molecular beacons

Publications


Table of contents


  1. Basic papers on molecular beacons

  2. Review papers on molecular beacons

  3. Papers on molecular beacons used for detection of DNA and RNA in living cells

  4. Papers on molecular beacons used in real-time PCR for SNP
    and mutation detection assays


  5. Papers on molecular beacons used in real-time PCR for DNA, RNA
    and pathogenic detection assays


  6. Papers on molecular beacons used in real-time NASBA assays

  7. Papers on molecular beacons used on arrays

  8. Papers on general application of molecular beacons




    I.   Basic papers on molecular beacons


  1. Bonnet G, Tyagi S, Libchaber A, and Kramer FR (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc Natl Acad Sci USA 96: 6171-6176. PubMed Link

  2. El-Hajj HH, Marras SA, Tyagi S, Shashkina E, Kamboj M, Kiehn TE, Glickman MS, Kramer FR, and Alland D (2009) Use of sloppy molecular beacon probes for identification of mycobacterial species. J Clin Microbiol 47: 1190-1198. PubMed Link

  3. Marras SAE, Kramer FR, and Tyagi S (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genet Anal 14: 151-156. PubMed Link

  4. Marras SAE, Kramer FR, and Tyagi S (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 30: e122. PubMed Link

  5. Mullah B and Livak K (1999) Efficient automated synthesis of molecular beacons. Nucleos Nucleot 18: 1311-1312.

  6. Ortiz E, Estrada G, and Lizardi PM (1998) PNA molecular beacons for rapid detection of PCR amplicons. Mol Cell Probes 12: 219-226. PubMed Link

  7. Tyagi S, Bratu DP, and Kramer FR (1998) Multicolor molecular beacons for allele discrimination. Nat Biotechnol 16: 49-53. PubMed Link

  8. Tyagi S and Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14: 303-308. PubMed Link

  9. Tyagi S, Marras SAE, and Kramer FR (2000) Wavelength-shifting molecular beacons. Nat Biotechnol 18: 1191-1196. PubMed Link


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    II.   Review papers on molecular beacons


  10. Abravaya K, Huff J, Marshall R, Merchant B, Mullen C, Schneider G, and Robinson J (2003) Molecular beacons as diagnostic tools: technology and applications. Clin Chem Lab Med 41: 468-474. PubMed Link

  11. Antony T and Subramaniam V (2001) Molecular beacons: nucleic acid hybridization and emerging applications. J Biomol Struct Dyn 19: 497-504. PubMed Link

  12. Barreiro LB, Henriques R, and Mhlanga MM (2009) High-throughput SNP genotyping: combining tag SNPs and molecular beacons. Methods Mol Biol 578: 255-276. PubMed Link

  13. Bratu DP (2006) Molecular beacons: fluorescent probes for detection of endogenous mRNAs in living cells. Methods Mol Biol 319: 1-14. PubMed Link

  14. Broude NE (2002) Stem-loop oligonucleotides: a robust tool for molecular biology and biotechnology. Trends Biotechnol 20: 249-256. PubMed Link

  15. Broude NE (2005) Molecular beacons and other hairpin probes. Encyclopedia of Diagnostic Genomics and Proteomics: 846 - 850.

  16. Drake T and Tan W (2004) Molecular beacon DNA probes and their bioanalytical applications. Applied Spectroscopy 58: 269-280.

  17. Fang X, Li JJ, Perlette J, Tan W, and Wang K (2000) Molecular beacons: novel fluorescent probes. Anal Chem 72: 747a-753a. PubMed Link

  18. Fang X, Mi Y, Li JJ, Beck T, Schuster S, and Tan W (2002) Molecular beacons: fluorogenic probes for living cell study. Cell Biochem Biophys 37: 71-81. PubMed Link

  19. Goel G, Kumar A, Puniya AK, Chen W, and Singh K (2005) Molecular beacon: a multitask probe. J Appl Microbiol 99: 435-442.

  20. Kim Y, Sohn D, and Tan W (2008) Molecular beacons in biomedical detection and clinical diagnosis. Int J Clin Exp Pathol 1: 105-116. PubMed Link

  21. Li Y, Zhou X, and Ye D (2008) Molecular beacons: an optimal multifunctional biological probe. Biochem Biophys Res Commun. PubMed Link

  22. Lucitti JL and Dickinson ME (2006) Moving toward the light: using new technology to answer old questions. Pediatr Res 60: 1-5. PubMed Link

  23. Manganelli R, Tyagi S, and Smith I (2001) Real-time PCR using molecular beacons. Methods Mol Med 54: 295-310.

  24. Marras SAE, Tyagi S, and Kramer FR (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin Chim Acta 363: 48-60. PubMed Link

  25. Marras SAE (2006) Selection of Fluorophore and Quencher Pairs for Fluorescent Nucleic Acid Hybridization Probes. Methods in Mol Biol 335: 3-16.

  26. Monroy-Contreras R and Vaca L (2011) Molecular beacons: powerful tools for imaging RNA in living cells. J Nucleic Acids 2011: 741723. PubMed Link

  27. Santangelo P, Nitin N, and Bao G (2006) Nanostructured probes for RNA detection in living cells. Ann Biomed Eng: 1-12. PubMed Link

  28. Santangelo PJ (2009) Molecular beacons and related probes for intracellular RNA imaging. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2: 11-19. PubMed Link

  29. Silverman AP and Kool ET (2005) Quenched probes for highly specific detection of cellular RNAs. Trends Biotechnol 23: 225-230. PubMed Link

  30. Tan W, Fang X, Li J, and Liu X (2000) Molecular beacons: a novel DNA probe for nucleic acid and protein studies. Chemistry 6: 1107-1111. PubMed Link

  31. Tan W, Wang K, and Drake TJ (2004) Molecular beacons. Curr Opin Chem Biol 8: 547-553. PubMed Link

  32. Tanke HJ, Dirks RW, and Raap T (2005) FISH and immunocytochemistry: towards visualising single target molecules in living cells. Curr Opin Biotechnol 16: 49-54. PubMed Link

  33. Tsourkas A and Bao G (2003) Shedding light on health and disease using molecular beacons. Brief Funct Genomic Proteomic 1: 372-384. PubMed Link

  34. Vet JA, Van der Rijt BJ, and Blom HJ (2002) Molecular beacons: colorful analysis of nucleic acids. Expert Rev Mol Diagn 2: 89-99. PubMed Link

  35. Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, and Tan W (2008) Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl. PubMed Link

  36. Yang CJ, Medley CD, and Tan W (2005) Monitoring nucleic acids using molecular beacons. Curr Pharm Biotechnol 6: 445-452. PubMed Link


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    III.   Papers on molecular beacons used for detection of DNA and RNA in living cells


  37. Alexander JC, Pandit A, Bao G, Connolly D, and Rochev Y (2011) Monitoring mRNA in living cells in a 3D in vitro model using TAT-peptide linked molecular beacons. Lab Chip 11: 3908-3914. PubMed Link

  38. Bratu DP, Catrina IE, and Marras SA (2011) Tiny Molecular Beacons for in vivo mRNA Detection. Methods Mol Biol 714: 141-157. PubMed Link

  39. Bratu DP, Cha BJ, Mhlanga MM, Kramer FR, and Tyagi S (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc Natl Acad Sci USA 100: 13308-13313. PubMed Link

  40. Catrina IE, Marras SA, and Bratu DP (2012) Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells. ACS Chem Biol 7: 1586-1595. PubMed Link

  41. Chen AK, Behlke MA, and Tsourkas A (2007) Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells. Nucleic Acids Res. PubMed Link

  42. Chen AK, Behlke MA, and Tsourkas A (2008) Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA. Nucleic Acids Res. PubMed Link

  43. Chen AK, Behlke MA, and Tsourkas A (2009) Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons. Nucleic Acids Res. PubMed Link

  44. Chen AK, Davydenko O, Behlke MA, and Tsourkas A (2010) Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells. Nucleic Acids Res 38: e148. PubMed Link

  45. Chen AK, Rhee WJ, Bao G, and Tsourkas A (2011) Delivery of molecular beacons for live-cell imaging and analysis of RNA. Methods Mol Biol 714: 159-174. PubMed Link

  46. Cui ZQ, Zhang ZP, Zhang XE, Wen JK, Zhou YF, and Xie WH (2005) Visualizing the dynamic behavior of poliovirus plus-strand RNA in living host cells. Nucleic Acids Res 33: 3245-3252. PubMed Link

  47. Kang WJ, Cho YL, Chae JR, Lee JD, Choi KJ, and Kim S (2011) Molecular beacon-based bioimaging of multiple microRNAs during myogenesis. Biomaterials 32: 1915-1922. PubMed Link

  48. Kihara T, Yoshida N, Kitagawa T, Nakamura C, Nakamura N, and Miyake J (2010) Development of a novel method to detect intrinsic mRNA in a living cell by using a molecular beacon-immobilized nanoneedle. Biosens Bioelectron 26: 1449-1454. PubMed Link

  49. Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S, and Etkin LD (2005) Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes. Development 132: 3445-3457. PubMed Link

  50. Matsuo T (1998) In situ visualization of messenger RNA for basic fibroblast growth factor in living cells. Biochim Biophys Acta 1379: 178-184. PubMed Link

  51. Mhlanga MM, Vargas DY, Fung CW, Kramer FR, and Tyagi S (2005) tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res 33: 1902-1912. PubMed Link

  52. Nitin N and Bao G (2008) NLS peptide conjugated molecular beacons for visualizing nuclear RNA in living cells. Bioconjug Chem. PubMed Link

  53. Nitin N, Rhee WJ, and Bao G (2009) Translation inhibition reveals interaction of 2'-deoxy and 2'-O-methyl molecular beacons with mRNA targets in living cells. Nucleic Acids Res. PubMed Link

  54. Nitin N, Santangelo PJ, Kim G, Nie S, and Bao G (2004) Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells. Nucleic Acids Res 32: e58. PubMed Link

  55. Peng XH, Cao ZH, Xia JT, Carlson GW, Lewis MM, Wood WC, and Yang L (2005) Real-time detection of gene expression in cancer cells using molecular beacon imaging: new strategies for cancer research. Cancer Res 65: 1909-1917. PubMed Link

  56. Perlette J and Tan W (2001) Real-time monitoring of intracellular mRNA hybridization inside single living cells. Anal Chem 73: 5544-5550. PubMed Link

  57. Rhee WJ and Bao G (2009) Simultaneous detection of mRNA and protein stem cell markers in live cells. BMC Biotechnol 9: 30. PubMed Link

  58. Rhee WJ, Santangelo PJ, Jo H, and Bao G (2008) Target accessibility and signal specificity in live-cell detection of BMP-4 mRNA using molecular beacons. Nucleic Acids Res. PubMed Link

  59. Riches LC, Lynch AM, and Gooderham NJ (2009) A molecular beacon approach to detecting RAD52 expression in response to DNA damage in human cells. Toxicol In Vitro. PubMed Link

  60. Rodriguez AJ, Condeelis J, Singer RH, and Dictenberg JB (2007) Imaging mRNA movement from transcription sites to translation sites. Semin Cell Dev Biol 18: 202-208. PubMed Link

  61. Santangelo P, Nitin N, Laconte L, Woolums A, and Bao G (2006) Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus, using molecular beacons. J Virol 80: 682-688. PubMed Link

  62. Santangelo PJ, Nitin N, and Bao G (2005) Direct visualization of mRNA colocalization with mitochondria in living cells using molecular beacons. J Biomed Opt 10: 44025. PubMed Link

  63. Santangelo PJ, Nix B, Tsourkas A, and Bao G (2004) Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res 32: e57. PubMed Link

  64. Simon B, Sandhu M, and Myhr KL (2009) Live FISH: Imaging mRNA in living neurons. J Neurosci Res. PubMed Link

  65. Sokol DL, Zhang X, Lu P, and Gewirtz AM (1998) Real time detection of DNA.RNA hybridization in living cells. Proc Natl Acad Sci USA 95: 11538-11543. PubMed Link

  66. Tyagi S and Alsmadi O (2004) Imaging native ß-actin mRNA in motile fibroblasts. Biophys J 78: 4153-4163. PubMed Link

  67. van den Bogaard PT and Tyagi S (2009) Using molecular beacons to study dispersal of mRNPs from the gene locus. Methods Mol Biol 464: 91-103. PubMed Link

  68. Vargas DY, Raj A, Marras SA, Kramer FR, and Tyagi S (2005) Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci U S A 102: 17008-17013. PubMed Link

  69. Veith R, Sorkalla T, Baumgart E, Anzt J, Haberlein H, Tyagi S, Siebrasse JP, and Kubitscheck U (2010) Balbiani ring mRNPs diffuse through and bind to clusters of large intranuclear molecular structures. Biophys J 99: 2676-2685. PubMed Link

  70. Wang A, Salazar AM, Yates MV, Mulchandani A, and Chen W (2005) Visualization and detection of infectious coxsackievirus replication using a combined cell culture-molecular beacon assay. Appl Environ Microbiol 71: 8397-8401. PubMed Link

  71. Wang W, Cui ZQ, Han H, Zhang ZP, Wei HP, Zhou YF, Chen Z, and Zhang XE (2008) Imaging and characterizing influenza A virus mRNA transport in living cells. Nucleic Acids Res. PubMed Link

  72. Wu Y, Yang CJ, Moroz LL, and Tan W (2008) Nucleic acid beacons for long-term real-time intracellular monitoring. Anal Chem. PubMed Link

  73. Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, Dorrestein PC, and Rosenfeld MG (2011) ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147: 773-788. PubMed Link

  74. Yeh HY, Yates MV, Mulchandani A, and Chen W (2008) Visualizing the dynamics of viral replication in living cells via Tat peptide delivery of nuclease-resistant molecular beacons. Proc Natl Acad Sci U S A 105: 17522-17525. PubMed Link


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    IV.   Papers on molecular beacons used in real-time PCR for SNP
    and mutation detection assays


  75. Alsmadi O, Muiya P, Khalak H, Al-Saud H, Meyer BF, Al-Mohanna F, Alshahid M, and Dzimiri N (2009) Haplotypes encompassing the KIAA0391 and PSMA6 gene cluster confer a genetic link for myocardial infarction and coronary artery disease. Ann Hum Genet. PubMed Link

  76. Ameziane N, Seguin C, Borgel D, Fumeron F, Moatti D, Alhenc-Gelas M, Grandchamp B, Aiach M, Emmerich J, and de Prost D (2002) The-33T -> C polymorphism in intron 7 of the TFPI gene influences the risk of venous thromboembolism, independently of the factor V Leiden and prothrombin mutations. Thrombosis and Haemostasis 88: 195-199.

  77. Chang HW, Ali SZ, Cho SK, Kurman RJ, and Shih Ie M (2002) Detection of allelic imbalance in ascitic supernatant by digital single nucleotide polymorphism analysis. Clin Cancer Res 8: 2580-2585. PubMed Link

  78. Dubertret B, Calame M, and Libchaber AJ (2001) Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat Biotechnol 19: 365-370. PubMed Link

  79. Durand R, Huart V, Jafari S, and Le Bras J (2002) Rapid detection of a molecular marker for chloroquine-resistant falciparum malaria. Antimicrob Agents Chemother 46: 2684-2686. PubMed Link

  80. El-Hajj HH, Marras SAE, Tyagi S, Kramer FR, and Alland D (2001) Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J Clin Microbiol 39: 4131-4137. PubMed Link

  81. Frei K, Szuhai K, Lucas T, Weipoltshammer K, Schofer C, Ramsebner R, Baumgartner WD, Raap AK, Bittner R, Wachtler FJ, and Kirschhofer K (2002) Connexin 26 mutations in cases of sensorineural deafness in eastern Austria. Eur J Hum Genet 10: 427-432. PubMed Link

  82. Giesendorf BA, Vet JA, Tyagi S, Mensink EJ, Trijbels FJ, and Blom HJ (1998) Molecular beacons: a new approach for semiautomated mutation analysis. Clin Chem 44: 482-486. PubMed Link

  83. Hodgson DR, Foy CA, Partridge M, Pateromichelakis S, and Gibson NJ (2002) Development of a facile fluorescent assay for the detection of 80 mutations within the p53 gene. Mol Med 8: 227-237. PubMed Link

  84. Jablonska E, Gromadzinska J, Reszka E, Wasowicz W, Sobala W, Szeszenia-Dabrowska N, and Boffetta P (2009) Association between GPx1 Pro198Leu polymorphism, GPx1 activity and plasma selenium concentration in humans. Eur J Nutr. PubMed Link

  85. Kostrikis LG, Tyagi S, Mhlanga MM, Ho DD, and Kramer FR (1998) Spectral genotyping of human alleles. Science 279: 1228-1229. PubMed Link

  86. Li X, Huang Y, Guan Y, Zhao M, and Li Y (2006) Universal molecular beacon-based tracer system for real-time polymerase chain reaction. Anal Chem 78: 7886-7890. PubMed Link

  87. Marras SAE, Kramer FR, and Tyagi S (2003) Genotyping SNPs with molecular beacons. Methods Mol Biol 212: 111-128. PubMed Link

  88. Mhlanga MM and Malmberg L (2001) Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR. Methods 25: 463-471. PubMed Link

  89. O'Shea MK, Ryan MA, Hawksworth AW, Alsip BJ, and Gray GC (2005) Symptomatic respiratory syncytial virus infection in previously healthy young adults living in a crowded military environment. Clin Infect Dis 41: 311-317. PubMed Link

  90. Orru G, Coghe F, Faa G, Pillai S, Manieli C, Montaldo C, Pilia F, Pichiri G, Piras V, and Coni P (2010) Rapid multiplex real-time PCR by molecular beacons for different BRAF allele detection in papillary thyroid carcinoma. Diagn Mol Pathol 19: 1-8. PubMed Link

  91. Orru G, Faa G, Pillai S, Pilloni L, Montaldo C, Pusceddu G, Piras V, and Coni P (2005) Rapid PCR real-time genotyping of M-Malton alpha1-antitrypsin deficiency alleles by molecular beacons. Diagn Mol Pathol 14: 237-242. PubMed Link

  92. Piatek AS, Telenti A, Murray MR, El-Hajj H, Jacobs WR, Jr., Kramer FR, and Alland D (2000) Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing. Antimicrob Agents Chemother 44: 103-110. PubMed Link

  93. Piatek AS, Tyagi S, Pol AC, Telenti A, Miller LP, Kramer FR, and Alland D (1998) Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat Biotechnol 16: 359-363. PubMed Link

  94. Rhee JT, Piatek AS, Small PM, Harris LM, Chaparro SV, Kramer FR, and Alland D (1999) Molecular epidemiologic evaluation of transmissibility and virulence of Mycobacterium tuberculosis. J Clin Microbiol 37: 1764-1770. PubMed Link

  95. Singer G, Kurman RJ, Chang HW, Cho SK, and Shih Ie M (2002) Diverse tumorigenic pathways in ovarian serous carcinoma. Am J Pathol 160: 1223-1228. PubMed Link

  96. Szuhai K, Ouweland J, Dirks R, Lemaitre M, Truffert J, Janssen G, Tanke H, Holme E, Maassen J, and Raap A (2001) Simultaneous A8344G heteroplasmy and mitochondrial DNA copy number quantification in Myoclonus Epilepsy and Ragged-Red Fibers (MERRF) syndrome by a multiplex molecular beacon based real-time fluorescence PCR. Nucleic Acids Res 29: e13. PubMed Link

  97. Szuhai K, Sandhaus E, Kolkman-Uljee SM, Lemaitre M, Truffert JC, Dirks RW, Tanke HJ, Fleuren GJ, Schuuring E, and Raap AK (2001) A novel strategy for human papillomavirus detection and genotyping with SybrGreen and molecular beacon polymerase chain reaction. Am J Pathol 159: 1651-1660. PubMed Link

  98. Tapp I, Malmberg L, Rennel E, Wik M, and Syvanen AC (2000) Homogeneous scoring of single-nucleotide polymorphisms: comparison of the 5'-nuclease TaqMan assay and molecular beacon probes. Biotechniques 28: 732-738. PubMed Link

  99. Vogelstein B and Kinzler KW (1999) Digital PCR. Proc Natl Acad Sci USA 96: 9236-9241.


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    V.   Papers on molecular beacons used in real-time PCR for DNA, RNA
    and pathogenic detection assays


  100. Abd el-Galil KH, El-Sokkary MA, Kheira SM, Salazar AM, Yates MV, Chen W, and Mulchandani A (2004) Combined immunomagnetic separation molecular beacon reverse transcription PCR assay for detection of hepatitis A virus from environmental samples. Appl Environ Microbiol 70: 4371-4374. PubMed Link

  101. Alsmadi O, Al-Rubeaan K, Wakil SM, Imtiaz F, Mohamed G, Al-Saud H, Al-Saud NA, Aldaghri N, Mohammad S, and Meyer BF (2007) Genetic study of saudi diabetes (GSSD): significant association of the KCNJ11 E23K polymorphism with type 2 diabetes. Diabetes Metab Res Rev. PubMed Link

  102. Alsmadi OA, Al-Kayal F, Al-Hamed M, and Meyer BF (2006) Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study. BMC Med Genet 7: 43-49. PubMed Link

  103. Arnold SF, Tims E, and McGrath BE (1999) Identification of bone morphogenetic proteins and their receptors in human breast cancer cell lines: importance of BMP2. Cytokine 11: 1031-1037. PubMed Link

  104. Balashov SV, Gardiner R, Park S, and Perlin DS (2005) Rapid, high-throughput, multiplex, real-time PCR for identification of mutations in the cyp51A gene of Aspergillus fumigatus that confer resistance to itraconazole. J Clin Microbiol 43: 214-222. PubMed Link

  105. Balashov SV, Park S, and Perlin DS (2006) Assessing resistance to the echinocandin antifungal drug caspofungin in candida albicans by profiling mutations in FKS1. Antimicrob Agents Chemother 50: 2058-2063. PubMed Link

  106. Banada PP, Chakravorty S, Shah D, Burday M, Mazzella FM, and Alland D (2012) Highly Sensitive Detection of Staphylococcus aureus Directly from Patient Blood. PLoS One 7: e31126. PubMed Link

  107. Banerjee R, Allen J, Lin SY, Westenhouse J, Desmond E, Schecter GF, Scott C, Raftery A, Mase S, Watt JP, and Flood J (2010) Rapid drug susceptibility testing with a molecular beacon assay is associated with earlier diagnosis and treatment of multidrug-resistant tuberculosis in California. J Clin Microbiol 48: 3779-3781. PubMed Link

  108. Belanger SD, Boissinot M, Clairoux N, Picard FJ, and Bergeron MG (2003) Rapid detection of clostridium difficile in feces by real-time PCR. J Clin Microbiol 41: 730-734. PubMed Link

  109. Belanger SD, Boissinot M, Menard C, Picard FJ, and Bergeron MG (2002) Rapid detection of shiga toxin-producing bacteria in feces by multiplex PCR with molecular beacons on the smart cycler. J Clin Microbiol 40: 1436-1440. PubMed Link

  110. Beloukas A, Paraskevis D, Haida C, Sypsa V, and Hatzakis A (2009) Development and assessment of a multiplex real-time PCR assay for the quantification of HIV-1 DNA. J Clin Microbiol. PubMed Link

  111. Bergeron MG and Ke D (2001) New DNA-based PCR approaches for rapid real-time detection and prevention of group B streptococcal infections in newborns and pregnant women. Expert Rev Mol Med 380: 5a.

  112. Besson G and Kazanji M (2009) One-step, multiplex, real-time PCR assay with molecular beacon probes for simultaneous detection, differentiation and quantification of human T-cell leukaemia viruses types 1, 2 and 3. J Clin Microbiol. PubMed Link

  113. Bhagwat AA, Patel J, Chua T, Chan A, Cruz SR, and Aguilar GA (2008) Detection of Salmonella species in foodstuffs. Methods Mol Biol 429: 33-43. PubMed Link

  114. Blackard JT, Komurian-Pradel F, Perret M, Sodoyer M, Smeaton L, Clair JB, Chapman S, Taylor LE, Paranhos-Baccala G, and Chung RT (2006) Intrahepatic cytokine expression is downregulated during HCV/HIV co-infection. J Med Virol 78: 202-207. PubMed Link

  115. Bonants PJM, van Gent-Pelzer MPE, Hooftman R, Cooke DEL, Guy DC, and Duncan JM (2004) A combination of baiting and different PCR formats, including measurement of real-time quantitative fluorescence, for the detection of Phytophthora fragariae in strawberry plants. European Journal of Plant Pathology 110: 689-702. PubMed Link

  116. Buitrago MJ, Merino P, Puente S, Gomez-Lopez A, Arribi A, Zancope-Oliveira RM, Gutierrez MC, Rodriguez-Tudela JL, and Cuenca-Estrella M (2009) Utility of Real-time PCR for the detection of Paracoccidioides brasiliensis DNA in the diagnosis of imported paracoccidioidomycosis. Med Mycol: 1-4. PubMed Link

  117. Castelli MV, Buitrago MJ, Bernal-Martinez L, Gomez-Lopez A, Rodriguez-Tudela JL, and Cuenca-Estrella M (2008) Development and validation of a quantitative PCR assay for the diagnosis of Scedosporiosis. J Clin Microbiol. PubMed Link

  118. Chakravorty S, Aladegbami B, Burday M, Levi M, Marras SA, Shah D, El-Hajj HH, Kramer FR, and Alland D (2010) Rapid universal diagnosis of bacterial pathogens from clinical Cultures using a novel sloppy molecular beacon melting temperature signature technique. J Clin Microbiol. PubMed Link

  119. Chakravorty S, Aladegbami B, Motiwala AS, Dai Y, Safi H, Brimacombe M, Helb D, and Alland D (2008) Rifampin-resistance, Beijing-W clade/SNP cluster group two phylogeny and the Rv2629 191-C allele in mycobacterium tuberculosis strains. J Clin Microbiol. PubMed Link

  120. Chakravorty S, Kothari H, Aladegbami B, Cho E, Lee JS, Roh SS, Kim H, Kwak H, Lee EG, Hwang S, Banada PP, Safi H, Via LE, Cho SN, Barry CE, 3rd, and Alland D (2012) Rapid, high throughput detection of Rifampicin resistance and hetero-resistance in Mycobacterium tuberculosis using Sloppy Molecular Beacon Melting Temperature coding. J Clin Microbiol. PubMed Link

  121. Chang HW, Yen CY, Liu SY, Singer G, and Shih Ie M (2002) Genotype analysis using human hair shaft. Cancer Epidemiol Biomarkers Prev 11: 925-929. PubMed Link

  122. Chen L, Mediavilla JR, Oliveira DC, Willey BM, de Lencastre H, and Kreiswirth BN (2009) Multiplex real-time PCR for rapid staphylococcal cassette chromosome mec (SCCmec) typing. J Clin Microbiol. PubMed Link

  123. Chen W, Martinez G, and Mulchandani A (2000) Molecular beacons: a real-time polymerase chain reaction assay for detecting Salmonella. Anal Biochem 280: 166-172. PubMed Link

  124. Chiba N, Murayama SY, Morozumi M, Nakayama E, Okada T, Iwata S, Sunakawa K, and Ubukata K (2009) Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR. J Infect Chemother 15: 92-98. PubMed Link

  125. Chowdhury TT, Arghandawi S, Brand J, Akanji OO, Bader DL, Salter DM, and Lee DA (2008) Dynamic compression counteracts IL-1beta induced iNOS and COX-2 expression in chondrocyte / agarose constructs. Arthritis Res Ther 10: R35. PubMed Link

  126. Claas EC, Schilham MW, de Brouwer CS, Hubacek P, Echavarria M, Lankester AC, van Tol MJ, and Kroes AC (2005) Internally controlled real-time PCR monitoring of adenovirus DNA load in serum or plasma of transplant recipients. J Clin Microbiol 43: 1738-1744. PubMed Link

  127. Clayton SJ, Scott FM, Walker J, Callaghan K, Hague K, Liloglou T, Xinarianos G, Shawcross S, Ceuppens P, Field JK, and Fox JC (2000) K-ras point mutation detection in lung cancer: comparison of two approaches to somatic mutation detection using ARMS allele-specific amplification. Clin Chem 46: 1929-1938.

  128. Dawes SS, Warner DF, Tsenova L, Timm J, McKinney JD, Kaplan G, Rubin H, and Mizrahi V (2003) Ribonucleotide reduction in Mycobacterium tuberculosis: function and expression of genes encoding class Ib and class II ribonucleotide reductases. Infect Immun 71: 6124-6131. PubMed Link

  129. Demetriou VL, van de Vijver DA, Kousiappa I, Balotta C, Clotet B, Grossman Z, Jorgensen LB, Lepej SZ, Levy I, Nielsen C, Paraskevis D, Poljak M, Roman F, Ruiz L, Schmidt JC, Vandamme AM, Van Laethem K, Vercauteren J, and Kostrikis LG (2010) Cellular HIV-1 DNA levels in drug sensitive strains are equivalent to those in drug resistant strains in newly-diagnosed patients in Europe. PLoS One 5: e10976. PubMed Link

  130. Devor EJ (2001) Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order primates. Genome Biol 2: 6.1-6.5. PubMed Link

  131. Dracheva S, Marras SAE, Elhakem AL, Kramer FR, Davis KL, and Haroutunian V (2001) N-Methyl-D-Aspartic Acid Receptor expression in Dorsolateral Prefrontal Cortex of elderly patients with schizophrenia. Am J Psychiatry 158: 1400-1410.

  132. Dracheva S, McGurk SR, and Haroutunian V (2005) mRNA expression of AMPA receptors and AMPA receptor binding proteins in the cerebral cortex of elderly schizophrenics. J Neurosci Res 79: 868-878.

  133. Durand R, Eslahpazire J, Jafari S, Delabre JF, Marmorat-Khuong A, di Piazza JP, and Le Bras J (2000) Use of molecular beacons to detect an antifolate resistance-associated mutation in Plasmodium falciparum. Antimicrob Agents Chemother 44: 3461-3464. PubMed Link

  134. Elsayed S, Chow BL, Hamilton NL, Gregson DB, Pitout JD, and Church DL (2003) Development and validation of a molecular beacon probe-based real-time polymerase chain reaction assay for rapid detection of methicillin resistance in Staphylococcus aureus. Arch Pathol Lab Med 127: 845-849. PubMed Link

  135. Elsayed S, Plewes K, Church D, Chow B, and Zhang K (2006) Use of molecular beacon probes for real-time PCR detection of Plasmodium falciparum and other plasmodium species in peripheral blood specimens. J Clin Microbiol 44: 622-624. PubMed Link

  136. Eun AJC and Wong SM (2000) Molecular Beacons: a new approach to plant virus detection. Phytopathology 90: 269-275.

  137. Fang Y, Wu WH, Pepper JL, Larsen JL, Marras SAE, Nelson EA, Epperson WB, and Christopher-Hennings J (2002) Comparison of real-time, quantitative PCR with molecular beacons to nested PCR and culture methods for detection of Mycobacterium avium subsp. paratuberculosis in bovine fecal samples. J Clin Microbiol 40: 287-291. PubMed Link

  138. Feldman SH and Bowman SG (2007) Molecular phylogeny of the pinworms of mice, rats and rabbits, and its use to develop molecular beacon assays for the detection of pinworms in mice. Lab Anim 36: 43-50. PubMed Link

  139. Fortin NY, Mulchandani A, and Chen W (2001) Use of real-time polymerase chain reaction and molecular beacons for the detection of Escherichia coli O157:H7. Anal Biochem 289: 281-288. PubMed Link

  140. Garcia-Effron G, Dilger A, Alcazar-Fuoli L, Park S, Mellado E, and Perlin DS (2008) Rapid detection of triazole antifungal resistance in Aspergillus fumigatus. J Clin Microbiol. PubMed Link

  141. Gatcombe RR, Jothikumar N, Dangoudoubiyam S, Kazacos KR, and Hill VR (2010) Evaluation of a molecular beacon real-time PCR assay for detection of Baylisascaris procyonis in different soil types and water samples. Parasitol Res 106: 499-504. PubMed Link

  142. Gomez DI, Fisher-Hoch SP, Bordt AS, Quitugua TN, Robledo J, Alvarez N, Correa N, McCormick JB, and Restrepo BI (2010) Systematic interpretation of molecular beacon polymerase chain reaction for identifying rpoB mutations in Mycobacterium tuberculosis isolates with mixed resistant and susceptible bacteria. Diagn Microbiol Infect Dis. PubMed Link

  143. Gonzalez E, Bamshad M, Sato N, Mummidi S, Dhanda R, Catano G, Cabrera S, McBride M, Cao XH, Merrill G, O'Connell P, Bowden DW, Freedman BI, Anderson SA, Walter EA, Evans JS, Stephan KT, Clark RA, Tyagi S, Ahuja SS, Dolan MJ, and Ahuja SK (1999) Race-specific HIV-1 disease-modifying effects associated with CCR5 haplotypes. Proc Natl Acad Sci USA 96: 12004-12009. PubMed Link

  144. Gubala AJ and Proll DF (2006) Molecular-beacon multiplex real-time PCR assay for detection of Vibrio cholerae. Appl Environ Microbiol 72: 6424-6428. PubMed Link

  145. Gullsby K, Storm M, and Bondeson K (2007) Simultaneous detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae using molecular beacons in a duplex real-time PCR. J Clin Microbiol. PubMed Link

  146. Hadjinicolaou AV, Demetriou VL, Emmanuel MA, Kakoyiannis CK, and Kostrikis LG (2009) Molecular beacon-based real-time PCR detection of primary isolates of Salmonella Typhimurium and Salmonella Enteritidis in environmental and clinical samples. BMC Microbiol 9: 97. PubMed Link

  147. Hadjinicolaou AV, Demetriou VL, Hezka J, Beyer W, Hadfield TL, and Kostrikis LG (2009) Use of molecular beacons and multi-allelic real-time PCR for detection of and discrimination between virulent bacillus anthracis and other bacillus isolates. J Microbiol Methods. PubMed Link

  148. Hadjinicolaou AV, Farcas GA, Demetriou VL, Mazzulli T, Poutanen SM, Willey BM, Low DE, Butany J, Asa SL, Kain KC, and Kostrikis LG (2011) Development of a molecular-beacon-based multi-allelic real-time RT-PCR assay for the detection of human coronavirus causing severe acute respiratory syndrome (SARS-CoV): a general methodology for detecting rapidly mutating viruses. Arch Virol 156: 671-680. PubMed Link

  149. Haldar S, Chakravorty S, Bhalla M, De Majumdar S, and Tyagi JS (2007) Simplified detection of Mycobacterium tuberculosis in sputum using smear microscopy and PCR with molecular beacons. J Med Microbiol 56: 1356-1362. PubMed Link

  150. Harms G, Layton AC, Dionisi HM, Gregory IR, Garrett VM, Hawkins SA, Robinson KG, and Sayler GS (2003) Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37: 343-351. PubMed Link

  151. Heil SG, Lievers KJ, Boers GH, Verhoef P, den Heijer M, Trijbels FJ, and Blom HJ (2000) Betaine-homocysteine methyltransferase (BHMT): genomic sequencing and relevance to hyperhomocysteinemia and vascular disease in humans. Mol Genet Metab 71: 511-519. PubMed Link

  152. Helps C, Reeves N, Tasker S, and Harbour D (2001) Use of real-time quantitative PCR to detect Chlamydophila felis infection. J Clin Microbiol 39: 2675-2676. PubMed Link

  153. Henry KM, Jiang J, Rozmajzl PJ, Azad AF, Macaluso KR, and Richards AL (2006) Development of quantitative real-time PCR assays to detect Rickettsia typhi and Rickettsia felis, the causative agents of murine typhus and flea-borne spotted fever. Mol Cell Probes 21: 17-23. PubMed Link

  154. Huletsky A, Giroux R, Rossbach V, Gagnon M, Vaillancourt M, Bernier M, Gagnon F, Truchon K, Bastien M, Picard FJ, van Belkum A, Ouellette M, Roy PH, and Bergeron MG (2004) New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J Clin Microbiol 42: 1875-1884. PubMed Link

  155. Jebbink J, Bai X, Rogers BB, Dawson DB, Scheuermann RH, and Domiati-Saad R (2003) Development of real-time PCR assays for the quantitative detection of Epstein-Barr virus and cytomegalovirus, comparison of TaqMan probes, and molecular beacons. J Mol Diagn 5: 15-20. PubMed Link

  156. Jin X, Bauer DE, Tuttleton SE, Lewin S, Gettie A, Blanchard J, Irwin CE, Safrit JT, Mittler J, Weinberger L, Kostrikis LG, Zhang L, Perelson AS, and Ho DD (1999) Dramatic rise in plasma viremia after CD8(+) T cell depletion in simian immunodeficiency virus-infected macaques. J Exp Med 189: 991-998. PubMed Link

  157. Jyoti A, Ram S, Vajpayee P, Singh G, Dwivedi PD, Jain SK, and Shanker R (2010) Contamination of surface and potable water in South Asia by Salmonellae: culture-independent quantification with molecular beacon real-time PCR. Sci Total Environ 408: 1256-1263. PubMed Link

  158. Kirs M and Smith DC (2007) Multiplex quantitative real-time RT-PCR for the F+ specific RNA coliphages: A method for use in microbial source tracking. Appl Environ Microbiol 73: 808-814. PubMed Link

  159. Komurian-Pradel F, Perret M, Deiman B, Sodoyer M, Lotteau V, Paranhos-Baccala G, and Andre P (2004) Strand specific quantitative real-time PCR to study replication of hepatitis C virus genome. J Virol Methods 116: 103-106. PubMed Link

  160. Kostrikis LG, Touloumi G, Karanicolas R, Pantazis N, Anastassopoulou C, Karafoulidou A, Goedert JJ, and Hatzakis A (2002) Quantitation of Human Immunodeficiency Virus type 1 DNA forms with the second template switch in peripheral blood cells predicts disease progression independently of plasma RNA load. J Virol 76: 10099-10108. PubMed Link

  161. Kota R, Holton TA, and Henry RJ (1999) Detection of transgenes in crop plants using molecular beacon assays. Plant Mol Biology Rep 17: 363-370.

  162. Kumar P, Nath K, Rath B, Sen MK, Vishalakshi P, Chauhan DS, Katoch VM, Singh S, Tyagi S, Sreenivas V, and Prasad HK (2009) Visual format for detection of Mycobacterium tuberculosis and M. bovis in clinical samples using molecular beacons. J Mol Diagn 11: 430-438. PubMed Link

  163. L'Homme Y, Leboeuf A, and Cameron J (2008) PrP genotype frequencies of Quebec sheep breeds determined by real-time PCR and molecular beacons. Can J Vet Res 72: 320-324. PubMed Link

  164. Lai JP, Douglas SD, Shaheen F, Pleasure DE, and Ho WZ (2002) Quantification of substance p mRNA in human immune cells by real-time reverse transcriptase PCR assay. Clin Diagn Lab Immunol 9: 138-143. PubMed Link

  165. Lai JP, Yang JH, Douglas SD, Wang X, Riedel E, and Ho WZ (2003) Quantification of CCR5 mRNA in human lymphocytes and macrophages by real-time reverse transcriptase PCR assay. Clinical and Diagnostic Laboratory Immunology 10: 1123-1128. PubMed Link

  166. Larsen MH, Vilcheze C, Kremer L, Besra GS, Parsons L, Salfinger M, Heifets L, Hazbon MH, Alland D, Sacchettini JC, and Jacobs WR, Jr. (2002) Overexpression of inhA, but not kasA, confers resistance to isoniazid and ethionamide in Mycobacterium smegmatis, M. bovis BCG and M. tuberculosis. Mol Microbiol 46: 453-466. PubMed Link

  167. Lasham A, Herbert M, Coppieters 't Wallant N, Patel R, Feng S, Eszes M, Cao H, and Reid G (2010) A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5' RACE and a molecular beacon probe. Nucleic Acids Res 38: e19. PubMed Link

  168. Lata P, Ram S, Agrawal M, and Shanker R (2009) Real time PCR for the rapid detection of vanA gene in surface waters and aquatic macrophyte by molecular beacon probe. Environ Sci Technol 43: 3343-3348. PubMed Link

  169. Lee DH, Li L, Andrus L, and Prince AM (2002) Stabilized viral nucleic acids in plasma as an alternative shipping method for NAT. Transfusion 42: 409-413. PubMed Link

  170. Lee DH, Mathew J, Pfahler W, Ma D, Valinsky J, Prince AM, and Andrus L (2005) Individual donor nucleic acid amplification testing for detection of West Nile virus. J Clin Microbiol 43: 5111-5116. PubMed Link

  171. Lerat S, England LS, Vincent ML, Pauls KP, Swanton CJ, Klironomos JN, and Trevors JT (2005) Real-time polymerase chain reaction quantification of the transgenes for roundup ready corn and roundup ready soybean in soil samples. J Agric Food Chem 53: 1337-1342. PubMed Link

  172. Levy-Booth DJ, Campbell RG, Gulden RH, Hart MM, Powell JR, Klironomos JN, Pauls KP, Swanton CJ, Trevors JT, and Dunfield KE (2008) Real-time polymerase chain reaction monitoring of recombinant DNA entry into soil from decomposing roundup ready leaf biomass. J Agric Food Chem. PubMed Link

  173. Lewin SR, Ribeiro RM, Walters T, Lau GK, Bowden S, Locarnini S, and Perelson AS (2001) Analysis of hepatitis B viral load decline under potent therapy: Complex decay profiles observed. Hepatology 34: 1012-1020. PubMed Link

  174. Lewin SR, Vesanen M, Kostrikis L, Hurley A, Duran M, Zhang L, Ho DD, and Markowitz M (1999) Use of real-time PCR and molecular beacons to detect virus replication in Human Immunodeficiency Virus type 1-infected individuals on prolonged effective antiretroviral therapy. J Virol 73: 6099-6103. PubMed Link

  175. Li Q, Liang J, Luan G, Zhang Y, and Wang K (2000) Molecular beacon-based homogeneous flourescence PCR assay for the diagnosis of infectious diseases. Anal Sci 16: 245-248.

  176. Liming SH and Bhagwat AA (2004) Application of a molecular beacon real-time PCR technology to detect Salmonella species contaminating fruits and vegetables. Int J Food Microbiol 95: 177-187. PubMed Link

  177. Lin SY, Probert W, Lo M, and Desmond E (2004) Rapid detection of isoniazid and rifampin resistance mutations in Mycobacterium tuberculosis complex from cultures or smear-positive sputa by use of molecular beacons. J Clin Microbiol 42: 4204-4208. PubMed Link

  178. Macia-Vicente JG, Jansson HB, Talbot NJ, and Lopez-Llorca LV (2009) Real-time PCR quantification and live-cell imaging of endophytic colonization of barley (Hordeum vulgare) roots by Fusarium equiseti and Pochonia chlamydosporia. New Phytol. PubMed Link

  179. Manganelli R, Dubnau E, Tyagi S, Kramer FR, and Smith I (1999) Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Mol Microbiol 31: 715-724. PubMed Link

  180. Martinez-Lopez J, Lahuerta JJ, Salama P, Ayala R, and Bautista JM (2004) The use of fluorescent molecular beacons in real-time PCR of IgH gene rearrangements for quantitative evaluation of multiple myeloma. Clin Lab Haematol 26: 31-35. PubMed Link

  181. Martinson JJ, Hong L, Karanicolas R, Moore JP, and Kostrikis LG (2000) Global distribution of the CCR2-64I/CCR5-59653T HIV-1 disease-protective haplotype. Aids 14: 483-489. PubMed Link

  182. Mathema B, Bifani P, Driscoll J, Steinlein L, Kurepina N, Moghazeh SL, Shashkina E, Marras SAE, Campbell S, Mangura B, Shilkret K, Crawford JT, Frothingham R, and Kreiswirth BN (2002) Identification and evolution of an IS6110 low-copy number Mycobacterium tuberculosis cluster. J Infect Dis 185: 641-649.

  183. McKillen J, Hjertner B, Millar A, McNeilly F, Belak S, Adair B, and Allan G (2007) Molecular beacon real-time PCR detection of swine viruses. J Virol Methods 140: 155-165. PubMed Link

  184. McKillip JL and Drake M (2000) Molecular beacon polymerase chain reaction detection of Escherichia coli O157:H7 in milk. J Food Prot 63: 855-859. PubMed Link

  185. Metzner KJ, Jin X, Lee FV, Gettie A, Bauer DE, Di Mascio M, Perelson AS, Marx PA, Ho DD, Kostrikis LG, and Connor RI (2000) Effects of in vivo CD8(+) T cell depletion on virus replication in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine. J Exp Med 191: 1921-1931. PubMed Link

  186. Morandi L, Ferrari D, Lombardo C, Pession A, and Tallini G (2006) Monitoring HCV RNA viral load by locked nucleic acid molecular beacons real time PCR. J Virol Methods 140: 148-154. PubMed Link

  187. Morandi L, Franceschi E, De Biase D, Marucci G, Tosoni A, Ermani M, Pession A, Tallini G, and Brandes AA (2010) Promoter methylation analysis of O6-methylguanine-DNA methyltransferase in glioblastoma: detection by locked nucleic acid based quantitative PCR using an imprinted gene (SNURF) as a reference. BMC Cancer 10: 48. PubMed Link

  188. Morozumi M, Nakayama E, Iwata S, Aoki Y, Hasegawa K, Kobayashi R, Chiba N, Tajima T, and Ubukata K (2006) Simultaneous detection of pathogens in clinical samples from patients with community-acquired pneumonia by real-time PCR with pathogen-specific molecular beacon probes. J Clin Microbiol 44: 1440-1446. PubMed Link

  189. Nascimento AM, Goldman GH, Park S, Marras SAE, Delmas G, Oza U, Lolans K, Dudley MN, Mann PA, and Perlin DS (2003) Multiple resistance mechanisms among Aspergillus fumigatus mutants with high-level resistance to itraconazole. Antimicrob Agents Chemother 47: 1719-1726. PubMed Link

  190. Nogueras MM, Pons I, Ortuno A, Lario S, and Segura F (2010) Rickettsia felis in Fleas from Catalonia (Northeast Spain). Vector Borne Zoonotic Dis. PubMed Link

  191. Ntziora F, Paraskevis D, Haida C, Magiorkinis E, Manesis E, Papatheodoridis G, Manolakopoulos S, Beloukas A, Chryssoy S, Magiorkinis G, Sypsa V, and Hatzakis A (2009) Quantitative detection of the M204V HBV minor variants by amplification refractory mutation system real-time polymerase chain reaction (ARMS rt-PCR) combined with molecular beacon. J Clin Microbiol. PubMed Link

  192. O'Shea MK and Cane PA (2004) Development of a highly sensitive semi-quantitative real-time PCR and molecular beacon probe assay for the detection of respiratory syncytial virus. J Virol Methods 118: 101-110. PubMed Link

  193. O'Shea MK, Pipkin C, Cane PA, and Gray GC (2007) Respiratory syncytial virus: an important cause of acute respiratory illness among young adults undergoing military training. Influenza Other Respir Viruses 1: 193-197. PubMed Link

  194. Oh YH, Kim Y, Kim YP, Seo SW, Mitsudomi T, Ahn MJ, Park K, and Kim HS (2010) Rapid detection of the epidermal growth factor receptor mutation in non-small-cell lung cancer for analysis of acquired resistance using molecular beacons. J Mol Diagn 12: 644-652. PubMed Link

  195. Orru G, Ferrando ML, Meloni M, Liciardi M, Savini G, and De Santis P (2006) Rapid detection and quantitation of bluetongue virus (BTV) using a molecular beacon fluorescent probe assay. J Virol Methods 137: 34-42. PubMed Link

  196. Paillard D, McKain N, Rincon MT, Shingfield KJ, Givens DI, and Wallace RJ (2007) Quantification of ruminal Clostridium proteoclasticum by real-time PCR using a molecular beacon approach. J Appl Microbiol 103: 1251-1261. PubMed Link

  197. Papaparaskevas J, Houhoula DP, Siatelis A, and Tsakris A (2008) Molecular beacon based real-time PCR for detection and quantification of Mycobacterium tuberculosis DNA in clinical samples. J Clin Microbiol. PubMed Link

  198. Paraskevis D, Beloukas A, Haida C, Katsoulidou A, Moschidis Z, Hatzitheodorou H, Varaklioti A, Sypsa V, and Hatzakis A (2010) Development of a new ultra sensitive real-time PCR assay (ultra sensitive RTQ-PCR) for the quantification of HBV-DNA. Virol J 7: 57. PubMed Link

  199. Park S and Perlin DS (2005) Establishing surrogate markers for fluconazole resistance in Candida albicans. Microb Drug Resist 11: 232-238. PubMed Link

  200. Park S, Wong M, Marras SAE, Cross EW, Kiehn TE, Chaturvedi V, Tyagi S, and Perlin DS (2000) Rapid identification of Candida dubliniensis using a species-specific molecular beacon. J Clin Microbiol 38: 2829-2836. PubMed Link

  201. Pas SD, Noppornpanth S, Eijk AA, Man RA, and Niesters HGM (2005) Quantification of the newly detected lamivudine resistant YSDD variants of Hepatitis B virus using molecular beacons. J Clin Virol 32: 166-172. PubMed Link

  202. Patel JR and Bhagwat AA (2008) Rapid real-time PCR assay for detecting Salmonella in raw and ready-to-eat meats. Acta Vet Hung 56: 451-458. PubMed Link

  203. Patel JR, Bhagwat AA, Sanglay GC, and Solomon MB (2006) Rapid detection of Salmonella from hydrodynamic pressure-treated poultry using molecular beacon real-time PCR. Food Microbiol 23: 39-46. PubMed Link

  204. Perlin DS, Balashov S, and Park S (2008) Multiplex detection of mutations. Methods Mol Biol 429: 23-31. PubMed Link

  205. Peyerl FW, Barouch DH, Bazick HS, Manuel E, and Letvin NL (2005) Use of molecular beacons for rapid, real-time, quantitative monitoring of cytotoxic T-lymphocyte epitope mutations in simian immunodeficiency virus. J Clin Microbiol 43: 4773-4779. PubMed Link

  206. Pierce KE, Rice JE, Sanchez JA, Brenner C, and Wangh LJ (2000) Real-time PCR using molecular beacons for accurate detection of the Y chromosome in single human blastomeres. Mol Hum Reprod 6: 1155-1164. PubMed Link

  207. Pierce KE, Rice JE, Sanchez JA, and Wangh LJ (2002) QuantiLyse: reliable DNA amplification from single cells. Biotechniques 32: 1106-1111. PubMed Link

  208. Pierce KE, Rice JE, Sanchez JA, and Wangh LJ (2003) Detection of cystic fibrosis alleles from single cells using molecular beacons and a novel method of asymmetric real-time PCR. Mol Hum Reprod 9: 815-820. PubMed Link

  209. Pierce KE and Wangh LJ (2007) Linear-after-the-exponential polymerase chain reaction and allied technologies: real-time detection strategies for rapid, reliable diagnosis from single cells. Methods Mol Med 132: 65-86. PubMed Link

  210. Poddar SK (1999) Detection of adenovirus using PCR and molecular beacon. J Virol Methods 82: 19-26. PubMed Link

  211. Poddar SK (2000) Symmetric vs asymmetric PCR and molecular beacon probe in the detection of a target gene of adenovirus. Mol Cell Probes 14: 25-32. PubMed Link

  212. Poddar SK (2003) Detection and discrimination of B-pertussis and B-holmesii by real-time PCR targeting IS481 using a beacon probe and probe-target melting analysis. Molecular and Cellular Probes 17: 91-98. PubMed Link

  213. Poddar SK and Le CT (2001) Bordetella pertussis detection by spectrofluorometry using polymerase chain reaction (PCR) and a molecular beacon probe. Mol Cell Probes 15: 161-167. PubMed Link

  214. Poe BG, Navratil M, and Arriaga EA (2007) Absolute quantitation of a heteroplasmic mitochondrial DNA deletion using a multiplex three-primer real-time PCR assay. Anal Biochem 362: 193-200. PubMed Link

  215. Ram S, Singh RL, and Shanker R (2008) In silico comparison of real-time PCR probes for detection of pathogens. In Silico Biol 8: 251-259. PubMed Link

  216. Ram S, Vajpayee P, and Shanker R (2008) Rapid culture-independent quantitative detection of enterotoxigenic Escherichia coli in surface waters by real-time PCR with molecular beacon. Environ Sci Technol 42: 4577-4582. PubMed Link

  217. Rice JE, Sanchez JA, Pierce KE, and Wangh LJ (2002) Real-time PCR with molecular beacons provides a highly accurate assay for detection of Tay-Sachs alleles in single cells. Prenat Diagn 22: 1130-1134. PubMed Link

  218. Rousseau S and Brunel D (2003) Use of molecular beacon for the detection of fertile male plants in batches of sterile male rapeseed. Molecular Breeding 12: 91-96. PubMed Link

  219. Roy S, Kabir M, Mondal D, Ali IK, Petri WA, Jr., and Haque R (2005) Real-time PCR assay for diagnosis of Entamoeba histolytica infection. J Clin Microbiol 43: 2168-2172. PubMed Link

  220. Saidac DS, Marras SA, and Parveen N (2009) Detection and quantification of Lyme spirochetes using sensitive and specific molecular beacon probes. BMC Microbiol 9: 43. PubMed Link

  221. Sanchez JA, Pierce KE, Rice JE, and Wangh LJ (2004) Linear-After-The-Exponential (LATE)-PCR: An advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc Natl Acad Sci USA 101: 1933-1938.

  222. Sandhya S, Chen W, and Mulchandani A (2008) Molecular beacons: a real-time polymerase chain reaction assay for detecting Escherichia coli from fresh produce and water. Anal Chim Acta 614: 208-212. PubMed Link

  223. Santi-Rocca J, Weber C, Guigon G, Sismeiro O, Coppee JY, and Guillen N (2007) The lysine-and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis. Cell Microbiol. PubMed Link

  224. Sebti A, Kiehn TE, Perlin D, Chaturvedi V, Wong M, Doney A, Park S, and Sepkowitz KA (2001) Candida dubliniensis at a cancer center. Clin Infect Dis 32: 1034-1038. PubMed Link

  225. Shi L, Jung YJ, Tyagi S, Gennaro ML, and North RJ (2003) Expression of Th1-mediated immunity in mouse lungs induces a Mycobacterium tuberculosis transcription pattern characteristic of nonreplicating persistence. Proc Natl Acad Sci USA 100: 241-246. PubMed Link

  226. Shi M, Caprau D, Dagle J, Christiansen L, Christensen K, and Murray JC (2004) Application of kinetic polymerase chain reaction and molecular beacon assays to pooled analyses and high-throughput genotyping for candidate genes. Birth Defects Res Part A Clin Mol Teratol 70: 65-74. PubMed Link

  227. Shih IM, Zhou W, Goodman SN, Lengauer C, Kinzler KW, and Vogelstein B (2001) Evidence that genetic instability occurs at an early stage of colorectal tumorigenesis. Cancer Res 61: 818-822. PubMed Link

  228. Sidon P, El Housni H, Dessars B, and Heimann P (2006) The JAK2V617F mutation is detectable at very low level in peripheral blood of healthy donors. Leukemia 20: 1622. PubMed Link

  229. Singh A, Singh Y, Pine R, Shi L, Chandra R, and Drlica K (2006) Protein kinase I of Mycobacterium tuberculosis: Cellular localization and expression during infection of macrophage-like cells. Tuberculosis (Edinb) 86: 28-33. PubMed Link

  230. Singh J, Batish VK, and Grover S (2009) A molecular beacon-based duplex real-time polymerase chain reaction assay for simultaneous detection of escherichia coli O157:H7 and listeria monocytogenes in milk and milk products. Foodborne Pathog Dis. PubMed Link

  231. Sinsimer D, Leekha S, Park S, Marras SA, Koreen L, Willey B, Naidich S, Musser KA, and Kreiswirth BN (2005) Use of a multiplex molecular beacon platform for rapid detection of methicillin and vancomycin resistance in Staphylococcus aureus. J Clin Microbiol 43: 4585-4591. PubMed Link

  232. Smit ML, Giesendorf BA, Vet JA, Trijbels FJ, and Blom HJ (2001) Semiautomated DNA mutation analysis using a robotic workstation and molecular beacons. Clin Chem 47: 739-744. PubMed Link

  233. Span PN, Manders P, Heuvel JJ, Thomas CM, Bosch RR, Beex LV, and Sweep CG (2003) Molecular beacon reverse transcription-PCR of human chorionic gonadotropin-beta-3, -5, and -8 mRNAs has prognostic value in breast cancer. Clin Chem 49: 1074-1080. PubMed Link

  234. Steuerwald N, Cohen J, Herrera RJ, and Brenner CA (1999) Analysis of gene expression in single oocytes and embryos by real-time rapid cycle fluorescence monitored RT-PCR. Mol Hum Reprod 5: 1034-1039. PubMed Link

  235. Sum SS, Wong DK, Yuen MF, Yuan HJ, Yu J, Lai CL, Ho D, and Zhang L (2004) Real-time PCR assay using molecular beacon for quantitation of hepatitis B virus DNA. J Clin Microbiol 42: 3438-3440. PubMed Link

  236. Takacs T, Jeney C, Kovacs L, Mozes J, Benczik M, and Sebe A (2008) Molecular beacon-based real-time PCR method for detection of 15 high-risk and 5 low-risk HPV types. J Virol Methods. PubMed Link

  237. Taylor JM, Paterson LJ, and Havis ND (2010) A quantitative real-time PCR assay for the detection of Ramularia collo-cygni from barley (Hordeum vulgare). Lett Appl Microbiol. PubMed Link

  238. Templeton KE, Scheltinga SA, Beersma MF, Kroes AC, and Claas EC (2004) Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4. J Clin Microbiol 42: 1564-1569. PubMed Link

  239. Templeton KE, Scheltinga SA, Graffelman AW, Van Schie JM, Crielaard JW, Sillekens P, Van Den Broek PJ, Goossens H, Beersma MF, and Claas EC (2003) Comparison and evaluation of real-time PCR, real-time nucleic acid sequence-based amplification, conventional PCR, and serology for diagnosis of Mycoplasma pneumoniae. J Clin Microbiol 41: 4366-4371. PubMed Link

  240. Templeton KE, Scheltinga SA, Sillekens P, Crielaard JW, van Dam AP, Goossens H, and Claas EC (2003) Development and clinical evaluation of an internally controlled, single-tube multiplex real-time PCR assay for detection of Legionella pneumophila and other Legionella species. J Clin Microbiol 41: 4016-4021. PubMed Link

  241. Templeton KE, Scheltinga SA, Van Der Zee A, Diederen BM, Kruijssen AM, Goossens H, Kuijper E, and Claas EC (2003) Evaluation of real-time PCR for detection of and discrimination between Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii for clinical diagnosis. J Clin Microbiol 41: 4121-4126. PubMed Link

  242. Terrell KA, Rasmussen TA, Trygg C, Bunnell BA, and Buck WR (2007) Molecular beacon genotyping for globoid cell leukodystrophy from hair roots in the twitcher mouse and rhesus macaque. J Neurosci Methods 163: 60-66. PubMed Link

  243. Uyttendaele M, Vanwildemeersch K, and Debevere J (2003) Evaluation of real-time PCR vs automated ELISA and a conventional culture method using a semi-solid medium for detection of Salmonella. Letters in Applied Microbiology 37: 386-391.

  244. Valentin A, Trivedi H, Lu W, Kostrikis LG, and Pavlakis GN (2000) CXCR4 mediates entry and productive infection of syncytia-inducing (X4) HIV-1 strains in primary macrophages. Virology 269: 294-304. PubMed Link

  245. van Schie RC, Marras SAE, Conroy JM, Nowak NJ, Catanese JJ, and de Jong PJ (2000) Semiautomated clone verification by real-time PCR using molecular beacons. Biotechniques 29: 1296-1306. PubMed Link

  246. Varma-Basil M, El-Hajj H, Colangeli R, Hazbon MH, Kumar S, Bose M, Bobadilla-del-Valle M, Garcia LG, Hernandez A, Kramer FR, Osornio JS, Ponce-de-Leon A, and Alland D (2004) Rapid detection of rifampin resistance in Mycobacterium tuberculosis isolates from India and Mexico by a molecular beacon assay. J Clin Microbiol 42: 5512-5516. PubMed Link

  247. Varma-Basil M, El-Hajj H, Marras SAE, Hazbon MH, Mann JM, Connell ND, Kramer FR, and Alland D (2004) Molecular beacons for multiplex detection of four bacterial bioterrorism agents. Clin Chem 50: 1060-1062. PubMed Link

  248. Vet JA, Majithia AR, Marras SAE, Tyagi S, Dube S, Poiesz BJ, and Kramer FR (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc Natl Acad Sci USA 96: 6394-6399. PubMed Link

  249. Waltz TL, Marras SAE, Rochford G, Nolan J, Lee E, Melegari M, and Pollack H (2005) Development of a molecular-beacon assay to detect the G1896A precore mutation in Hepatitis B virus-infected individuals. J Clin Microbiol 43: 254-258. PubMed Link

  250. Wang XW, Ao JQ, Li QG, and Chen XH (2006) Quantitative detection of a marine fish iridovirus isolated from large yellow croaker, pseudosciaena crocea, using a molecular beacon. J Virol Methods 133: 76-81. PubMed Link

  251. Warren DK, Liao RS, Merz LR, Eveland M, and Dunne WM, Jr. (2004) Detection of methicillin-resistant Staphylococcus aureus directly from nasal swab specimens by a real-time PCR assay. J Clin Microbiol 42: 5578-5581. PubMed Link

  252. Xiao G, Chicas A, Olivier M, Taya Y, Tyagi S, Kramer FR, and Bargonetti J (2000) A DNA damage signal is required for p53 to activate gadd45. Cancer Res 60: 1711-1719. PubMed Link

  253. Yang JH, Lai JP, Douglas SD, Metzger D, Zhu XH, and Ho WZ (2002) Real-time RT-PCR for quantitation of hepatitis C virus RNA. J Virol Methods 102: 119-128. PubMed Link

  254. Yeh HY, Hwang YC, Yates MV, Mulchandani A, and Chen W (2008) Detection of hepatitis A virus using a combined cell-culture - molecular beacon assay. Appl Environ Microbiol. PubMed Link

  255. Yeo AC, Chan KP, Kumarasinghe G, and Yap HK (2005) Rapid detection of codon 460 mutations in the UL97 gene of ganciclovir-resistant cytomegalovirus clinical isolates by real-time PCR using molecular beacons. Mol Cell Probes 19: 389-393. PubMed Link

  256. Yesilkaya H, Meacci F, Niemann S, Hillemann D, Rusch-Gerdes S, Barer MR, Andrew PW, and Oggioni MR (2006) Evaluation of molecular-beacon, TaqMan, and fluorescence resonance energy transfer probes for detection of antibiotic resistance-conferring single nucleotide polymorphisms in mixed Mycobacterium tuberculosis DNA extracts. J Clin Microbiol 44: 3826-3829. PubMed Link

  257. Zhan G, Shaheen F, Mackiewicz M, Fenik P, and Veasey SC (2002) Single cell laser dissection with molecular beacon polymerase chain reaction identifies 2A as the predominant serotonin receptor subtype in hypoglossal motoneurons. Neuroscience 113: 145-154. PubMed Link

  258. Zhang L, Lewin SR, Markowitz M, Lin HH, Skulsky E, Karanicolas R, He Y, Jin X, Tuttleton S, Vesanen M, Spiegel H, Kost R, van Lunzen J, Stellbrink HJ, Wolinsky S, Borkowsky W, Palumbo P, Kostrikis LG, and Ho DD (1999) Measuring recent thymic emigrants in blood of normal and HIV-1-infected individuals before and after effective therapy. J Exp Med 190: 725-732. PubMed Link

  259. Zhang X, Yu RM, Jones PD, Lam GK, Newsted JL, Gracia T, Hecker M, Hilscherova K, Sanderson T, Wu RS, and Giesy JP (2005) Quantitative RT-PCR methods for evaluating toxicant-induced effects on steroidogenesis using the H295R cell line. Environ Sci Technol 39: 2777-2785. PubMed Link


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    VI.   Papers on molecular beacons used in NASBA


  260. Abd el-Galil KH, el-Sokkary MA, Kheira SM, Salazar AM, Yates MV, Chen W, and Mulchandani A (2005) Real-time nucleic acid sequence-based amplification assay for detection of hepatitis A virus. Appl Environ Microbiol 71: 7113-7116. PubMed Link

  261. Antunes R, Figueiredo S, Bartolo I, Pinheiro M, Rosado L, Soares I, Lourenco H, and Taveira N (2003) Evaluation of the clinical sensitivities of three viral load assays with plasma samples from a pediatric population predominantly infected with human immunodeficiency virus type 1 subtype G and BG recombinant forms. J Clin Microbiol 41: 3361-3367. PubMed Link

  262. Ayele W, Baar MP, Goudsmit J, Kliphuis A, Tilahun T, Dorigo-Zetsma W, Wolday D, Abebe A, Mengistu Y, and Pollakis G (2005) Surveillance technology for HIV-1 subtype C in Ethiopia: an env-based NASBA molecular beacon assay to discriminate between subcluster C and C'. J Virol Methods 130: 22-29. PubMed Link

  263. Ayele W, Pollakis G, Abebe A, Fisseha B, Tegbaru B, Tesfaye G, Mengistu Y, Wolday D, van Gemen B, Goudsmit J, Dorigo-Zetsma W, and de Baar MP (2004) Development of a nucleic acid sequence-based amplification assay that uses gag-based molecular beacons to distinguish between Human Immunodeficiency Virus type 1 subtype C and C' infections in Ethiopia. J Clin Microbiol 42: 1534-1541. PubMed Link

  264. Berard C, Cazalis MA, Leissner P, and Mougin B (2004) DNA nucleic acid sequence-based amplification-based genotyping for polymorphism analysis. Biotechniques 37: 680-686. PubMed Link

  265. Capaul SE and Gorgievski-Hrisoho M (2005) Detection of enterovirus RNA in cerebrospinal fluid (CSF) using NucliSens EasyQ Enterovirus assay. J Clin Virol 32: 236-240. PubMed Link

  266. Casper ET, Paul JH, Smith MC, and Gray M (2004) Detection and quantification of the red tide dinoflagellate Karenia brevis by real-time nucleic acid sequence-based amplification. Applied and Environmental Microbiology 70: 4727-4732. PubMed Link

  267. Chantratita W, Pongtanapisit W, Piroj W, Srichunrasmi C, and Seesuai S (2004) Development and comparison of the real-time amplification based methods--NASBA-Beacon, RT-PCR taqman and RT-PCR hybridization probe assays--for the qualitative detection of SARS coronavirus. Southeast Asian J Trop Med Public Health 35: 623-629. PubMed Link

  268. Churruca E, Girbau C, Martinez I, Mateo E, Alonso R, and Fernandez-Astorga A (2007) Detection of Campylobacter jejuni and Campylobacter coli in chicken meat samples by real-time nucleic acid sequence-based amplification with molecular beacons. Int J Food Microbiol. PubMed Link

  269. Cuschieri KS, Whitley MJ, and Cubie HA (2004) Human papillomavirus type specific DNA and RNA persistence-implications for cervical disease progression and monitoring. J Med Virol 73: 65-70. PubMed Link

  270. de Baar MP, Timmermans EC, Bakker M, de Rooij E, van Gemen B, and Goudsmit J (2001) One-tube real-time isothermal amplification assay to identify and distinguish human immunodeficiency virus type 1 subtypes A, B, and C and circulating recombinant forms AE and AG. J Clin Microbiol 39: 1895-1902. PubMed Link

  271. de Baar MP, van Dooren MW, de Rooij E, Bakker M, van Gemen B, Goudsmit J, and de Ronde A (2001) Single rapid real-time monitored isothermal RNA amplification assay for quantification of Human Immunodeficiency Virus type 1 isolates from groups M, N, and O. J Clin Microbiol 39: 1378-1384. PubMed Link

  272. de Mendoza C, Koppelman M, Montes B, Ferre V, Soriano V, Cuypers H, Segondy M, and Oosterlaken T (2005) Multicenter evaluation of the NucliSens EasyQ HIV-1 v1.1 assay for the quantitative detection of HIV-1 RNA in plasma. J Virol Methods 127: 54-59. PubMed Link

  273. de Ronde A, van Dooren M, van Der Hoek L, Bouwhuis D, de Rooij E, van Gemen B, de Boer R, and Goudsmit J (2001) Establishment of new transmissible and drug-sensitive Human Immunodeficiency Virus type 1 wild types due to transmission of nucleoside analogue-resistant virus. J Virol 75: 595-602. PubMed Link

  274. Deiman B, Jay C, Zintilini C, Vermeer S, van Strijp D, Venema F, and van de Wiel P (2008) Efficient amplification with NASBA((R)) of hepatitis B virus, herpes simplex virus and methicillin resistant Staphylococcus aureus DNA. J Virol Methods 151: 283-293. PubMed Link

  275. Deiman B, Schrover C, Moore C, Westmoreland D, and van de Wiel P (2007) Rapid and highly sensitive qualitative real-time assay for detection of respiratory syncytial virus A and B using NASBA and molecular beacon technology. J Virol Methods. PubMed Link

  276. Dimov IK, Garcia-Cordero JL, O'Grady J, Poulsen CR, Viguier C, Kent L, Daly P, Lincoln B, Maher M, O'Kennedy R, Smith TJ, Ricco AJ, and Lee LP (2008) Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics. Lab Chip 8: 2071-2078. PubMed Link

  277. Fihman V, Hannouche D, Bousson V, Bardin T, Liote F, Raskine L, Riahi J, Sanson-Le Pors MJ, and Bercot B (2007) Improved diagnosis specificity in bone and joint infections using molecular techniques. J Infect. PubMed Link

  278. Fox JD, Han S, Samuelson A, Zhang Y, Neale ML, and Westmoreland D (2002) Development and evaluation of nucleic acid sequence based amplification (NASBA) for diagnosis of enterovirus infections using the NucliSens Basic Kit. J Clin Virol 24: 117-130. PubMed Link

  279. Fradet Y, Saad F, Aprikian A, Dessureault J, Elhilali M, Trudel C, Masse B, Piche L, and Chypre C (2004) uPM3, a new molecular urine test for the detection of prostate cancer. Urology 64: 311-316.

  280. Fykse EM, Skogan G, Davies W, Olsen JS, and Blatny JM (2007) Detection of vibrio cholerae by real-time nucleic acid sequence-based amplification. Appl Environ Microbiol 73: 1457-1466. PubMed Link

  281. Ginocchio CC, Manji R, Lotlikar M, and Zhang F (2008) Clinical evaluation of NucliSENS magnetic extraction and NucliSENS analytic specific reagents for the real time detection of human metapneumovirus (hMPV) in pediatric respiratory specimens. J Clin Microbiol. PubMed Link

  282. Goncalves MC, Klerks MM, Verbeek M, Vega J, and van den Heuvel J (2002) The use of molecular beacons combined with NASBA for the sensitive detection of sugarcane yellow leaf virus. European Journal of Plant Pathology 108: 401-407. PubMed Link

  283. Gore HM, Wakeman CA, Hull RM, and McKillip JL (2003) Real-time molecular beacon NASBA reveals hblC expression from Bacillus spp. in milk. Biochem Biophys Res Commun 311: 386-390. PubMed Link

  284. Gottesman BS, Grossman Z, Lorber M, Levi I, Shitrit P, Katzir M, Shahar E, Gottesman G, and Chowers M (2006) Comparative performance of the Amplicor HIV-1 monitor assay versus NucliSens EasyQ in HIV subtype C-infected patients. J Med Virol 78: 883-887. PubMed Link

  285. Greijer AE, Adriaanse HM, Dekkers CA, and Middeldorp JM (2002) Multiplex real-time NASBA for monitoring expression dynamics of human cytomegalovirus encoded IE1 and pp67 RNA. J Clin Virol 24: 57-66. PubMed Link

  286. Gulliksen A, Solli L, Karlsen F, Rogne H, Hovig E, Nordstrom T, and Sirevag R (2004) Real-time nucleic acid sequence-based amplification in nanoliter volumes. Anal Chem 76: 9-14. PubMed Link

  287. Heijnen L and Medema G (2009) Method for rapid detection of viable Escherichia coli in water using real-time NASBA. Water Res. PubMed Link

  288. Hibbitts S, Rahman A, John R, Westmoreland D, and Fox JD (2003) Development and evaluation of NucliSens basic kit NASBA for diagnosis of parainfluenza virus infection with 'end-point' and 'real-time' detection. J Virol Methods 108: 145-155. PubMed Link

  289. Keightley MC, Sillekens P, Schippers W, Rinaldo C, and George KS (2005) Real-time NASBA detection of SARS-associated coronavirus and comparison with real-time reverse transcription-PCR. J Med Virol 77: 602-608. PubMed Link

  290. Klerks MM, Leone GO, Verbeek M, van den Heuvel JF, and Schoen CD (2001) Development of a multiplex AmpliDet RNA for the simultaneous detection of potato leafroll virus and potato virus Y in potato tubers. J Virol Methods 93: 115-125. PubMed Link

  291. Klerks MM, Lindner JL, Vaskova D, Spak J, Thompson JR, Jelkmann W, and Schoen CD (2004) Detection and tentative grouping of strawberry crinkle virus isolates. Eur J Plant Pathol 110: 45-52.

  292. Lam HY, Chen JH, Wong KH, Chan K, Li P, Lee MP, Tsang DN, Yuen KY, and Yam WC (2006) Evaluation of NucliSens EasyQtrade mark HIV-1 assay for quantification of HIV-1 subtypes prevalent in South-east Asia. J Clin Virol 38: 39-43. PubMed Link

  293. Lamhoujeb S, Charest H, Fliss I, Ngazoa S, and Jean J (2009) Real-time molecular beacon NASBA for rapid and sensitive detection of norovirus GII in clinical samples. Can J Microbiol 55: 1375-1380. PubMed Link

  294. Lamhoujeb S, Fliss I, Ngazoa SE, and Jean J (2008) Evaluation of the persistence of infectious human noroviruses on food surfaces using molecular beacon-based nucleic acid sequence-based amplification. Appl Environ Microbiol. PubMed Link

  295. Lanciotti RS and Kerst AJ (2001) Nucleic acid sequence-based amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses. J Clin Microbiol 39: 4506-4513. PubMed Link

  296. Landry ML, Garner R, and Ferguson D (2005) Real-time nucleic acid sequence-based amplification using molecular beacons for detection of enterovirus RNA in clinical specimens. J Clin Microbiol 43: 3136-3139. PubMed Link

  297. Leone G, van Schijndel H, van Gemen B, Kramer FR, and Schoen CD (1998) Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res 26: 2150-2155. PubMed Link

  298. Loens K, Beck T, Goossens H, Ursi D, Overdijk M, Sillekens P, and Ieven M (2006) Development of conventional and real-time nucleic acid sequence-based amplification assays for detection of Chlamydophila pneumoniae in respiratory specimens. J Clin Microbiol 44: 1241-1244. PubMed Link

  299. Loens K, Beck T, Goossens H, Ursi D, Overdijk M, Sillekens P, and Ieven M (2006) Development of conventional and real-time NASBA(R) for the detection of Legionella species in respiratory specimens. J Microbiol Methods 67: 408-415. PubMed Link

  300. Loens K, Beck T, Ursi D, Overdijk M, Sillekens P, Goossens H, and Ieven M (2007) Development of real-time multiplex NASBA(R) for the detection of Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella spp. in respiratory specimens. J Clin Microbiol. PubMed Link

  301. Loens K, Ieven M, Ursi D, Beck T, Overdijk M, Sillekens P, and Goossens H (2003) Detection of Mycoplasma pneumoniae by real-time nucleic acid sequence-based amplification. J Clin Microbiol 41: 4448-4450. PubMed Link

  302. McClernon DR, Vavro C, and St Clair M (2006) Evaluation of a real-time nucleic acid sequence-based amplification assay using molecular beacons for detection of human immunodeficiency virus type 1. J Clin Microbiol 44: 2280-2282. PubMed Link

  303. Mohlala BK, Tucker TJ, Besser MJ, Williamson C, Yeats J, Smit L, Anthony J, and Puren A (2005) Investigation of HIV in amniotic fluid from HIV-infected pregnant women at full term. J Infect Dis 192: 488-491. PubMed Link

  304. Molden T, Kraus I, Skomedal H, Nordstrom T, and Karlsen F (2007) PreTecttrade mark HPV-Proofer: Real-time detection and typing of E6/E7 mRNA from carcinogenic human papillomaviruses. J Virol Methods 142: 204-212. PubMed Link

  305. Moore C, Hibbitts S, Owen N, Corden SA, Harrison G, Fox J, Gelder C, and Westmoreland D (2004) Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A. J Med Virol 74: 619-628. PubMed Link

  306. Moore C, Valappil M, Corden S, and Westmoreland D (2006) Enhanced clinical utility of the NucliSens EasyQ RSV A+B Assay for rapid detection of respiratory syncytial virus in clinical samples. Eur J Clin Microbiol Infect Dis 25: 167-174. PubMed Link

  307. Nadal A, Coll A, Cook N, and Pla M (2007) A molecular beacon-based real time NASBA assay for detection of listeria monocytogenes in food products: Role of target mRNA secondary structure on NASBA design. J Microbiol Methods 68: 623-632. PubMed Link

  308. Patterson SS, Casper ET, Garcia-Rubio L, Smith MC, and Paul JH, 3rd (2005) Increased precision of microbial RNA quantification using NASBA with an internal control. J Microbiol Methods 60: 343-352. PubMed Link

  309. Patterson SS, Smith MW, Casper ET, Huffman D, Stark L, Fries D, and Paul JH (2006) A nucleic acid sequence-based amplification assay for real-time detection of norovirus genogroup II. J Appl Microbiol 101: 956-963. PubMed Link

  310. Polstra AM, Goudsmit J, and Cornelissen M (2002) Development of real-time NASBA assays with molecular beacon detection to quantify mRNA coding for HHV-8 lytic and latent genes. BMC Infect Dis 2: 18-28. PubMed Link

  311. Rodes B, Sheldon J, Toro C, Cuevas L, Perez-Pastrana E, Herrera I, and Soriano V (2007) Quantitative detection of plasma human immunodeficiency virus type 2 subtype A RNA by the Nuclisens EasyQ Assay (version 1.1). J Clin Microbiol 45: 88-92. PubMed Link

  312. Rodriguez-Lazaro D, D'Agostino M, Pla M, and Cook N (2004) Construction strategy for an internal amplification control for real-time diagnostic assays using nucleic acid sequence-based amplification: development and clinical application. J Clin Microbiol 42: 5832-5836. PubMed Link

  313. Rodriguez-Lazaro D, Lloyd J, Herrewegh A, Ikonomopoulos J, D'Agostino M, Pla M, and Cook N (2004) A molecular beacon-based real-time NASBA assay for detection of Mycobacterium avium subsp. paratuberculosis in water and milk. FEMS Microbiol Lett 237: 119-126. PubMed Link

  314. Rutjes SA, Italiaander R, van den Berg HH, Lodder WJ, and de Roda Husman AM (2005) Isolation and detection of enterovirus RNA from large-volume water samples by using the NucliSens miniMAG system and real-time nucleic acid sequence-based amplification. Appl Environ Microbiol 71: 3734-3740. PubMed Link

  315. Schneider P, Wolters L, Schoone G, Schallig H, Sillekens P, Hermsen R, and Sauerwein R (2005) Real-time nucleic acid sequence-based amplification is more convenient than real-time PCR for quantification of Plasmodium falciparum. J Clin Microbiol 43: 402-405. PubMed Link

  316. Starkey WG, Millar RM, Jenkins ME, Ireland JH, Muir KF, and Richards RH (2004) Detection of piscine nodaviruses by real-time nucleic acid sequence based amplification (NASBA). Dis Aquat Organ 59: 93-100. PubMed Link

  317. Starkey WG, Smail DA, Bleie H, Muir KF, Ireland JH, and Richards RH (2006) Detection of infectious salmon anaemia virus by real-time nucleic acid sequence based amplification. Dis Aquat Organ 72: 107-113. PubMed Link

  318. Stevens W, Horsfield P, and Scott LE (2007) Evaluation of the performance of the automated NucliSENS EasyMAG and EasyQ systems versus the Roche Ampliprep/Amplicor combination for high throughput HIV viral load monitoring. J Clin Microbiol 45: 1244-1249. PubMed Link

  319. Stevens W, Wiggill T, Horsfield P, Coetzee L, and Scott LE (2005) Evaluation of the NucliSens EasyQ assay in HIV-1-infected individuals in South Africa. J Virol Methods 124: 105-110. PubMed Link

  320. Szemes M, Klerks MM, van den Heuvel JF, and Schoen CD (2002) Development of a multiplex AmpliDet RNA assay for simultaneous detection and typing of potato virus Y isolates. J Virol Methods 100: 83-96. PubMed Link

  321. Szemes M and Schoen CD (2003) Design of molecular beacons for AmpliDet RNA assay-characterization of binding stability and probe specificity. Anal Biochem 315: 189-201. PubMed Link

  322. van Beckhoven JR, Stead DE, and van der Wolf JM (2002) Detection of Clavibacter michiganensis subsp. sepedonicus by AmpliDet RNA, a new technology based on real-time monitoring of NASBA amplicons with a molecular beacon. J Appl Microbiol 93: 840-849. PubMed Link

  323. van Beuningen R, Marras SAE, Kramer FR, Oosterlaken T, Weusten J, Borst G, and van de Wiel P (2001) Development of a high-throughput detection system for HIV-1 using real-time NASBA based on molecular beacons. SPIE 4264: 66-71.

  324. Van der Wolf JM, Van Beckhoven J, De Haan EG, Van den Bovenkamp GW, and Leone GOM (2004) Specific detection of Ralstonia solanacearum 16S rRNA sequences by AmpliDet RNA. European Journal of Plant Pathology 110: 25-33. PubMed Link

  325. Vaskova D, Spak J, Klerks MM, Schoen CD, Thompson JR, and Jelkmann W (2004) Real-time NASBA for detection of strawberry vein banding virus. European Journal of Plant Pathology 110: 213-221. PubMed Link

  326. Weusten JJ, Carpay WM, Oosterlaken TA, van Zuijlen MC, and van de Wiel PA (2002) Principles of quantitation of viral loads using nucleic acid sequence-based amplification in combination with homogeneous detection using molecular beacons. Nucleic Acids Res 30: e26. PubMed Link

  327. Weusten JJ, Wouters PA, van Zuijlen MC, and van de Wiel PA (2002) Stochastic processes defining sensitivity and variability of internally calibrated quantitative NASBA-based viral load assays. Nucleic Acids Res 30: e137. PubMed Link

  328. Yao J, Liu Z, Ko LS, Pan G, and Jiang Y (2005) Quantitative detection of HIV-1 RNA using NucliSens EasyQ HIV-1 assay. J Virol Methods 129: 40-46. PubMed Link

  329. Yates S, Penning M, Goudsmit J, Frantzen I, van de Weijer B, van Strijp D, and van Gemen B (2001) Quantitative detection of hepatitis B virus DNA by real-time nucleic acid sequence-based amplification with molecular beacon detection. J Clin Microbiol 39: 3656-3665. PubMed Link

  330. Zhao Y, Park S, Kreiswirth BN, Ginocchio CC, Veyret R, Laayoun A, Troesch A, and Perlin DS (2009) A rapid real-time nucleic acid sequence-based amplification (NASBA)-molecular beacons platform to detect fungal and bacterial bloodstream infections. J Clin Microbiol. PubMed Link

  331. Zhao Y, Park S, Warn P, Shrief R, Harrison E, and Perlin DS (2010) Detection of Aspergillus fumigatus in a rat model of invasive pulmonary aspergillosis by real-time nucleic acid sequence-based amplification (NASBA). J Clin Microbiol. PubMed Link


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    VII.   Papers on molecular beacons used on arrays


  332. Beaucage SL (2001) Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications. Current Medicinal Chemistry 8: 1213-1244.

  333. Bockisch B, Grunwald T, Spillner E, and Bredehorst R (2005) Immobilized stem-loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA. Nucleic Acids Res 33: e101. PubMed Link

  334. Brown LJ, Cummins J, Hamilton A, and Brown T (2000) Molecular beacons attached to glass beads flouresce upon hybridisation to target DNA. Chem Commun (Camb) 7: 621-622.

  335. Culha M, Stokes DL, Griffin GD, and Vo-Dinh T (2004) Application of a miniature biochip using the molecular beacon probe in breast cancer gene BRCA1 detection. Biosens Bioelectron 19: 1007-1012. PubMed Link

  336. Culha M, Stokes DL, Griffin GD, and Vo-Dinh T (2004) Screening for the breast cancer gene (BRCA1) using a biochip system and molecular beacon probes immobilized on solid surfaces. J Biomed Opt 9: 439-443. PubMed Link

  337. Dai A, Yang W, Firlar E, Marras SAE, and Libera M (2012) Surface-patterned microgel-tethered molecular beacons. Soft Matter 8: 3067-3076.

  338. Du H, Disney MD, Miller BL, and Krauss TD (2003) Hybridization-based unquenching of DNA hairpins on au surfaces: prototypical molecular beacon biosensors. J Am Chem Soc 125: 4012-4013. PubMed Link

  339. Du H, Strohsahl CM, Camera J, Miller BL, and Krauss TD (2005) Sensitivity and specificity of metal surface-immobilized molecular beacon biosensors. J Am Chem Soc 127: 7932-7940. PubMed Link

  340. Epstein JR, Leung AP, Lee KH, and Walt DR (2003) High-density, microsphere-based fiber optic DNA microarrays. Biosens Bioelectron 18: 541-546. PubMed Link

  341. Fang XH, Liu XJ, Schuster S, and Tan WH (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. Journal of the American Chemical Society 121: 2921-2922.

  342. Kim H, Kane MD, Kim S, Dominguez W, Applegate BM, and Savikhin S (2006) A molecular beacon DNA microarray system for rapid detection of E. coli O157:H7 that eliminates the risk of a false negative signal. Biosens Bioelectron 22: 1041-1047. PubMed Link

  343. Li J, Tan W, Wang K, Xiao D, Yang X, He X, and Tang Z (2001) Ultrasensitive optical DNA biosensor based on surface immobilization of molecular beacon by a bridge structure. Anal Sci 17: 1149-1153. PubMed Link

  344. Liu X, Farmerie W, Schuster S, and Tan W (2000) Molecular beacons for DNA biosensors with micrometer to submicrometer dimensions. Anal Biochem 283: 56-63. PubMed Link

  345. Liu X and Tan W (1999) A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons. Anal Chem 71: 5054-5059. PubMed Link

  346. Martinez K, Estevez MC, Wu Y, Phillips JA, Medley CD, and Tan W (2009) Locked nucleic acid based beacons for surface interaction studies and biosensor development. Anal Chem 81: 3448-3454. PubMed Link

  347. Palecek E (2004) Surface-attached molecular beacons light the way for DNA sequencing. Trends Biotechnol 22: 55-58. PubMed Link

  348. Situma C, Moehring AJ, Noor MA, and Soper SA (2006) Immobilized molecular beacons: A new strategy using UV-activated poly(methyl methacrylate) surfaces to provide large fluorescence sensitivities for reporting on molecular association events. Anal Biochem 363: 35-45. PubMed Link

  349. Steemers FJ, Ferguson JA, and Walt DR (2000) Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat Biotechnol 18: 91-94. PubMed Link

  350. Wang H, Li J, Liu H, Liu Q, Mei Q, Wang Y, Zhu J, He N, and Lu Z (2002) Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res 30: e61. PubMed Link

  351. Yao G and Tan W (2004) Molecular beacon-based array for sensitive DNA analysis. Anal Biochem 331: 216-223. PubMed Link

  352. Zhao X, Tapec-Dytioco R, Wang K, and Tan W (2003) Collection of trace amounts of DNA/mRNA molecules using genomagnetic nanocapturers. Anal Chem 75: 3144-3151. PubMed Link


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    VIII.   Papers on general application of molecular beacons


  353. Alexander JC, Browne S, Pandit A, and Rochev Y (2013) Biomaterial constructs for delivery of multiple therapeutic genes: a spatiotemporal evaluation of efficacy using molecular beacons. PLoS One 8: e65749. PMI: 23755278: PubMed Link

  354. Andersen CB, Holst-Jensen A, Berdal KG, Thorstensen T, and Tengs T (2006) Equal performance of TaqMan, MGB, molecular beacon, and SYBR green-based detection assays in detection and quantification of roundup ready soybean. J Agric Food Chem 54: 9658-9663. PMI: 17177484: PubMed Link

  355. Angelatos AS, Johnston AP, Wang Y, and Caruso F (2007) Probing the permeability of polyelectrolyte multilayer capsules via a molecular beacon approach. Langmuir 23: 4554-4562. PMI: 17338557: PubMed Link

  356. Antony T and Subramaniam V (2002) A molecular beacon strategy for real-time monitoring of triplex DNA formation kinetics. Antisense Nucleic Acid Drug Dev 12: 145-154. PMI: 12162697: PubMed Link

  357. Antony T, Thomas T, Sigal LH, Shirahata A, and Thomas TJ (2001) A molecular beacon strategy for the thermodynamic characterization of triplex DNA: triplex formation at the promoter region of cyclin D1. Biochemistry 40: 9387-9395. PMI: 11478908: PubMed Link

  358. Asanuma H, Osawa T, Kashida H, Fujii T, Liang X, Niwa K, Yoshida Y, Shimada N, and Maruyama A (2012) A polycation-chaperoned in-stem molecular beacon system. Chem Commun (Camb) 48: 1760-1762. PMI: 22218646: PubMed Link

  359. Avila Figueroa A and Delaney S (2010) Mechanistic studies of hairpin to duplex conversion for trinucleotide repeat sequences. J Biol Chem. PMI: 20228068: PubMed Link

  360. Baker MB, Bao G, and Searles CD (2012) In vitro quantification of specific microRNA using molecular beacons. Nucleic Acids Res 40: e13. PMI: 22110035: PubMed Link

  361. Baker MB, Bao G, and Searles CD (2013) The use of molecular beacons to detect and quantify microRNA. Methods Mol Biol 1039: 279-287. PMI: 24026703: PubMed Link

  362. Ban K, Wile B, Kim S, Park HJ, Byun J, Cho KW, Saafir T, Song MK, Yu SP, Wagner M, Bao G, and Yoon YS (2013) Purification of cardiomyocytes from differentiating pluripotent stem cells using molecular beacons that target cardiomyocyte-specific mRNA. Circulation 128: 1897-1909. PMI: 23995537: PubMed Link

  363. Bang GS, Cho S, and Kim BG (2005) A novel electrochemical detection method for aptamer biosensors. Biosens Bioelectron 21: 863-870. PMI: 16257654: PubMed Link

  364. Bar-Ziv R and Libchaber A (2001) Effects of DNA sequence and structure on binding of RecA to single-stranded DNA. Proc Natl Acad Sci USA 98: 9068-9073. PMI: 11470894: PubMed Link

  365. Barilero T, Le Saux T, Gosse C, and Jullien L (2009) Fluorescent thermometers for dual-emission-wavelength measurements: molecular engineering and application to thermal imaging in a microsystem. Anal Chem. PMI: 19711963: PubMed Link

  366. Bates JA and Taylor EJ (2001) Scorpion ARMS primers for SNP real-time PCR detection and quantification of Pyrenophora teres. Mol Plant Pathol 2: 275-280. PMI: 20573015: PubMed Link

  367. Belon C and Frick D (2008) Monitoring helicase activity with molecular beacons. Biotechniques 45: 433-440, 442. PMI: 18855770: PubMed Link

  368. Belon CA and Frick DN (2009) Fuel specificity of the hepatitis C virus NS3 helicase. J Mol Biol. PMI: 19332076: PubMed Link

  369. Beni V, Hayes K, Lerga TM, and O'Sullivan CK (2010) Development of a gold nano-particle-based fluorescent molecular beacon for detection of cystic fibrosis associated mutation. Biosens Bioelectron 26: 307-313. PMI: 20829026: PubMed Link

  370. Beni V, Zewdu T, Joda H, Katakis I, and O'Sullivan CK (2012) Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing. Anal Bioanal Chem 402: 1001-1009. PMI: 22086396: PubMed Link

  371. Bercovici M, Kaigala GV, Mach KE, Han CM, Liao JC, and Santiago JG (2011) Rapid detection of urinary tract infections using isotachophoresis and molecular beacons. Anal Chem 83: 4110-4117. PMI: 21545089: PubMed Link

  372. Bernacchi S, Ennifar E, Toth K, Walter P, Langowski J, and Dumas P (2005) Mechanism of hairpin-duplex conversion for the HIV-1 dimerization initiation site. J Biol Chem 280: 40112-40121. PMI: 16169845: PubMed Link

  373. Bernacchi S and Mely Y (2001) Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure. Nucleic Acids Res 29: e62. PMI: 11433038: PubMed Link

  374. Bhadra S and Ellington AD (2014) A Spinach molecular beacon triggered by strand displacement. RNA 20: 1183-1194. PMI: 24942625: PubMed Link

  375. Biggins JB, Prudent JR, Marshall DJ, Ruppen M, and Thorson JS (2000) A continuous assay for DNA cleavage: The application of 'break lights' to enediynes, iron-dependent agents, and nucleases. Proceedings of the National Academy of Sciences of the USA 97: 13537-13542. PMI: ISI:000165728800018: PubMed Link

  376. Bilodeau GJ, Levesque CA, de Cock AW, Duchaine C, Briere S, Uribe P, Martin FN, and Hamelin RC (2007) Molecular Detection of Phytophthora ramorum by Real-Time Polymerase Chain Reaction Using TaqMan, SYBR Green, and Molecular Beacons. Phytopathology 97: 632-642. PMI: 18943583: PubMed Link

  377. Biner SM and Haner R (2011) A two-color, self-controlled molecular beacon. Chembiochem 12: 2733-2736. PMI: 22076865: PubMed Link

  378. Biner SM, Kummer D, Malinovskii VL, and Haner R (2011) Signal control by self-assembly of fluorophores in a molecular beacon--a model study. Org Biomol Chem 9: 2628-2633. PMI: 21350744: PubMed Link

  379. Blackstock D, Sun Q, and Chen W (2014) Fluorescent protein-based molecular beacons by zinc finger protein-guided assembly. Biotechnol Bioeng. PMI: 25163615: PubMed Link

  380. Bonnet G, Krichevsky O, and Libchaber A (1998) Kinetics of conformational fluctuations in DNA hairpin-loops. Proc Natl Acad Sci USA 95: 8602-8606. PMI: 9671724: PubMed Link

  381. Bose D, Jayaraj GG, Kumar S, and Maiti S (2013) A molecular-beacon-based screen for small molecule inhibitors of miRNA maturation. ACS Chem Biol 8: 930-938. PMI: 23402670: PubMed Link

  382. Bourdoncle A, Estevez Torres A, Gosse C, Lacroix L, Vekhoff P, Le Saux T, Jullien L, and Mergny JL (2006) Quadruplex-based molecular beacons as tunable DNA probes. J Am Chem Soc 128: 11094-11105. PMI: 16925427: PubMed Link

  383. Brody JR, Witkiewicz AK, and Yeo CJ (2011) The past, present, and future of biomarkers: a need for molecular beacons for the clinical management of pancreatic cancer. Adv Surg 45: 301-321. PMI: 21954696: PubMed Link

  384. Browne KA (2005) Sequence-specific, self-reporting hairpin inversion probes. J Am Chem Soc 127: 1989-1994. PMI: 15701035: PubMed Link

  385. Brunner J and Kraemer R (2004) Copper(II)-quenched oligonucleotide probes for fluorescent DNA sensing. J Am Chem Soc 126: 13626-13627. PMI: 15493914: PubMed Link

  386. Buranachai C, Thavarungkul P, and Kanatharana P (2012) A novel reconfigurable optical biosensor based on DNA aptamers and a DNA molecular beacon. J Fluoresc 22: 1617-1625. PMI: 22811040: PubMed Link

  387. Burris KP, Wu TC, Vasudev M, Stroscio MA, Millwood RJ, and Stewart CN, Jr. (2013) Mega-nano detection of foodborne pathogens and transgenes using molecular beacon and semiconductor quantum dot technologies. IEEE Trans Nanobioscience 12: 233-238. PMI: 23722479: PubMed Link

  388. Burucoa C, Garnier M, Silvain C, and Fauchere JL (2008) Quadruplex real-time PCR assay using allele-specific scorpion primers for detection of mutations conferring clarithromycin resistance to Helicobacter pylori. J Clin Microbiol 46: 2320-2326. PMI: 18463216: PubMed Link

  389. Bustamante LY, Crooke A, Martinez J, Diez A, and Bautista JM (2004) Dual-function stem molecular beacons to assess mRNA expression in AT-rich transcripts of Plasmodium falciparum. Biotechniques 36: 488-494. PMI: 15038165: PubMed Link

  390. Cady NC (2009) Quantum dot molecular beacons for DNA detection. Methods Mol Biol 544: 367-379. PMI: 19488712: PubMed Link

  391. Cady NC, Strickland AD, and Batt CA (2006) Optimized linkage and quenching strategies for quantum dot molecular beacons. Mol Cell Probes 21: 116-124. PMI: 17084590: PubMed Link

  392. Cai Z, Song Y, Wu Y, Zhu Z, Yang CJ, and Chen X (2013) An electrochemical sensor based on label-free functional allosteric molecular beacons for detection target DNA/miRNA. Biosens Bioelectron 41: 783-788. PMI: 23102830: PubMed Link

  393. Cao J, Feng C, Liu Y, Wang S, and Liu F (2014) Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes. Biosens Bioelectron 57: 133-138. PMI: 24583317: PubMed Link

  394. Carters R, Ferguson J, Gaut R, Ravetto P, Thelwell N, and Whitcombe D (2008) Design and use of scorpions fluorescent signaling molecules. Methods Mol Biol 429: 99-115. PMI: 18695962: PubMed Link

  395. Cazzato A, Capobianco ML, Zambianchi M, Favaretto L, Bettini C, and Barbarella G (2007) Oligothiophene molecular beacons. Bioconjug Chem 18: 318-322. PMI: 17300170: PubMed Link

  396. Cederquist KB and Keating CD (2010) Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length. Langmuir 26: 18273-18280. PMI: 21038880: PubMed Link

  397. Cederquist KB, Stoermer Golightly R, and Keating CD (2008) Molecular beacon-metal nanowire interface: effect of probe sequence and surface coverage on sensor performance. Langmuir. PMI: 18624416: PubMed Link

  398. Chakravorty S, Aladegbami B, Thoms K, Lee JS, Lee EG, Rajan V, Cho EJ, Kim H, Kwak H, Kurepina N, Cho SN, Kreiswirth B, Via LE, Barry CE, 3rd, and Alland D (2011) Rapid detection of fluoroquinolone-resistant and heteroresistant Mycobacterium tuberculosis by use of sloppy molecular beacons and dual melting-temperature codes in a real-time PCR assay. J Clin Microbiol 49: 932-940. PMI: 21191047: PubMed Link

  399. Chang CY and Stellwagen NC (2011) Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability. Biochemistry 50: 9148-9157. PMI: 21942650: PubMed Link

  400. Chang E, Zhu MQ, and Drezek R (2007) Novel siRNA-based molecular beacons for dual imaging and therapy. Biotechnol J 2: 2-5. PMI: 17330221: PubMed Link

  401. Chang IH, Tulock JJ, Liu J, Kim WS, Cannon DM, Jr., Lu Y, Bohn PW, Sweedler JV, and Cropek DM (2005) Miniaturized lead sensor based on lead-specific DNAzyme in a nanocapillary interconnected microfluidic device. Environ Sci Technol 39: 3756-3761. PMI: 15952382: PubMed Link

  402. Chen J, Jarvi M, Lo PC, Stefflova K, Wilson BC, and Zheng G (2007) Using the singlet oxygen scavenging property of carotenoid in photodynamic molecular beacons to minimize photodamage to non-targeted cells. Photochem Photobiol Sci 6: 1311-1317. PMI: 18046487: PubMed Link

  403. Chen J, Liu TW, Lo PC, Wilson BC, and Zheng G (2009) "Zipper" molecular beacons: a generalized strategy to optimize the performance of activatable protease probes. Bioconjug Chem 20: 1836-1842. PMI: 19754039: PubMed Link

  404. Chen J, Lovell JF, Lo PC, Stefflova K, Niedre M, Wilson BC, and Zheng G (2008) A tumor mRNA-triggered photodynamic molecular beacon based on oligonucleotide hairpin control of singlet oxygen production. Photochem Photobiol Sci 7: 775-781. PMI: 18597024: PubMed Link

  405. Chen Q, Wu N, Xie M, Zhang B, Chen M, Li J, Zhuo L, Kuang H, and Fu W (2012) A novel asymmetric-loop molecular beacon-based two-phase hybridization assay for accurate and high-throughput detection of multiple drug resistance-conferring point mutations in Mycobacterium tuberculosis. Med Sci Monit 18: HY5-8. PMI: 22460100: PubMed Link

  406. Cheng G, Shen B, Zhang F, Wu J, Xu Y, He P, and Fang Y (2010) A new electrochemically active-inactive switching aptamer molecular beacon to detect thrombin directly in solution. Biosens Bioelectron. PMI: 20378327: PubMed Link

  407. Cheng W, Zhang W, Yan Y, Shen B, Zhu D, Lei P, and Ding S (2014) A novel electrochemical biosensor for ultrasensitive and specific detection of DNA based on molecular beacon mediated circular strand displacement and rolling circle amplification. Biosens Bioelectron 62: 274-279. PMI: 25022510: PubMed Link

  408. Chinnappan R, Dube A, Lemay JF, and Lafontaine DA (2013) Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay. Nucleic Acids Res 41: e106. PMI: 23525464: PubMed Link

  409. Choi Y, Kim HS, Woo J, Hwang EH, Cho KW, Kim S, and Moon WK (2014) Real-Time Imaging of the Epithelial-Mesenchymal Transition Using microRNA-200a Sequence-Based Molecular Beacon-Conjugated Magnetic Nanoparticles. PLoS One 9: e102164. PMI: 25048580: PubMed Link

  410. Conde J, Rosa J, de la Fuente JM, and Baptista PV (2013) Gold-nanobeacons for simultaneous gene specific silencing and intracellular tracking of the silencing events. Biomaterials 34: 2516-2523. PMI: 23312904: PubMed Link

  411. Conley NR, Pomerantz AK, Wang H, Twieg RJ, and Moerner WE (2007) Bulk and single-molecule characterization of an improved molecular beacon utilizing H-dimer excitonic behavior. J Phys Chem B 111: 7929-7931. PMI: 17583944: PubMed Link

  412. Conlon P, Yang CJ, Wu Y, Chen Y, Martinez K, Kim Y, Stevens N, Marti AA, Jockusch S, Turro NJ, and Tan W (2008) Pyrene excimer signaling molecular beacons for probing nucleic acids. J Am Chem Soc 130: 336-342. PMI: 18078339: PubMed Link

  413. Cornett EM and Kolpashchikov DM (2013) SNP analysis using a molecular beacon-based operating cooperatively (OC) sensor. Methods Mol Biol 1039: 81-86. PMI: 24026687: PubMed Link

  414. Crey-Desbiolles C, Ahn DR, and Leumann CJ (2005) Molecular beacons with a homo-DNA stem: improving target selectivity. Nucleic Acids Res 33: e77. PMI: 15879349: PubMed Link

  415. Dahl F, Baner J, Gullberg M, Mendel-Hartvig M, Landegren U, and Nilsson M (2004) Circle-to-circle amplification for precise and sensitive DNA analysis. Proc Natl Acad Sci U S A 101: 4548-4553. PMI: 15070755: PubMed Link

  416. Darby RA, Sollogoub M, McKeen C, Brown L, Risitano A, Brown N, Barton C, Brown T, and Fox KR (2002) High throughput measurement of duplex, triplex and quadruplex melting curves using molecular beacons and a LightCycler. Nucleic Acids Res 30: e39. PMI: 11972354: PubMed Link

  417. Dave N and Liu J (2010) Fast molecular beacon hybridization in organic solvents with improved target specificity. J Phys Chem B 114: 15694-15699. PMI: 21062084: PubMed Link

  418. Deerinck TJ (2008) The application of fluorescent quantum dots to confocal, multiphoton, and electron microscopic imaging. Toxicol Pathol 36: 112-116. PMI: 18337229: PubMed Link

  419. Deng D, Zhang D, Li Y, Achilefu S, and Gu Y (2013) Gold nanoparticles based molecular beacons for in vitro and in vivo detection of the matriptase expression on tumor. Biosens Bioelectron 49: 216-221. PMI: 23770391: PubMed Link

  420. Deng P, Lee YK, and Cheng P (2005) Two-dimensional micro-bubble actuator array to enhance the efficiency of molecular beacon based DNA micro-biosensors. Biosens Bioelectron 21: 1443-1450. PMI: 16099153: PubMed Link

  421. Deng S, Cheng L, Lei J, Cheng Y, Huang Y, and Ju H (2013) Label-free electrochemiluminescent detection of DNA by hybridization with a molecular beacon to form hemin/G-quadruplex architecture for signal inhibition. Nanoscale 5: 5435-5441. PMI: 23662297: PubMed Link

  422. Dodge A, Turcatti G, Lawrence I, de Rooij NF, and Verpoorte E (2004) A microfluidic platform using molecular beacon-based temperature calibration for thermal dehybridization of surface-bound DNA. Anal Chem 76: 1778-1787. PMI: 15018583: PubMed Link

  423. Dong D, Pang Y, Gao Q, Huang X, Xu Y, and Li R (2010) Rapid monitoring of mRNA levels with a molecular beacon during microbial fermentation. J Biotechnol 145: 310-316. PMI: 19941914: PubMed Link

  424. Dong H, Ding L, Yan F, Ji H, and Ju H (2011) The use of polyethylenimine-grafted graphene nanoribbon for cellular delivery of locked nucleic acid modified molecular beacon for recognition of microRNA. Biomaterials 32: 3875-3882. PMI: 21354613: PubMed Link

  425. Dong H, Gao W, Yan F, Ji H, and Ju H (2010) Fluorescence resonance energy transfer between quantum dots and graphene oxide for sensing biomolecules. Anal Chem 82: 5511-5517. PMI: 20524633: PubMed Link

  426. Dong H, Hao K, Tian Y, Jin S, Lu H, Zhou SF, and Zhang X (2014) Label-free and ultrasensitive microRNA detection based on novel molecular beacon binding readout and target recycling amplification. Biosens Bioelectron 53: 377-383. PMI: 24185256: PubMed Link

  427. Drake TJ, Medley CD, Sen A, Rogers RJ, and Tan W (2005) Stochasticity of manganese superoxide dismutase mRNA expression in breast carcinoma cells by molecular beacon imaging. Chembiochem 6: 2041-2047. PMI: 16206227: PubMed Link

  428. Dummitt B and Chang YH (2006) Molecular beacons for DNA binding proteins: an emerging technology for detection of DNA binding proteins and their ligands. Assay Drug Dev Technol 4: 343-349. PMI: 16834539: PubMed Link

  429. Dunams D, Sarkar P, Chen W, and Yates MV (2012) Simultaneous detection of infectious human echoviruses and adenoviruses by an in situ nuclease-resistant molecular beacon-based assay. Appl Environ Microbiol 78: 1584-1588. PMI: 22194298: PubMed Link

  430. El-Yazbi AF and Loppnow GR (2013) Chimeric RNA-DNA molecular beacons for quantification of nucleic acids, single nucleotide polymophisms, and nucleic acid damage. Anal Chem 85: 4321-4327. PMI: 23544988: PubMed Link

  431. Englund EA and Appella DH (2005) Synthesis of gamma-substituted peptide nucleic acids: A new place to attach fluorophores without affecting DNA binding. Org Lett 7: 3465-3467. PMI: 16048318: PubMed Link

  432. Fang M, Lu QR, and Hong ZQ (2010) [Establishment and application of molecular beacon real-time PCR in the detection of Mycobacteriun tuberculosis]. Sichuan Da Xue Xue Bao Yi Xue Ban 41: 162-165. PMI: 20369495: PubMed Link

  433. Fang X, Li JJ, and Tan W (2000) Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Anal Chem 72: 3280-3285. PMI: 10939400: PubMed Link

  434. Fang X and Tan W (1999) Imaging single fluorescent molecules at the interface of an optical fiber probe by evanescent wave excitation. Anal Chem 71: 3101-3105. PMI: PubMed Link

  435. Fang XH, Sen A, Vicens M, and Tan WH (2003) Synthetic DNA aptamers to detect protein molecular variants in a high-throughput fluorescence quenching assay. Chembiochem 4: 829-834. PMI: ISI:000185455600006: PubMed Link

  436. Farjami E, Clima L, Gothelf KV, and Ferapontova EE (2010) DNA interactions with a Methylene Blue redox indicator depend on the DNA length and are sequence specific. Analyst. PMI: 20369213: PubMed Link

  437. Feng S, Shang Y, Wu F, Ding F, Li B, Xu J, Xu L, and Zhou X (2014) DNA nanomachines as evolved molecular beacons for in vitro and in vivo detection. Talanta 120: 141-147. PMI: 24468353: PubMed Link

  438. Feng X, Duan X, Liu L, An L, Feng F, and Wang S (2008) Cationic conjugated polyelectrolyte/molecular beacon complex for sensitive, sequence-specific, real-time DNA detection. Langmuir 24: 12138-12141. PMI: 18834161: PubMed Link

  439. Frauendorf C and Jaschke A (2001) Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem 9: 2521-2524. PMI: 11557338: PubMed Link

  440. Fu R, Li T, Lee SS, and Park HG (2011) DNAzyme molecular beacon probes for target-induced signal-amplifying colorimetric detection of nucleic acids. Anal Chem 83: 494-500. PMI: 21158421: PubMed Link

  441. Fujimoto K, Shimizu H, and Inouye M (2004) Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons. J Org Chem 69: 3271-3275. PMI: 15132531: PubMed Link

  442. Ganguli PS, Chen W, and Yates MV (2011) Detection of murine norovirus-1 by using TAT peptide-delivered molecular beacons. Appl Environ Microbiol 77: 5517-5520. PMI: 21652740: PubMed Link

  443. Ganguly S, Ghosh S, Chattopadhyay D, and Das P (2004) Antisense molecular beacon strategy for in situ visualization of snRNA and fibrillarin protein interaction in Giardia lamblia. RNA Biol 1: 48-53. PMI: 17194934: PubMed Link

  444. Gao F, Lei J, and Ju H (2013) Assistant DNA recycling with nicking endonuclease and molecular beacon for signal amplification using a target-complementary arched structure. Chem Commun (Camb) 49: 4006-4008. PMI: 23563493: PubMed Link

  445. Gao Q, Lin K, Zhang H, Qi H, and Zhang C (2010) Label-free fluorescent molecular beacon based on a small fluorescent molecule non-covalently bound to the intentional gap site in the stem moiety. Talanta 83: 535-540. PMI: 21111170: PubMed Link

  446. Gao W, Tyagi S, Kramer FR, and Goldman E (1997) Messenger RNA release from ribosomes during 5'-translational blockage by consecutive low-usage arginine but not leucine codons in Escherichia coli. Mol Microbiol 25: 707-716. PMI: 9379900: PubMed Link

  447. Gao Y, Li Y, Zou X, Huang H, and Su X (2012) Highly sensitive and selective detection of biothiols using graphene oxide-based "molecular beacon"-like fluorescent probe. Anal Chim Acta 731: 68-74. PMI: 22652266: PubMed Link

  448. Gao Y, Qiao G, Zhuo L, Li N, Liu Y, and Tang B (2011) A tumor mRNA-mediated bi-photosensitizer molecular beacon as an efficient imaging and photosensitizing agent. Chem Commun (Camb) 47: 5316-5318. PMI: 21451872: PubMed Link

  449. Gerasimova YV, Ballantyne J, and Kolpashchikov DM (2013) Detection of SNP-containing human DNA sequences using a split sensor with a universal molecular beacon reporter. Methods Mol Biol 1039: 69-80. PMI: 24026686: PubMed Link

  450. Gerasimova YV, Hayson A, Ballantyne J, and Kolpashchikov DM (2010) A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences. Chembiochem 11: 1762-1768. PMI: 20665615: PubMed Link

  451. Gerasimova YV and Kolpashchikov DM (2013) Detection of bacterial 16S rRNA using a molecular beacon-based X sensor. Biosens Bioelectron 41: 386-390. PMI: 23021850: PubMed Link

  452. Ghosn B, Haselton FR, Gee KR, and Monroe WT (2005) Control of DNA hybridization with photocleavable adducts. Photochem Photobiol 81: 953-959. PMI: 15869326: PubMed Link

  453. Goddard NL, Bonnet G, Krichevsky O, and Libchaber A (2000) Sequence dependent rigidity of single stranded DNA. Phys Rev Lett 85: 2400-2403. PMI: 10978020: PubMed Link

  454. Gold B, Rodriguez GM, Marras SAE, Pentecost M, and Smith I (2001) The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages. Mol Microbiol 42: 851-865. PMI: 11722747: PubMed Link

  455. Grossmann TN, Roglin L, and Seitz O (2007) Triplex molecular beacons as modular probes for DNA detection. Angew Chem Int Ed Engl 46: 5223-5225. PMI: 17535003: PubMed Link

  456. Guetschow ED, Black W, Walsh CM, and Furchak JR (2012) Detection of prolactin inducible protein mRNA, a biomarker for breast cancer metastasis, using a molecular beacon-based assay. Anal Bioanal Chem 404: 399-406. PMI: 22692591: PubMed Link

  457. Guo J and Yang R (2012) An OR logic gate based on two molecular beacons. Mol Biosyst 8: 927-930. PMI: 22278176: PubMed Link

  458. Guo Y, Wang H, Sun Y, and Qu B (2012) A disulfide bound-molecular beacon as a fluorescent probe for the detection of reduced glutathione and its application in cells. Chem Commun (Camb) 48: 3221-3223. PMI: 22354149: PubMed Link

  459. Hall B, Cater S, Levy M, and Ellington AD (2009) Kinetic optimization of a protein-responsive aptamer beacon. Biotechnol Bioeng. PMI: 19431189: PubMed Link

  460. Hall B, Hesselberth JR, and Ellington AD (2007) Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 22: 1939-1947. PMI: 16996258: PubMed Link

  461. Hamaguchi N, Ellington A, and Stanton M (2001) Aptamer beacons for the direct detection of proteins. Anal Biochem 294: 126-131. PMI: 11444807: PubMed Link

  462. Han D, Kim YR, Oh JW, Kim TH, Mahajan RK, Kim JS, and Kim H (2009) A regenerative electrochemical sensor based on oligonucleotide for the selective determination of mercury(II). Analyst 134: 1857-1862. PMI: 19684910: PubMed Link

  463. Han S, Li L, Jia X, Ou W, Ma J, Wang H, Zhao J, and Zhu Q (2012) A molecular beacon-based method for screening cervical cancer. J Nanosci Nanotechnol 12: 8282-8286. PMI: 23421207: PubMed Link

  464. Han SX, Jia X, Ma JL, and Zhu Q (2013) Molecular beacons: a novel optical diagnostic tool. Arch Immunol Ther Exp (Warsz) 61: 139-148. PMI: 23292078: PubMed Link

  465. Haner R, Biner SM, Langenegger SM, Meng T, and Malinovskii VL (2009) A highly sensitive, excimer-controlled molecular beacon. Angew Chem Int Ed Engl. PMI: 20069619: PubMed Link

  466. Hara Y, Fujii T, Kashida H, Sekiguchi K, Liang X, Niwa K, Takase T, Yoshida Y, and Asanuma H (2010) Coherent quenching of a fluorophore for the design of a highly sensitive in-stem molecular beacon. Angew Chem Int Ed Engl 49: 5502-5506. PMI: 20602380: PubMed Link

  467. Hart KW, Williams OM, Thelwell N, Fiander AN, Brown T, Borysiewicz LK, and Gelder CM (2001) Novel method for detection, typing, and quantification of human papillomaviruses in clinical samples. J Clin Microbiol 39: 3204-3212. PMI: 11526152: PubMed Link

  468. Hartig JS, Grune I, Najafi-Shoushtari SH, and Famulok M (2004) Sequence-specific detection of microRNAs by signal-amplifying ribozymes. J Am Chem Soc 126: 722-723. PMI: ISI:000188318300014: PubMed Link

  469. Hayden T (2007) Nanowires and molecular beacons for DNA analysis. Anal Chem 79: 1789. PMI: 17375394: PubMed Link

  470. He HQ, Ma XH, Liu B, Zhang XY, Chen WZ, Wang CX, and Cheng SH (2007) High-throughput real-time assay based on molecular beacons for HIV-1 integrase 3'-processing reaction. Acta Pharmacol Sin 28: 811-817. PMI: 17506940: PubMed Link

  471. He JL, Wu ZS, Zhang SB, Shen GL, and Yu RQ (2010) Fluorescence aptasensor based on competitive-binding for human neutrophil elastase detection. Talanta 80: 1264-1268. PMI: 20006085: PubMed Link

  472. He L, Yang X, Wang K, Wang Q, Zhao F, Huang J, and Liu J (2014) A self-assembled conformational switch: a host-guest stabilized triple stem molecular beacon via a photoactivated and thermal regeneration mode. Chem Commun (Camb) 50: 7803-7805. PMI: 24903573: PubMed Link

  473. He X, Ni X, Wang Y, Wang K, and Jian L (2011) Electrochemical detection of nicotinamide adenine dinucleotide based on molecular beacon-like DNA and E. coli DNA ligase. Talanta 83: 937-942. PMI: 21147340: PubMed Link

  474. He Y, Wang ZG, Tang HW, and Pang DW (2011) Low background signal platform for the detection of ATP: when a molecular aptamer beacon meets graphene oxide. Biosens Bioelectron 29: 76-81. PMI: 21889887: PubMed Link

  475. Hianik T, Ostatna V, Sonlajtnerova M, and Grman I (2006) Influence of ionic strength, pH and aptamer configuration for binding affinity to thrombin. Bioelectrochemistry 70: 127-133. PMI: 16725379: PubMed Link

  476. Holzhauser C and Wagenknecht HA (2011) In-stem-labeled molecular beacons for distinct fluorescent color readout. Angew Chem Int Ed Engl 50: 7268-7272. PMI: 21717540: PubMed Link

  477. Hong Y, Haubetaler M, Lam JW, Li Z, Sin KK, Dong Y, Tong H, Liu J, Qin A, Renneberg R, and Tang BZ (2008) Label-free fluorescent probing of G-quadruplex formation and real-time monitoring of DNA folding by a quaternized tetraphenylethene salt with aggregation-induced emission characteristics. Chemistry. PMI: 18512826: PubMed Link

  478. Hopkins JF, Panja S, McNeil SA, and Woodson SA (2009) Effect of salt and RNA structure on annealing and strand displacement by Hfq. Nucleic Acids Res. PMI: 19671524: PubMed Link

  479. Hopkins JF and Woodson SA (2005) Molecular beacons as probes of RNA unfolding under native conditions. Nucleic Acids Res 33: 5763-5770. PMI: 16221975: PubMed Link

  480. Horejsh D, Martini F, Poccia F, Ippolito G, Di Caro A, and Capobianchi MR (2005) A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry. Nucleic Acids Res 33: e13. PMI: 15659574: PubMed Link

  481. Hou J, Liu X, Wang J, Liu J, and Duan T (2007) Molecular beacons for isothermal fluorescence enhancement by the cleavage of RNase HII from Chlamydia pneumoniae. Anal Biochem. PMI: 17923101: PubMed Link

  482. Hou J, Liu X, Zheng Y, and Liu J (2007) A method for HLA genotyping using the specific cleavage of DNA-rN(1)-DNA/DNA with RNase HII from Chlamydia pneumoniae. Oligonucleotides 17: 433-444. PMI: 18154453: PubMed Link

  483. Hou P, Long Y, Zhao J, Wang J, and Zhou F (2012) A thymidine-terminated molecular beacon for selective Hg2+ or sequence-specific DNA assay. Spectrochim Acta A Mol Biomol Spectrosc 86: 76-79. PMI: 22055557: PubMed Link

  484. Hsieh AT, Pan PJ, and Lee AP (2014) A real-time characterization method to rapidly optimize molecular beacon signal for sensitive nucleic acids analysis. Anal Bioanal Chem 406: 3059-3067. PMI: 24722874: PubMed Link

  485. Hu D, Huang Z, Pu F, Ren J, and Qu X (2011) A label-free, quadruplex-based functional molecular beacon (LFG4-MB) for fluorescence turn-on detection of DNA and nuclease. Chemistry 17: 1635-1641. PMI: 21268166: PubMed Link

  486. Hu Q, Lyu D, Shi X, Jiang Y, Lin Y, Li Y, Qiu Y, He L, Zhang R, and Li Q (2014) A modified molecular beacons-based multiplex real-time PCR assay for simultaneous detection of eight foodborne pathogens in a single reaction and its application. Foodborne Pathog Dis 11: 207-214. PMI: 24328501: PubMed Link

  487. Hu R, Liu YR, Zhang XB, Tan W, Shen GL, and Yu RQ (2013) An efficient fluorescent sensing platform for biomolecules based on fenton reaction triggered molecular beacon cleavage strategy. Biosens Bioelectron 41: 442-445. PMI: 23062552: PubMed Link

  488. Huang J, He Y, Yang X, Wang K, Quan K, and Lin X (2014) Split aptazyme-based catalytic molecular beacons for amplified detection of adenosine. Analyst 139: 2994-2997. PMI: 24807151: PubMed Link

  489. Huang J, Zheng Q, Kim JK, and Li Z (2013) A molecular beacon and graphene oxide-based fluorescent biosensor for Cu(2+) detection. Biosens Bioelectron 43: 379-383. PMI: 23357003: PubMed Link

  490. Huang K and Marti AA (2012) Recent trends in molecular beacon design and applications. Anal Bioanal Chem 402: 3091-3102. PMI: 22159461: PubMed Link

  491. Huang K and Marti AA (2012) Optimizing the sensitivity of photoluminescent probes using time-resolved spectroscopy: a molecular beacon case study. Anal Chem 84: 8075-8082. PMI: 22934684: PubMed Link

  492. Huang PJ and Liu J (2012) Molecular beacon lighting up on graphene oxide. Anal Chem 84: 4192-4198. PMI: 22489847: PubMed Link

  493. Huang Q, Liu Z, Liao Y, Chen X, and Li Q (2010) Multiplex fluorescence melting curve analysis for mutation detection with dual-labeled, self-quenched probes. PlosOne 6: e19206. PMI: PubMed Link

  494. Huang Q and Quinones E (2008) A spectroscopic method to determine the activity of the restriction endonuclease EcoRV that involves a single reaction. Anal Biochem. PMI: 18489897: PubMed Link

  495. Hunt EA and Deo SK (2011) Bioluminescent stem-loop probes for highly sensitive nucleic acid detection. Chem Commun (Camb) 47: 9393-9395. PMI: 21769413: PubMed Link

  496. Hwang DW, Song IC, Lee DS, and Kim S (2009) Smart magnetic fluorescent nanoparticle imaging probes to monitor microRNAs. Small. PMI: 19911390: PubMed Link

  497. Hwang GT, Seo YJ, and Kim BH (2004) A highly discriminating quencher-free molecular beacon for probing DNA. J Am Chem Soc 126: 6528-6529. PMI: 15161261: PubMed Link

  498. Ilieva M, Della Vedova P, Hansen O, and Dufva M (2013) Tracking neuronal marker expression inside living differentiating cells using molecular beacons. Front Cell Neurosci 7: 266. PMI: 24431988: PubMed Link

  499. Ilieva M and Dufva M (2013) SOX2 and OCT4 mRNA-expressing cells, detected by molecular beacons, localize to the center of neurospheres during differentiation. PLoS One 8: e73669. PMI: 24013403: PubMed Link

  500. Ishchenko AA, Deprez E, Maksimenko A, Brochon JC, Tauc P, and Saparbaev MK (2006) Uncoupling of the base excision and nucleotide incision repair pathways reveals their respective biological roles. Proc Natl Acad Sci U S A 103: 2564-2569. PMI: 16473948: PubMed Link

  501. Jacroux T, Rieck DC, Cui R, Ouyang Y, and Dong WJ (2013) Enzymatic amplification of DNA/RNA hybrid molecular beacon signaling in nucleic acid detection. Anal Biochem 432: 106-114. PMI: 23000602: PubMed Link

  502. Jaumot J, Eritja R, Tauler R, and Gargallo R (2006) Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand. Nucleic Acids Res 34: 206-216. PMI: 16397299: PubMed Link

  503. Jeong HS, Seo YJ, Bang EK, Hwang GT, Jung JH, Jang SK, and Kim BH (2008) Cholesterol-linked pyrene excimer molecular beacon with enhanced cell permeability. Nucleic Acids Symp Ser (Oxf): 351-352. PMI: 18776398: PubMed Link

  504. Ji H, Dong H, Yan F, Lei J, Ding L, Gao W, and Ju H (2011) Visual scanometric detection of DNA through silver enhancement regulated by gold-nanoparticle aggregation with a molecular beacon as the trigger. Chemistry 17: 11344-11349. PMI: 21850726: PubMed Link

  505. Jiang YL, McGoldrick CA, Yin D, Zhao J, Patel V, Brannon MF, Lightner JW, Krishnan K, and Stone WL (2012) A specific molecular beacon probe for the detection of human prostate cancer cells. Bioorg Med Chem Lett 22: 3632-3638. PMI: 22572577: PubMed Link

  506. Jin Y, Wang K, Tan W, Wu P, Wang Q, Huang H, Huang S, Tang Z, and Guo Q (2004) Monitoring molecular beacon/DNA interactions using atomic force microscopy. Anal Chem 76: 5721-5725. PMI: 15456291: PubMed Link

  507. Jo SM, Kim Y, Jeong YS, Hee Oh Y, Park K, and Kim HS (2013) Rapid detection of exon 2-deleted AIMP2 mutation as a potential biomarker for lung cancer by molecular beacons. Biosens Bioelectron 46: 142-149. PMI: 23537880: PubMed Link

  508. Jockusch S, Marti AA, Turro NJ, Li Z, Li X, Ju J, Stevens N, and Akins DL (2006) Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences. Photochem Photobiol Sci 5: 493-498. PMI: 16685327: PubMed Link

  509. Johansson MK, Fidder H, Dick D, and Cook RM (2002) Intramolecular dimers: A new strategy to fluorescence quenching in dual-labeled oligonucleotide probes. J Am Chem Soc 124: 6950-6956. PMI: ISI:000176198200041: PubMed Link

  510. Johnson SC, Sherrill CB, Marshall DJ, Moser MJ, and Prudent JR (2004) A third base pair for the polymerase chain reaction: inserting isoC and isoG. Nucleic Acids Res 32: 1937-1941. PMI: 15051811: PubMed Link

  511. Johnston AP and Caruso F (2005) A molecular beacon approach to measuring the DNA permeability of thin films. J Am Chem Soc 127: 10014-10015. PMI: 16011361: PubMed Link

  512. Jones R, Baker MB, Weber M, Harrison DG, Bao G, and Searles CD (2008) Molecular beacons can assess changes in expression and 3' polyadenylation of human eNOS mRNA. Am J Physiol Cell Physiol. PMI: 19109525: PubMed Link

  513. Joo HN and Seo YJ (2015) A multiplex fluorophore molecular beacon: detection of the target sequence using large Stokes shift and multiple emission signal properties. Chem Commun (Camb) 51: 2939-2942. PMI: 25588113: PubMed Link

  514. Jordens JZ, Lanham S, Pickett MA, Amarasekara S, Abeywickrema I, and Watt PJ (2000) Amplification with molecular beacon primers and reverse line blotting for the detection and typing of human papillomaviruses. J Virol Methods 89: 29-37. PMI: 10996637: PubMed Link

  515. Joshi HS and Tor Y (2001) Metal-containing DNA hairpins as hybridization probes. Chemical Comm 6: 550-559. PMI: PubMed Link

  516. Joshi KB, Vlachos A, Mikat V, Deller T, and Heckel A (2012) Light-activatable molecular beacons with a caged loop sequence. Chem Commun (Camb) 48: 2746-2748. PMI: 22159276: PubMed Link

  517. Jun BH, Kim JE, Rho C, Byun JW, Kim YH, Kang H, Kim JH, Kang T, Cho MH, and Lee YS (2011) Immobilization of aptamer-based molecular beacons onto optically-encoded micro-sized beads. J Nanosci Nanotechnol 11: 6249-6252. PMI: 22121695: PubMed Link

  518. Jung J, Chen L, Lee S, Kim S, Seong GH, Choo J, Lee EK, and Oh CH (2007) Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel. Anal Bioanal Chem 387: 2609-2615. PMI: 17318519: PubMed Link

  519. Kaboev OK, Luchkina LA, Tret'iakov AN, and Bahrmand AR (2000) PCR hot start using primers with the structure of molecular beacons (hairpin-like structure). Nucleic Acids Res 28: e94. PMI: 11058144: PubMed Link

  520. Kam Y, Rubinstein A, Naik S, Djavsarov I, Halle D, Ariel I, Gure AO, Stojadinovic A, Pan H, Tsivin V, Nissan A, and Yavin E (2014) Detection of a long non-coding RNA (CCAT1) in living cells and human adenocarcinoma of colon tissues using FIT-PNA molecular beacons. Cancer Lett 352: 90-96. PMI: 23416875: PubMed Link

  521. Kam Y, Rubinstein A, Nissan A, Halle D, and Yavin E (2012) Detection of endogenous K-ras mRNA in living cells at a single base resolution by a PNA molecular beacon. Mol Pharm 9: 685-693. PMI: 22289057: PubMed Link

  522. Kamboj A, Pateriya AK, Mishra A, Ranaware P, Kulkarni DD, and Raut AA (2014) Novel molecular beacon probe-based real-time RT-PCR assay for diagnosis of Crimean-Congo hemorrhagic fever encountered in India. Biomed Res Int 2014: 496219. PMI: 24877102: PubMed Link

  523. Kara IO, Duman BB, and Afsar CU (2013) The evaluation of minimal residual disease in multiple myeloma by fluorescent molecular beacons in real time PCR of IgH gene rearrangements and correlation with flow cytometry. J BUON 18: 442-447. PMI: 23818359: PubMed Link

  524. Karlsen KK, Okholm A, Kjems J, and Wengel J (2013) A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Bioorg Med Chem 21: 6186-6190. PMI: 23693070: PubMed Link

  525. Kashida H, Takatsu T, Fujii T, Sekiguchi K, Liang X, Niwa K, Takase T, Yoshida Y, and Asanuma H (2009) In-stem molecular beacon containing a pseudo base pair of threoninol nucleotides for the removal of background emission. Angew Chem Int Ed Engl. PMI: 19705388: PubMed Link

  526. Kashida H, Yamaguchi K, Hara Y, and Asanuma H (2012) Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation. Bioorg Med Chem 20: 4310-4315. PMI: 22705023: PubMed Link

  527. Ke G, Wang C, Ge Y, Zheng N, Zhu Z, and Yang CJ (2012) L-DNA molecular beacon: a safe, stable, and accurate intracellular nano-thermometer for temperature sensing in living cells. J Am Chem Soc 134: 18908-18911. PMI: 23126671: PubMed Link

  528. Keegan H, Pilkington L, McInerney J, Jeney C, Benczik M, Cleary S, von Bunau G, Turner M, D'Arcy T, S OT, Pal-Szenthe B, Kaltenecker B, Mozes J, Kovacs A, Solt A, Bolger N, O'Leary J, and Martin C (2014) Human papillomavirus detection and genotyping, by HC2, full-spectrum HPV and molecular beacon real-time HPV assay in an Irish colposcopy clinic. J Virol Methods 201: 93-100. PMI: 24583109: PubMed Link

  529. Kehlenbach RH (2003) In vitro analysis of nuclear mRNA export using molecular beacons for target detection. Nucleic Acids Res 31: e64. PMI: 12771228: PubMed Link

  530. Kerby MB, Freeman S, Prachanronarong K, Artenstein AW, Opal SM, and Tripathi A (2008) Direct sequence detection of structured h5 influenza viral RNA. J Mol Diagn 10: 225-235. PMI: 18403607: PubMed Link

  531. Kim B, Jung IH, Kang M, Shim HK, and Woo HY (2012) Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection. J Am Chem Soc 134: 3133-3138. PMI: 22280349: PubMed Link

  532. Kim JH, Lee MJ, Hwang I, and Hwang HJ (2013) In-cell protease assay systems based on trans-localizing molecular beacon proteins using HCV protease as a model system. PLoS One 8: e59710. PMI: 23555756: PubMed Link

  533. Kim JH, Morikis D, and Ozkan M (2004) Adaptation of inorganic quantum dots for stable molecular beacons. Sensors and Actuators B 102: 315-319. PMI: PubMed Link

  534. Kim JK, Choi KJ, Lee M, Jo MH, and Kim S (2012) Molecular imaging of a cancer-targeting theragnostics probe using a nucleolin aptamer- and microRNA-221 molecular beacon-conjugated nanoparticle. Biomaterials 33: 207-217. PMI: 21944470: PubMed Link

  535. Kim KH, Kim J, Choi JS, Bae S, Kwon D, Park I, Kim DH, and Seo TS (2015) Rapid, High-Throughput, and Direct Molecular Beacon Delivery to Human Cancer Cells Using a Nanowire-Incorporated and Pneumatic Pressure-Driven Microdevice. Small. PMI: 26484480: PubMed Link

  536. Kim KT, Veedu RN, Seo YJ, and Kim BH (2014) Quencher-free molecular beacons as probes for oligonucleotides containing CAG repeat sequences. Chem Commun (Camb) 50: 1561-1563. PMI: 24382518: PubMed Link

  537. Kim MY, Kim J, and Hah SS (2012) Poly(A)-targeting molecular beacons: fluorescence resonance energy transfer-based in vitro quantitation and time-dependent imaging in live cells. Anal Biochem 429: 92-98. PMI: 22828410: PubMed Link

  538. Kim S, Chen L, Lee S, Seong GH, Choo J, Lee EK, and Oh CH (2007) Rapid DNA hybridization analysis using a PDMS microfluidic sensor and a molecular beacon. Anal Sci 23: 401-405. PMI: 17420542: PubMed Link

  539. Kim Y, Yang CJ, and Tan W (2007) Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem. Nucleic Acids Res. PMI: 17959649: PubMed Link

  540. King FW, Liszewski W, Ritner C, and Bernstein HS (2011) High-throughput tracking of pluripotent human embryonic stem cells with dual fluorescence resonance energy transfer molecular beacons. Stem Cells Dev 20: 475-484. PMI: 20624034: PubMed Link

  541. Kitagawa F, Ohori Y, Ikeda H, Fujimori H, Murakami Y, and Nakamura Y (2002) Design of a molecular beacon PNA. Nucleic Acids Res Suppl 2: 143-144. PMI: 12903146: PubMed Link

  542. Knemeyer JP, Marme N, and Sauer M (2000) Probes for detection of specific DNA sequences at the single-molecule level. Anal Chem 72: 3717-3724. PMI: 10959954: PubMed Link

  543. Ko HY, Lee J, Joo JY, Lee YS, Heo H, Ko JJ, and Kim S (2014) A color-tunable molecular beacon to sense miRNA-9 expression during neurogenesis. Sci Rep 4: 4626. PMI: 24713846: PubMed Link

  544. Kolpashchikov DM (2012) An elegant biosensor molecular beacon probe: challenges and recent solutions. Scientifica (Cairo) 2012: 928783. PMI: 24278758: PubMed Link

  545. Kong D, Jin Y, Yin Y, Mi H, and Shen H (2007) Real-time PCR detection of telomerase activity using specific molecular beacon probes. Anal Bioanal Chem 388: 699-709. PMI: 17437092: PubMed Link

  546. Kong DM, Gu L, Shen HX, and Mi HF (2002) A modified molecular beacon combining the properties of TaqMan probe. Chem Commun (Camb): 854-855. PMI: 12123012: PubMed Link

  547. Kong RM, Zhang XB, Zhang LL, Huang Y, Lu DQ, Tan W, Shen GL, and Yu RQ (2011) Molecular beacon-based junction probes for efficient detection of nucleic acids via a true target-triggered enzymatic recycling amplification. Anal Chem 83: 14-17. PMI: 21117628: PubMed Link

  548. Kovacs J, Jentzsch E, and Mokhir A (2008) Cu(2+)-controlled hybridization of peptide nucleic acids. Inorg Chem. PMI: 19053337: PubMed Link

  549. Krasnoperov LN, Marras SA, Kozlov M, Wirpsza L, and Mustaev A (2010) Luminescent probes for ultrasensitive detection of nucleic acids. Bioconjug Chem. PMI: 20085336: PubMed Link

  550. Krusinski T, Laskowska A, Ozyhar A, and Dobryszycki P (2008) The application of an immobilized molecular beacon for the analysis of the DNA binding domains from the ecdysteroid receptor proteins Usp and EcR's interaction with the hsp27 response element. J Biomol Screen. PMI: 18812572: PubMed Link

  551. Krusinski T, Wietrzych M, Grad I, Ozyhar A, and Dobryszycki P (2007) Equilibrium analysis of the DNA binding domain of the ultraspiracle protein interaction with the response element from the hsp27 gene promoter - the application of molecular beacon technology. J Fluoresc. PMI: 18049881: PubMed Link

  552. Kuechenmeister LJ, Anderson KL, Morrison JM, and Dunman PM (2008) The use of molecular beacons to directly measure bacterial mRNA abundances and transcript degradation. J Microbiol Methods. PMI: 18992285: PubMed Link

  553. Kuhn H, Demidov VV, Coull JM, Fiandaca MJ, Gildea BD, and Frank-Kamenetskii MD (2002) Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets. J Am Chem Soc 124: 1097-1103. PMI: 11829619: PubMed Link

  554. Kuhn H, Demidov VV, Gildea BD, Fiandaca MJ, Coull JC, and Frank-Kamenetskii MD (2001) PNA beacons for duplex DNA. Antisense Nucleic Acid Drug Dev 11: 265-270. PMI: 11572603: PubMed Link

  555. Kundu LM, Burgdorf LT, Kleiner O, Batschauer A, and Carell T (2002) Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity. Chembiochem 3: 1053-1060. PMI: 12404629: PubMed Link

  556. Kuo CY and Tseng WL (2013) Adenosine-based molecular beacons as light-up probes for sensing heparin in plasma. Chem Commun (Camb) 49: 4607-4609. PMI: 23563586: PubMed Link

  557. Kwon K, Nagarajan R, and Stivers JT (2004) Ribonuclease activity of vaccinia DNA topoisomerase IB: kinetic and high-throughput inhibition studies using a robust continuous fluorescence assay. Biochemistry 43: 14994-15004. PMI: 15554707: PubMed Link

  558. La Paz JL, Esteve T, and Pla M (2007) Comparison of real-time PCR detection chemistries and cycling modes using Mon810 event-specific assays as model. J Agric Food Chem 55: 4312-4318. PMI: 17488028: PubMed Link

  559. Lagally ET, Lee SH, and Soh HT (2005) Integrated microsystem for dielectrophoretic cell concentration and genetic detection. Lab Chip 5: 1053-1058. PMI: 16175260: PubMed Link

  560. Landre JBP, Ruryk A, Schlicksbier T, Russwurm S, and Deigner H-P (2005) Design and applications of a novel type of hairpin probes: adressable bipartite molecular hook (ABMH). NSTI-Nanotech 1: 385-388. PMI: PubMed Link

  561. Larios-Sanz M, Kourentzi KD, Warmflash D, Jones J, Pierson DL, Willson RC, and Fox GE (2007) 16S rRNA beacons for bacterial monitoring during human space missions. Aviat Space Environ Med 78: A43-47. PMI: 17511298: PubMed Link

  562. Latorre A, Posch C, Garcimartin Y, Ortiz-Urda S, and Somoza A (2014) Single-point mutation detection in RNA extracts using gold nanoparticles modified with hydrophobic molecular beacon-like structures. Chem Commun (Camb) 50: 3018-3020. PMI: 24496380: PubMed Link

  563. Lee IH, Lee SH, Park TH, and Zhang BT (2013) Non-linear molecular pattern classification using molecular beacons with multiple targets. Biosystems 114: 206-213. PMI: 23743339: PubMed Link

  564. Lee J, Cho HY, and Hwang GT (2013) Highly efficient quencher-free molecular beacon systems containing 2-ethynyldibenzofuran- and 2-ethynyldibenzothiophene-labeled 2'-deoxyuridine units. Chembiochem 14: 1353-1362. PMI: 23824637: PubMed Link

  565. Lenaerts J, Lappin-Scott HM, and Porter J (2007) Improved fluorescent in situ hybridisation detection of bacteria from activated sludge and river water using DNA molecular beacons and flow cytometry. Appl Environ Microbiol 73: 2020-2023. PMI: 17277208: PubMed Link

  566. Lennon FE, Hermann CD, Olivares-Navarrete R, Rhee WJ, Schwartz Z, Bao G, and Boyan BD (2010) Use of molecular beacons to image effects of titanium surface microstructure on beta1 integrin expression in live osteoblast-like cells. Biomaterials 31: 7640-7647. PMI: 20674005: PubMed Link

  567. Lerga TM and O'Sullivan CK (2008) Rapid determination of total hardness in water using fluorescent molecular aptamer beacon. Anal Chim Acta 610: 105-111. PMI: 18267146: PubMed Link

  568. Levy M, Cater SF, and Ellington AD (2005) Quantum-dot aptamer beacons for the detection of proteins. Chembiochem 6: 2163-2166. PMI: 16254932: PubMed Link

  569. Li B, Li Z, Situ B, Dai Z, Liu Q, Wang Q, Gu D, and Zheng L (2014) Sensitive HIV-1 detection in a homogeneous solution based on an electrochemical molecular beacon coupled with a nafion-graphene composite film modified screen-printed carbon electrode. Biosens Bioelectron 52: 330-336. PMI: 24099877: PubMed Link

  570. Li C, Long Y, Liu B, Xiang D, and Zhu H (2014) Real time monitoring uracil excision using uracil-containing molecular beacons. Anal Chim Acta 819: 71-77. PMI: 24636413: PubMed Link

  571. Li F, Huang Y, Yang Q, Zhong Z, Li D, Wang L, Song S, and Fan C (2010) A graphene-enhanced molecular beacon for homogeneous DNA detection. Nanoscale 2: 1021-1026. PMI: 20648302: PubMed Link

  572. Li F, Li P, Yang L, and Tang B (2012) Simple and sensitive fluorescence detection of the RNA endonuclease activity of mammalian argonaute2 protein based on an RNA molecular beacon. Chem Commun (Camb) 48: 12192-12194. PMI: 23145433: PubMed Link

  573. Li J, Cao ZC, Tang Z, Wang K, and Tan W (2008) Molecular beacons for protein-DNA interaction studies. Methods Mol Biol 429: 209-224. PMI: 18695969: PubMed Link

  574. Li J, Zhou W, Ouyang X, Yu H, Yang R, Tan W, and Yuan J (2011) Design of a room-temperature phosphorescence-based molecular beacon for highly sensitive detection of nucleic acids in biological fluids. Anal Chem 83: 1356-1362. PMI: 21247075: PubMed Link

  575. Li JJ, Chu Y, Lee BY, and Xie XS (2008) Enzymatic signal amplification of molecular beacons for sensitive DNA detection. Nucleic Acids Res. PMI: 18304948: PubMed Link

  576. Li JJ, Fang X, Schuster SM, and Tan W (2000) Molecular beacons: A novel approach to detect protein - DNA interactions. Angew Chem Int Ed Engl 39: 1049-1052. PMI: 10760918: PubMed Link

  577. Li JJ, Fang X, and Tan W (2002) Molecular aptamer beacons for real-time protein recognition. Biochem Biophys Res Commun 292: 31-40. PMI: 11890667: PubMed Link

  578. Li JJ, Geyer R, and Tan W (2000) Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA. Nucleic Acids Res 28: e52. PMI: 10871351: PubMed Link

  579. Li JJ and Tan W (2003) A real-time assay for DNA sticky-end pairing using molecular beacons. Anal Biochem 312: 251-254. PMI: 12531213: PubMed Link

  580. Li N and Wong PK (2010) Transfection of molecular beacons in microchannels for single-cell gene-expression analysis. Bioanalysis 2: 1689-1699. PMI: 21083321: PubMed Link

  581. Li X, Deng D, Xue J, Qu L, Achilefu S, and Gu Y (2014) Quantum dots based molecular beacons for in vitro and in vivo detection of MMP-2 on tumor. Biosens Bioelectron 61: 512-518. PMI: 24951921: PubMed Link

  582. Li X, Huang Y, Guan Y, Zhao M, and Li Y (2007) A novel one cycle allele specific primer extension-molecular beacon displacement method for DNA point mutation detection with improved specificity. Anal Chim Acta 584: 12-18. PMI: 17386579: PubMed Link

  583. Li X, Huang Y, Song C, Zhao M, and Li Y (2007) Several concerns about the primer design in the universal molecular beacon real-time PCR assay and its application in HBV DNA detection. Anal Bioanal Chem 388: 979-985. PMI: 17468857: PubMed Link

  584. Li X, Li Z, Marti AA, Jockusch S, Stevens N, Akins DL, Turro NJ, and Ju J (2006) Combinatorial fluorescence energy transfer molecular beacons for probing nucleic acid sequences. Photochem Photobiol Sci 5: 896-902. PMI: 17019467: PubMed Link

  585. Li X, Morgenroth E, and Raskin L (2008) Quantitative rRNA-targeted solution-based hybridization assay using peptide nucleic acid molecular beacons. Appl Environ Microbiol. PMI: 18820054: PubMed Link

  586. Li X, Song C, Zhao M, and Li Y (2008) Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction. Anal Biochem. PMI: 18611388: PubMed Link

  587. Li YQ, Guan LY, Wang JH, Zhang HL, Chen J, Lin S, Chen W, and Zhao YD (2011) Simultaneous detection of dual single-base mutations by capillary electrophoresis using quantum dot-molecular beacon probe. Biosens Bioelectron 26: 2317-2322. PMI: 21115340: PubMed Link

  588. Liao N, Gao JH, Zeng WS, Lu F, and Luo SQ (2011) [Establishment of molecular beacon real-time PCR for detecting p53 gene single nucleotide polymorphism]. Nan Fang Yi Ke Da Xue Xue Bao 31: 1875-1878. PMI: 22126769: PubMed Link

  589. Lim HW, Lee SH, Yang KA, Yoo SI, Park TH, and Zhang BT (2013) Biomolecular computation with molecular beacons for quantitative analysis of target nucleic acids. Biosystems 111: 11-17. PMI: 23123676: PubMed Link

  590. Lin JH and Tseng WL (2014) Design of two and three input molecular logic gates using non-Watson-Crick base pairing-based molecular beacons. Analyst 139: 1436-1441. PMI: 24490204: PubMed Link

  591. Lin X, Konno T, and Ishihara K (2014) Cell-membrane-permeable and cytocompatible phospholipid polymer nanoprobes conjugated with molecular beacons. Biomacromolecules 15: 150-157. PMI: 24308501: PubMed Link

  592. Lin X, Zhang C, Huang Y, Zhu Z, Chen X, and Yang CJ (2013) Backbone-modified molecular beacons for highly sensitive and selective detection of microRNAs based on duplex specific nuclease signal amplification. Chem Commun (Camb) 49: 7243-7245. PMI: 23842896: PubMed Link

  593. Lin Y, Shi X, Zhu Y, Qiu Y, Li Y, Lv D, and Hu Q (2011) [Development of modified molecular beacon based real-time PCR assay for the rapid detection of Salmonella choleraesuis and Salmonella paratyphi C]. Wei Sheng Yan Jiu 40: 514-516. PMI: 21861361: PubMed Link

  594. Lin YH and Tseng WL (2012) A room-temperature adenosine-based molecular beacon for highly sensitive detection of nucleic acids. Chem Commun (Camb) 48: 6262-6264. PMI: 22531390: PubMed Link

  595. Lin YW, Ho HT, Huang CC, and Chang HT (2008) Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon. Nucleic Acids Res 36: e123. PMI: 18753149: PubMed Link

  596. Lindquist JN, Kauschke SG, Stefanovic B, Burchardt ER, and Brenner DA (2000) Characterization of the interaction between alphaCP(2) and the 3'-untranslated region of collagen alpha1(I) mRNA. Nucleic Acids Res 28: 4306-4316. PMI: 11058131: PubMed Link

  597. Liu A, Sun Z, Wang K, Chen X, Xu X, Wu Y, Lin X, Chen Y, and Du M (2012) Molecular beacon-based fluorescence biosensor for the detection of gene fragment and PCR amplification products related to chronic myelogenous leukemia. Anal Bioanal Chem 402: 805-812. PMI: 22015477: PubMed Link

  598. Liu B, Xiang D, Long Y, and Tong C (2013) Real time monitoring of junction ribonuclease activity of RNase H using chimeric molecular beacons. Analyst 138: 3238-3245. PMI: 23608820: PubMed Link

  599. Liu CW, Lin YW, Huang CC, and Chang HT (2009) Fluorescence detection of single-nucleotide polymorphisms using a thymidine-based molecular beacon. Biosens Bioelectron. PMI: 19200710: PubMed Link

  600. Liu J, Feldman P, and Chung TD (2002) Real-time monitoring in vitro transcription using molecular beacons. Anal Biochem 300: 40-45. PMI: 11743690: PubMed Link

  601. Liu J, Liu XM, Xiao SY, Tong CY, Tang DY, and Zhao LJ (2005) Bioconjugated nanoparticle for DNA protection from ultrasound damage. Anal Sci 21: 193-195. PMI: 15790096: PubMed Link

  602. Liu J and Lu Y (2006) Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons. Methods Mol Biol 335: 275-288. PMI: 16785634: PubMed Link

  603. Liu JJ, Song XR, Wang YW, Chen GN, and Yang HH (2012) A graphene oxide (GO)-based molecular beacon for DNA-binding transcription factor detection. Nanoscale 4: 3655-3659. PMI: 22581162: PubMed Link

  604. Liu L, Li H, Qiu T, Zhou G, Wong KY, He Z, and Liu Z (2011) Construction of a molecular beacon based on two-photon excited fluorescence resonance energy transfer with quantum dot as donor. Chem Commun (Camb) 47: 2622-2624. PMI: 21234481: PubMed Link

  605. Liu L, Tang Z, Wang K, Tan W, Li J, Guo Q, Meng X, and Ma C (2005) Using molecular beacon to monitor activity of E. coli DNA ligase. Analyst 130: 350-357. PMI: 15724164: PubMed Link

  606. Liu TW, Akens MK, Chen J, Wise-Milestone L, Wilson BC, and Zheng G (2011) Imaging of specific activation of photodynamic molecular beacons in breast cancer vertebral metastases. Bioconjug Chem 22: 1021-1030. PMI: 21585206: PubMed Link

  607. Liu TW, Chen J, and Zheng G (2011) Peptide-based molecular beacons for cancer imaging and therapy. Amino Acids 41: 1123-1134. PMI: 20169374: PubMed Link

  608. Liu XP, Hou JL, and Liu JH (2009) A novel single nucleotide polymorphism detection of a double-stranded DNA target by a ribonucleotide-carrying molecular beacon and thermostable RNase HII. Anal Biochem. PMI: 19891952: PubMed Link

  609. Lo PC, Chen J, Stefflova K, Warren MS, Navab R, Bandarchi B, Mullins S, Tsao M, Cheng JD, and Zheng G (2008) Photodynamic molecular beacon triggered by fibroblast activation protein on cancer-associated fibroblasts for diagnosis and treatment of epithelial cancers. J Med Chem. PMI: 19093877: PubMed Link

  610. Lockett MR, Shortreed MR, and Smith LM (2007) Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions. Anal Chem 79: 6031-6036. PMI: 17595056: PubMed Link

  611. Lou HJ, Brister JR, Li JJ, Chen W, Muzyczka N, and Tan W (2004) Adeno-associated virus Rep78/Rep68 promotes localized melting of the rep binding element in the absence of adenosine triphosphate. Chembiochem 5: 324-332. PMI: 14997524: PubMed Link

  612. Lovell JF, Chen J, Huynh E, Jarvi MT, Wilson BC, and Zheng G (2010) Facile synthesis of advanced photodynamic molecular beacon architectures. Bioconjug Chem. PMI: 20509598: PubMed Link

  613. Lovell JF, Jin H, Ng KK, and Zheng G (2010) Programmed nanoparticle aggregation using molecular beacons. Angew Chem Int Ed Engl 49: 7917-7919. PMI: 20853381: PubMed Link

  614. Lu CH, Li J, Liu JJ, Yang HH, Chen X, and Chen GN (2010) Increasing the sensitivity and single-base mismatch selectivity of the molecular beacon using graphene oxide as the "Nanoquencher". Chemistry. PMI: 20301144: PubMed Link

  615. Lv C, Yu L, Wang J, and Tang X (2010) A dumbbell molecular beacon for the specific recognition of nucleic acids. Bioorg Med Chem Lett 20: 6547-6550. PMI: 20933418: PubMed Link

  616. Ma C (2012) Highly sensitive detection of alkaline phosphatase using molecular beacon probes based on enzymatic polymerization. Mol Cell Probes 26: 113-115. PMI: 22464925: PubMed Link

  617. Ma C, Fang H, Wang K, Xia K, Chen H, He H, and Zeng W (2013) Simultaneous detection of kinase and phosphatase activities of polynucleotide kinase using molecular beacon probes. Anal Biochem 443: 166-168. PMI: 24036036: PubMed Link

  618. Ma C, Tang Z, Huo X, Yang X, Li W, and Tan W (2008) Real-time monitoring of double-stranded DNA cleavage using molecular beacons. Talanta 76: 458-461. PMI: 18585306: PubMed Link

  619. Ma C, Tang Z, Wang K, Tan W, Li J, Li W, Li Z, Yang X, Li H, and Liu L (2006) Real-time monitoring of DNA polymerase activity using molecular beacon. Anal Biochem 353: 141-143. PMI: 16624242: PubMed Link

  620. Ma C, Tang Z, Wang K, Tan W, Yang X, Li W, Li Z, Li H, and Lv X (2007) Real-time monitoring of nucleic acid dephosphorylation by using molecular beacons. Chembiochem 8: 1487-1490. PMI: 17685374: PubMed Link

  621. Ma C, Tang Z, Wang K, Tan W, Yang X, Li W, Li Z, and Lv X (2007) Real-time monitoring of restriction endonuclease activity using molecular beacon. Anal Biochem 363: 294-296. PMI: 17313935: PubMed Link

  622. Ma C, Tang Z, Wang K, Yang X, and Tan W (2013) A novel sensitive and selective ligation-based ATP assay using a molecular beacon. Analyst 138: 3013-3017. PMI: 23563079: PubMed Link

  623. Ma C, Yang X, Wang K, Tang Z, Li W, Tan W, and Lv X (2007) A novel kinase-based ATP assay using molecular beacon. Anal Biochem. PMI: 17889821: PubMed Link

  624. Magdalena S and Chalupa A (2015) Biosensors based on molecular beacons. Chemical Papers 69: 62 - 76. PMI: PubMed Link

  625. Maksimenko A, Ishchenko AA, Sanz G, Laval J, Elder RH, and Saparbaev MK (2004) A molecular beacon assay for measuring base excision repair activities. Biochem Biophys Res Commun 319: 240-246. PMI: 15158468: PubMed Link

  626. Mao X, Jiang J, Xu X, Chu X, Luo Y, Shen G, and Yu R (2008) Enzymatic amplification detection of DNA based on molecular beacon biosensors. Biosens Bioelectron. PMI: 18304797: PubMed Link

  627. Mao X, Xu H, Zeng Q, Zeng L, and Liu G (2009) Molecular beacon-functionalized gold nanoparticles as probes in dry-reagent strip biosensor for DNA analysis. Chem Commun (Camb): 3065-3067. PMI: 19462088: PubMed Link

  628. Marras SA, Gold B, Kramer FR, Smith I, and Tyagi S (2004) Real-time measurement of in vitro transcription. Nucleic Acids Res 32: e72. PMI: 15155820: PubMed Link

  629. Marti AA, Jockusch S, Li Z, Ju J, and Turro NJ (2006) Molecular beacons with intrinsically fluorescent nucleotides. Nucleic Acids Res 34: e50. PMI: 16595796: PubMed Link

  630. Marti AA, Jockusch S, Stevens N, Ju J, and Turro NJ (2007) Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc Chem Res 40: 402-409. PMI: 17458926: PubMed Link

  631. Marti AA, Li X, Jockusch S, Stevens N, Li Z, Raveendra B, Kalachikov S, Morozova I, Russo JJ, Akins DL, Ju J, and Turro NJ (2007) Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection. Tetrahedron 63: 3591-3600. PMI: 19907676: PubMed Link

  632. Marx A and Seitz O (2008) Molecular beacons: signalling nucleic acid probes, methods, and protocols. Preface. Methods Mol Biol 429: v-vii. PMI: 18700328: PubMed Link

  633. Matsumoto K, Shinohara Y, Bag SS, Takeuchi Y, Morii T, Saito Y, and Saito I (2009) Pyrene-labeled deoxyguanosine as a fluorescence sensor to discriminate single and double stranded DNA structures: design of ends free molecular beacons. Bioorg Med Chem Lett 19: 6392-6395. PMI: 19828314: PubMed Link

  634. Matsumoto K, Shinohara Y, Numajiri K, Ishioroshi S, Morii T, Saito Y, and Saito I (2009) Design of extremely facile 3'- and 5'- ends free molecular beacons using C8 alkylamino substituted 2'-deoxyguanosine. Nucleic Acids Symp Ser (Oxf): 141-142. PMI: 19749300: PubMed Link

  635. May JP, Brown LJ, Rudloff I, and Brown T (2003) A new dark quencher for use in genetic analysis. Chem Commun (Camb): 970-971. PMI: 12744324: PubMed Link

  636. McGown E, Su M, and Dennis R (2000) Measurement of molecular beacons in the SRECTRAmax (R) GEMINI spectrofluorometer. Journal of Chemical Technology and Biotechnology 75: 942-944. PMI: ISI:000089717200010: PubMed Link

  637. McKeen CM, Brown LJ, Nicol JT, Mellor JM, and Brown T (2003) Synthesis of fluorophore and quencher monomers for use in scorpion primers and nucleic acid structural probes. Org Biomol Chem 1: 2267-2275. PMI: 12945696: PubMed Link

  638. McNally B, Singer A, Yu Z, Sun Y, Weng Z, and Meller A (2010) Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett. PMI: 20459065: PubMed Link

  639. Medintz IL, Berti L, Pons T, Grimes AF, English DS, Alessandrini A, Facci P, and Mattoussi H (2007) A reactive peptidic linker for self-assembling hybrid quantum dot-DNA bioconjugates. Nano Lett 7: 1741-1748. PMI: 17530814: PubMed Link

  640. Medley CD, Drake TJ, Tomasini JM, Rogers RJ, and Tan W (2005) Simultaneous monitoring of the expression of multiple genes inside of single breast carcinoma cells. Anal Chem 77: 4713-4718. PMI: 16053280: PubMed Link

  641. Menacher F and Wagenknecht HA (2011) Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution. Photochem Photobiol Sci 10: 1275-1278. PMI: 21547330: PubMed Link

  642. Meng HM, Fu T, Zhang XB, Wang NN, Tan W, Shen GL, and Yu RQ (2012) Efficient fluorescence turn-on probe for zirconium via a target-triggered DNA molecular beacon strategy. Anal Chem 84: 2124-2128. PMI: 22394089: PubMed Link

  643. Meng XC, Pang R, Wang C, and Wang LQ (2010) Rapid and direct quantitative detection of viable bifidobacteria in probiotic yogurt by combination of ethidium monoazide and real-time PCR using a molecular beacon approach. J Dairy Res 77: 498-504. PMI: 20822571: PubMed Link

  644. Metelev V, Weissleder R, and Bogdanov A, Jr. (2004) Synthesis and properties of fluorescent NF-kappaB-recognizing hairpin oligodeoxyribonucleotide decoys. Bioconjug Chem 15: 1481-1487. PMI: 15546218: PubMed Link

  645. Mhlanga MM and Tyagi S (2006) Using tRNA-linked molecular beacons to image cytoplasmic mRNAs in live cells. Nat Protoc 1: 1392-1398. PMI: 17406426: PubMed Link

  646. Miao X, Guo X, Xiao Z, and Ling L (2014) Electrochemical molecular beacon biosensor for sequence-specific recognition of double-stranded DNA. Biosens Bioelectron 59: 54-57. PMI: 24690562: PubMed Link

  647. Mirbahai L, Kershaw RM, Green RM, Hayden RE, Meldrum RA, and Hodges NJ (2009) Use of a molecular beacon to track the activity of base excision repair protein OGG1 in live cells. DNA Repair (Amst). PMI: 20042377: PubMed Link

  648. Misra A, Kumar P, and Gupta KC (2007) Design and synthesis of hairpin probe for specific mis-match discrimination. Nucleic Acids Symp Ser (Oxf): 311-312. PMI: 18029711: PubMed Link

  649. Mohammadi-Yeganeh S, Paryan M, Mirab Samiee S, Kia V, and Rezvan H (2012) Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV. Iran J Microbiol 4: 47-54. PMI: 22973469: PubMed Link

  650. Monroe WT and Haselton FR (2003) Molecular beacon sequence design algorithm. Biotechniques 34: 68-73. PMI: 12545542: PubMed Link

  651. Morse DP (2007) Direct selection of RNA beacon aptamers. Biochem Biophys Res Commun 359: 94-101. PMI: 17533112: PubMed Link

  652. Mukewar P, Wang G, Henning P, Bao G, and Wang M (2004) Segmentation of bionano images for understanding cell dynamics. Conf Proc IEEE Eng Med Biol Soc 3: 1759-1762. PMI: 17272047: PubMed Link

  653. Muradrasoli S, Mohamed N, Belak S, Czifra G, Herrmann B, Berencsi G, and Blomberg J (2009) Broadly targeted triplex real-time PCR detection of influenza A, B and C viruses based on the nucleoprotein gene and a novel "MegaBeacon" probe strategy. J Virol Methods. PMI: 19879296: PubMed Link

  654. Narita A, Ogawa K, Sando S, and Aoyama Y (2007) Cis-regulatory hairpin-shaped mRNA encoding a reporter protein: catalytic sensing of nucleic acid sequence at single nucleotide resolution. Nat Protoc 2: 1105-1116. PMI: 17546001: PubMed Link

  655. Nazarenko IA, Bhatnagar SK, and Hohman RJ (1997) A closed tube format for amplification and detection of DNA based on energy transfer. Nucleic Acids Res 25: 2516-2521. PMI: 9171107: PubMed Link

  656. Nellaker C, Wallgren U, and Karlsson H (2007) Molecular beacon-based temperature control and automated analyses for improved resolution of melting temperature analysis using SYBR I green chemistry. Clin Chem 53: 98-103. PMI: 17110472: PubMed Link

  657. Nesterova IV, Erdem SS, Pakhomov S, Hammer RP, and Soper SA (2009) Phthalocyanine dimerization-based molecular beacons using near-IR fluorescence. J Am Chem Soc 131: 2432-2433. PMI: 19191492: PubMed Link

  658. Ng CT, Gilchrist CA, Lane A, Roy S, Haque R, and Houpt ER (2005) Multiplex real-time PCR assay using Scorpion probes and DNA capture for genotype-specific detection of Giardia lamblia on fecal samples. J Clin Microbiol 43: 1256-1260. PMI: 15750093: PubMed Link

  659. Nguyen C, Grimes J, Gerasimova YV, and Kolpashchikov DM (2011) Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. Chemistry 17: 13052-13058. PMI: 21956816: PubMed Link

  660. Nguyen LV, Giannetti S, Warren-Smith S, Cooper A, Selleri S, Cucinotta A, and Monro T (2014) Genotyping Single Nucleotide Polymorphisms Using Different Molecular Beacon Multiplexed within a Suspended Core Optical Fiber. Sensors (Basel) 14: 14488-14499. PMI: 25111240: PubMed Link

  661. Nguyen LV, Warren-Smith SC, Cooper A, and Monro TM (2012) Molecular beacons immobilized within suspended core optical fiber for specific DNA detection. Opt Express 20: 29378-29385. PMI: 23388765: PubMed Link

  662. Nieh CC and Tseng WL (2014) Thymine-based molecular beacon for sensing adenosine based on the inhibition of S-adenosylhomocysteine hydrolase activity. Biosens Bioelectron 61: 404-409. PMI: 24914852: PubMed Link

  663. Niemeyer CM and Adler M (2002) Nanomechanical devices based on DNA. Angew Chem Int Ed 41: 3779-3782. PMI: PubMed Link

  664. Nilsson M, Gullberg M, Dahl F, Szuhai K, and Raap AK (2002) Real-time monitoring of rolling-circle amplification using a modified molecular beacon design. Nucleic Acids Res 30: e66. PMI: 12136114: PubMed Link

  665. Nutiu R and Li Y (2002) Tripartite molecular beacons. Nucleic Acids Res 30: e94. PMI: 12235396: PubMed Link

  666. Oh KJ, Cash KJ, Lubin AA, and Plaxco KW (2007) Chimeric peptide beacons: a direct polypeptide analog of DNA molecular beacons. Chem Commun (Camb): 4869-4871. PMI: 18361352: PubMed Link

  667. Oh KJ, Cash KJ, and Plaxco KW (2009) Beyond molecular beacons: optical sensors based on the binding-induced folding of proteins and polypeptides. Chemistry 15: 2244-2251. PMI: 19191230: PubMed Link

  668. Okamoto A, Tanabe K, Inasaki T, and Saito I (2003) Phototriggered drug release from functionalized oligonucleotides by a molecular beacon strategy. Angew Chem Int Ed Engl 42: 2502-2504. PMI: 12800170: PubMed Link

  669. Oladepo SA and Loppnow GR (2010) The effect of tryptophan on UV-induced DNA photodamage. Photochem Photobiol. PMI: 20492563: PubMed Link

  670. Paiboonskuwong K and Kato Y (2006) Detection of the mature, but not precursor, RNA using a fluorescent DNA probe. Nucleic Acids Symp Ser (Oxf): 327-328. PMI: 17150950: PubMed Link

  671. Park KS, Seo MW, Jung C, Lee JY, and Park HG (2012) Simple and universal platform for logic gate operations based on molecular beacon probes. Small 8: 2203-2212, 2129. PMI: 22517593: PubMed Link

  672. Paryan M, Mohammadi-Yeganeh S, Mirab Samiee S, and Rezvan H (2012) Design and Development of a Multiplex Real-Time PCR Assay for Detection of HIV-1 and HCV Using Molecular Beacons. Indian J Microbiol 52: 456-463. PMI: 23997339: PubMed Link

  673. Pattanayak V, Gifford LK, Lu P, and Gewirtz AM (2008) Observed versus predicted structure of fluorescent self-quenching reporter molecules (SQRM): caveats with respect to the use of "stem-loop" oligonucleotides as probes for mRNA folding. RNA 14: 657-665. PMI: 18359781: PubMed Link

  674. Pattyn F, Speleman F, De Paepe A, and Vandesompele J (2003) RTPrimerDB: The Real-Time PCR primer and probe database. Nucleic Acids Res 31: 122-123. PMI: ISI:000181079700027: PubMed Link

  675. Peng Z, Soper SA, Pingle MR, Barany F, and Davis LM (2010) Ligase detection reaction generation of reverse molecular beacons for near real-time analysis of bacterial pathogens using single-pair fluorescence resonance energy transfer and a cyclic olefin copolymer microfluidic chip. Anal Chem 82: 9727-9735. PMI: 21047095: PubMed Link

  676. Peng Z, Young B, Baird AE, and Soper SA (2013) Single-pair fluorescence resonance energy transfer analysis of mRNA transcripts for highly sensitive gene expression profiling in near real time. Anal Chem 85: 7851-7858. PMI: 23869556: PubMed Link

  677. Persat A and Santiago JG (2011) MicroRNA profiling by simultaneous selective isotachophoresis and hybridization with molecular beacons. Anal Chem 83: 2310-2316. PMI: 21329391: PubMed Link

  678. Petersen K, Vogel U, Rockenbauer E, Nielsen KV, Kolvraa S, Bolund L, and Nexo B (2004) Short PNA molecular beacons for real-time PCR allelic discrimination of single nucleotide polymorphisms. Mol Cell Probes 18: 117-122. PMI: 15051121: PubMed Link

  679. Piao Y, Liu F, and Seo TS (2012) A novel molecular beacon bearing a graphite nanoparticle as a nanoquencher for in situ mRNA detection in cancer cells. ACS Appl Mater Interfaces 4: 6785-6789. PMI: 23145791: PubMed Link

  680. Prosseda G, Mazzola A, Di Martino ML, Tielker D, Micheli G, and Colonna B (2010) A temperature-induced narrow DNA curvature range sustains maximum activity of a bacterial promoter in vitro. Biochemistry. PMI: 20170130: PubMed Link

  681. Puleo CM and Wang TH (2009) Microfluidic means of achieving attomolar detection limits with molecular beacon probes. Lab Chip 9: 1065-1072. PMI: 19350088: PubMed Link

  682. Qi L, Zhao Y, Yuan H, Bai K, Zhao Y, Chen F, Dong Y, and Wu Y (2012) Amplified fluorescence detection of mercury(II) ions (Hg2+) using target-induced DNAzyme cascade with catalytic and molecular beacons. Analyst 137: 2799-2805. PMI: 22551984: PubMed Link

  683. Qian R, Ding L, Yan L, Lin M, and Ju H (2014) A robust probe for lighting up intracellular telomerase via primer extension to open a nicked molecular beacon. J Am Chem Soc 136: 8205-8208. PMI: 24857561: PubMed Link

  684. Qiao G, Gao Y, Li N, Yu Z, Zhuo L, and Tang B (2011) Simultaneous detection of intracellular tumor mRNA with bi-color imaging based on a gold nanoparticle/molecular beacon. Chemistry 17: 11210-11215. PMI: 21850725: PubMed Link

  685. Qiao G, Zhuo L, Gao Y, Yu L, Li N, and Tang B (2011) A tumor mRNA-dependent gold nanoparticle-molecular beacon carrier for controlled drug release and intracellular imaging. Chem Commun (Camb) 47: 7458-7460. PMI: 21589964: PubMed Link

  686. Qiu L, Wu C, You M, Han D, Chen T, Zhu G, Jiang J, Yu R, and Tan W (2013) A targeted, self-delivered, and photocontrolled molecular beacon for mRNA detection in living cells. J Am Chem Soc 135: 12952-12955. PMI: 23931073: PubMed Link

  687. Raab M and Hancock WO (2007) Transport and detection of unlabeled nucleotide targets by microtubules functionalized with molecular beacons. Biotechnol Bioeng. PMI: 17879297: PubMed Link

  688. Radi AE, Acero Sanchez JL, Baldrich E, and O'Sullivan CK (2006) Reagentless, reusable, ultrasensitive electrochemical molecular beacon aptasensor. J Am Chem Soc 128: 117-124. PMI: 16390138: PubMed Link

  689. Rai V, Nyine YT, Hapuarachchi HC, Yap HM, Ng LC, and Toh CS (2012) Electrochemically amplified molecular beacon biosensor for ultrasensitive DNA sequence-specific detection of Legionella sp. Biosens Bioelectron 32: 133-140. PMI: 22196877: PubMed Link

  690. Rajendran M and Ellington AD (2003) In vitro selection of molecular beacons. Nucleic Acids Res 31: 5700-5713. PMI: 14500834: PubMed Link

  691. Rajendran M and Ellington AD (2007) Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal Bioanal Chem. PMI: 18049815: PubMed Link

  692. Ramachandran A, Flinchbaugh J, Ayoubi P, Olah GA, and Malayer JR (2004) Target discrimination by surface-immobilized molecular beacons designed to detect Francisella tularensis. Biosens Bioelectron 19: 727-736. PMI: 14709391: PubMed Link

  693. Ramachandran A, Zhang M, Goad D, Olah G, Malayer JR, and El-Rassi Z (2003) Capillary electrophoresis and fluorescence studies on molecular beacon-based variable length oligonucleotide target discrimination. Electrophoresis 24: 70-77. PMI: 12652574: PubMed Link

  694. Ramakrishnan A and Sadana A (2002) A kinetic study of analyte-receptor binding and dissociation for biosensor applications: a fractal analysis for two different DNA systems. Biosystems 66: 165-177. PMI: 12413747: PubMed Link

  695. Rani N, Vajpayee P, Bhatti S, Singh S, Shanker R, and Gupta KC (2014) Quantification of Salmonella Typhi in water and sediments by molecular-beacon based qPCR. Ecotoxicol Environ Saf 108C: 58-64. PMI: 25042245: PubMed Link

  696. Raphael MP, Christodoulides JA, Qadri SN, Qadri SA, Miller MM, Kurihara LK, and Byers JM (2008) The use of DNA molecular beacons as nanoscale temperature probes for microchip-based biosensors. Biosens Bioelectron 24: 894-898. PMI: 18760910: PubMed Link

  697. Rehman S, Kapur N, Durgapal H, and Panda SK (2007) Subcellular localization of hepatitis E virus (HEV) replicase. Virology. PMI: 17904184: PubMed Link

  698. Rinne JS, Kaminski TP, Kubitscheck U, and Heckel A (2013) Light-inducible molecular beacons for spatio-temporally highly defined activation. Chem Commun (Camb) 49: 5375-5377. PMI: 23652644: PubMed Link

  699. Rizzo J, Gifford LK, Zhang X, Gewirtz AM, and Lu P (2002) Chimeric RNA-DNA molecular beacon assay for ribonuclease H activity. Mol Cell Probes 16: 277-283. PMI: 12270269: PubMed Link

  700. Root DD, Vaccaro C, Zhang Z, and Castro M (2004) Detection of single nucleotide variations by a hybridization proximity assay based on molecular beacons and luminescence resonance energy transfer. Biopolymers 75: 60-70. PMI: 15307198: PubMed Link

  701. Rosa J, Conde J, de la Fuente JM, Lima JC, and Baptista PV (2012) Gold-nanobeacons for real-time monitoring of RNA synthesis. Biosens Bioelectron 36: 161-167. PMI: 22541812: PubMed Link

  702. Ryazantsev DY, Kvach MV, Tsybulsky DA, Prokhorenko IA, Stepanova IA, Martynenko YV, Gontarev SV, Shmanai VV, Zavriev SK, and Korshun VA (2014) Design of molecular beacons: 3' couple quenchers improve fluorogenic properties of a probe in real-time PCR assay. Analyst 139: 2867-2872. PMI: 24736939: PubMed Link

  703. Saha BK, Tian B, and Bucy RP (2001) Quantitation of HIV-1 by real-time PCR with a unique fluorogenic probe. J Virol Methods 93: 33-42. PMI: 11311341: PubMed Link

  704. Saito Y, Mizuno E, Bag SS, Suzuka I, and Saito I (2007) Design of a novel G-quenched molecular beacon: A simple and efficient strategy for DNA sequence analysis. Chem Commun (Camb): 4492-4494. PMI: 17971966: PubMed Link

  705. Saito Y, Numajiri K, Bag SS, Mizuno E, and Saito I (2008) Design of an efficient self-quenched molecular beacon for SNPs genotyping. Nucleic Acids Symp Ser (Oxf): 359-360. PMI: 18776402: PubMed Link

  706. Saito Y, Shinohara Y, Bag SS, Takeuchi Y, Matsumoto K, and Saito I (2008) Design of an ultimate quencher free molecular beacon containing pyrrolocytidine-guanine base pair. Nucleic Acids Symp Ser (Oxf): 361-362. PMI: 18776403: PubMed Link

  707. Sanzani SM, Reverberi M, Fanelli C, and Ippolito A (2015) Detection of ochratoxin A using molecular beacons and real-time PCR thermal cycler. Toxins (Basel) 7: 812-820. PMI: 25760080: PubMed Link

  708. Sato Y, Nishizawa S, and Teramae N (2008) Development of label-free molecular beacons based on abasic site-binding fluorescence molecules. Nucleic Acids Symp Ser (Oxf): 121-122. PMI: 18776283: PubMed Link

  709. Sato Y, Nishizawa S, and Teramae N (2011) Label-free molecular beacon system based on DNAs containing abasic sites and fluorescent ligands that bind abasic sites. Chemistry 17: 11650-11656. PMI: 21953933: PubMed Link

  710. Satterfield BC, Bartosiewicz M, West JA, and Caplan MR (2010) Surpassing specificity limits of nucleic acid probes via cooperativity. J Mol Diagn. PMI: 20304941: PubMed Link

  711. Satterfield BC, West JA, and Caplan MR (2007) Tentacle probes: eliminating false positives without sacrificing sensitivity. Nucleic Acids Res 35: e76. PMI: 17517788: PubMed Link

  712. Schofield P, Pell AN, and Krause DO (1997) Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria. Appl Environ Microbiol 63: 1143-1147. PMI: 9055429: PubMed Link

  713. Seitz O (2000) Solid-phase synthesis of doubly labeled peptide nucleic acids as probes for the real-time detection of hybridization. Angewandte Chemie-International Edition 39: 3249-3252. PMI: ISI:000089433600006: PubMed Link

  714. Seitz O and Kohler O (2001) Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase. Chemistry-a European Journal 7: 3911-3925. PMI: ISI:000171220600007: PubMed Link

  715. Seo YJ, Jeong HS, Bang EK, Hwang GT, Jung JH, Jang SK, and Kim BH (2006) Cholesterol-linked fluorescent molecular beacons with enhanced cell permeability. Bioconjug Chem 17: 1151-1155. PMI: 16984122: PubMed Link

  716. Sheng P, Yang Z, Kim Y, Wu Y, Tan W, and Benner SA (2008) Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet. Chem Commun (Camb): 5128-5130. PMI: 18956044: PubMed Link

  717. Shi C, Gu H, and Ma C (2009) An aptamer-based fluorescent biosensor for potassium ion detection using a pyrene-labeled molecular beacon. Anal Biochem. PMI: 20056100: PubMed Link

  718. Shi X, Wen J, Li Y, Zheng Y, Zhou J, Li X, and Yu HZ (2014) DNA Molecular Beacon-Based Plastic Biochip: A Versatile and Sensitive Scanometric Detection Platform. ACS Appl Mater Interfaces. PMI: 24852130: PubMed Link

  719. Shi XL, Hu QH, Zhang JF, Li QG, Wang B, Lin YM, Zhuang ZX, Liu XL, and Zhang SX (2006) [Rapid simultaneous detection of Salmonella and Shigella using modified molecular beacons and real-time PCR]. Zhonghua Liu Xing Bing Xue Za Zhi 27: 1053-1056. PMI: 17415984: PubMed Link

  720. Shin S, Nam HY, Lee EJ, Jung W, and Hah SS (2012) Molecular beacon-based quantitiation of epithelial tumor marker mucin 1. Bioorg Med Chem Lett 22: 6081-6084. PMI: 22959521: PubMed Link

  721. Shire ZJ and Loppnow GR (2012) Molecular beacon probes of oligonucleotides photodamaged by psoralen. Photochem Photobiol 88: 645-650. PMI: 22329786: PubMed Link

  722. Shire ZJ and Loppnow GR (2012) Molecular beacon probes for the detection of cisplatin-induced DNA damage. Anal Bioanal Chem 403: 179-184. PMI: 22349333: PubMed Link

  723. Sidon P, Heimann P, Lambert F, Dessars B, Robin V, and El Housni H (2006) Combined locked nucleic acid and molecular beacon technologies for sensitive detection of the JAK2V617F somatic single-base sequence variant. Clin Chem 52: 1436-1438. PMI: 16798973: PubMed Link

  724. Sidoti F, Bergallo M, Terlizzi ME, Piasentin Alessio E, Astegiano S, Gasparini G, and Cavallo R (2012) Development of a quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes. Mol Biotechnol 50: 221-228. PMI: 21728031: PubMed Link

  725. Sivaraman D, Yeh HY, Mulchandani A, Yates MV, and Chen W (2013) Use of flow cytometry for rapid, quantitative detection of poliovirus-infected cells via TAT peptide-delivered molecular beacons. Appl Environ Microbiol 79: 696-700. PMI: 23160127: PubMed Link

  726. Smith BD and Liu J (2010) Assembly of DNA-functionalized nanoparticles in alcoholic solvents reveals opposite thermodynamic and kinetic trends for DNA hybridization. J Am Chem Soc. PMI: 20402504: PubMed Link

  727. Song C, Zhang C, and Zhao MP (2010) Development of a high-throughput screening platform for DNA 3'-phosphatases and their inhibitors based on a universal molecular beacon and quantitative real-time PCR. Chem Asian J 5: 1146-1151. PMI: 20408165: PubMed Link

  728. Song P, Xiang Y, Xing H, Zhou Z, Tong A, and Lu Y (2012) Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules. Anal Chem 84: 2916-2922. PMI: 22400799: PubMed Link

  729. Song Y, Cui L, Wu J, Zhang W, Zhang WY, Kang H, and Yang CJ (2011) Allosteric molecular beacons for sensitive detection of nucleic acids, proteins, and small molecules in complex biological samples. Chemistry 17: 9042-9046. PMI: 21766367: PubMed Link

  730. Soni GV and Meller A (2007) Progress toward ultrafast DNA sequencing using solid-state nanopores. Clin Chem 53: 1996-2001. PMI: 17890440: PubMed Link

  731. Stefflova K, Chen J, and Zheng G (2007) Using molecular beacons for cancer imaging and treatment. Front Biosci 12: 4709-4721. PMI: 17485407: PubMed Link

  732. Stevaert A, Nurra S, Pala N, Carcelli M, Rogolino D, Shepard C, Domaoal RA, Kim B, Alfonso-Prieto M, Marras SA, Sechi M, and Naesens L (2015) An Integrated Biological Approach to Guide the Development of Metal-Chelating Inhibitors of Influenza Virus PA Endonuclease. Mol Pharmacol 87: 323-337. PMI: 25477342: PubMed Link

  733. Stobiecka M, Molinero AA, Chalupa A, and Hepel M (2012) Mercury/homocysteine ligation-induced ON/OFF-switching of a T-T mismatch-based oligonucleotide molecular beacon. Anal Chem 84: 4970-4978. PMI: 22524145: PubMed Link

  734. Stoermer RL, Cederquist KB, McFarland SK, Sha MY, Penn SG, and Keating CD (2006) Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. J Am Chem Soc 128: 16892-16903. PMI: 17177440: PubMed Link

  735. Stoermer RL and Keating CD (2006) Distance-dependent emission from dye-labeled oligonucleotides on striped au/ag nanowires: effect of secondary structure and hybridization efficiency. J Am Chem Soc 128: 13243-13254. PMI: 17017805: PubMed Link

  736. Stojanovic MN, de Prada P, and Landry DW (2001) Catalytic molecular beacons. Chembiochem 2: 411-415. PMI: 11828471: PubMed Link

  737. Strohsahl CM, Krauss TD, and Miller BL (2007) Identification of high-stringency DNA hairpin probes by partial gene folding. Biosens Bioelectron. PMI: 17512187: PubMed Link

  738. Strouse GF and Armstrong RE (2014) Rationally Manipulating Aptamer Binding Affinities in a Stem-loop Molecular Beacon. Bioconjug Chem. PMI: 25170558: PubMed Link

  739. Strouse RJ, Hakki FZ, Wang SC, DeFusco AW, Garrett JL, and Schenerman MA (2000) Using molecular beacons to quantify low levels of type I endonuclease activity. Biopharm 13: 40-47. PMI: PubMed Link

  740. Su S, Wei X, Zhong Y, Guo Y, Su Y, Huang Q, Lee ST, Fan C, and He Y (2012) Silicon nanowire-based molecular beacons for high-sensitivity and sequence-specific DNA multiplexed analysis. ACS Nano 6: 2582-2590. PMI: 22329677: PubMed Link

  741. Su X, Zhang C, and Zhao M (2011) Discrimination of the false-positive signals of molecular beacons by combination of heat inactivation and using single walled carbon nanotubes. Biosens Bioelectron 26: 3596-3601. PMI: 21382709: PubMed Link

  742. Su YC, Wang CH, Chang WH, Chen TY, and Lee GB (2014) Rapid and amplification-free detection of fish pathogens by utilizing a molecular beacon-based microfluidic system. Biosens Bioelectron 63C: 196-203. PMI: 25089817: PubMed Link

  743. Summerer D (2008) DNA polymerase profiling. Methods Mol Biol 429: 225-235. PMI: 18695970: PubMed Link

  744. Summerer D and Marx A (2002) A molecular beacon for quantitative monitoring of the DNA polymerase reaction in real-time. Angew Chem Int Ed Engl 41: 3620-3622. PMI: 12370909: PubMed Link

  745. Svilar D, Vens C, and Sobol RW (2012) Quantitative, real-time analysis of base excision repair activity in cell lysates utilizing lesion-specific molecular beacons. J Vis Exp: e4168. PMI: 22895410: PubMed Link

  746. Tan L, Li Y, Drake TJ, Moroz L, Wang K, Li J, Munteanu A, James Yang C, Martinez K, and Tan W (2005) Molecular beacons for bioanalytical applications. Analyst 130: 1002-1005. PMI: 15965520: PubMed Link

  747. Tan X, Chen W, Lu S, Zhu Z, Chen T, Zhu G, You M, and Tan W (2012) Molecular beacon aptamers for direct and universal quantitation of recombinant proteins from cell lysates. Anal Chem 84: 8272-8276. PMI: 22916953: PubMed Link

  748. Tang D, Liao D, Zhu Q, Wang F, Jiao H, Zhang Y, and Yu C (2011) Fluorescence turn-on detection of a protein through the displaced single-stranded DNA binding protein binding to a molecular beacon. Chem Commun (Camb) 47: 5485-5487. PMI: 21483905: PubMed Link

  749. Tang H, Yang X, Wang K, Tan W, Li H, He L, and Liu B (2008) RNA-templated single-base mutation detection based on T4 DNA ligase and reverse molecular beacon. Talanta 75: 1388-1393. PMI: 18585229: PubMed Link

  750. Tang Z, Liu P, Ma C, Yang X, Wang K, Tan W, and Lv X (2011) Molecular beacon based bioassay for highly sensitive and selective detection of nicotinamide adenine dinucleotide and the activity of alanine aminotransferase. Anal Chem 83: 2505-2510. PMI: 21401019: PubMed Link

  751. Tang Z, Wang K, Tan W, Li J, Liu L, Guo Q, Meng X, Ma C, and Huang S (2003) Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons. Nucleic Acids Res 31: e148. PMI: 14627838: PubMed Link

  752. Tang Z, Wang K, Tan W, Ma C, Li J, Liu L, Guo Q, and Meng X (2005) Real-time investigation of nucleic acids phosphorylation process using molecular beacons. Nucleic Acids Res 33: e97. PMI: 15961728: PubMed Link

  753. Taveau M, Stockholm D, Spencer M, and Richard I (2002) Quantification of splice variants using molecular beacon or scorpion primers. Anal Biochem 305: 227-235. PMI: 12054451: PubMed Link

  754. Thelwell N, Millington S, Solinas A, Booth J, and Brown T (2000) Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res 28: 3752-3761. PMI: 11000267: PubMed Link

  755. Thurley S, Roglin L, and Seitz O (2007) Hairpin peptide beacon: dual-labeled PNA-peptide-hybrids for protein detection. J Am Chem Soc 129: 12693-12695. PMI: 17927187: PubMed Link

  756. Toga T, Kuraoka I, Yasui A, and Iwai S (2013) A transfection reporter for the prevention of false-negative results in molecular beacon experiments. Anal Biochem 440: 9-11. PMI: 23685051: PubMed Link

  757. Tok J, Lai J, Leung T, and Li SF (2010) Molecular aptamer beacon for myotonic dystrophy kinase-related Cdc42-binding kinase alpha. Talanta 81: 732-736. PMI: 20188990: PubMed Link

  758. Tsourkas A, Behlke MA, and Bao G (2002) Structure-function relationships of shared-stem and conventional molecular beacons. Nucleic Acids Res 30: 4208-4215. PMI: 12364599: PubMed Link

  759. Tsourkas A, Behlke MA, and Bao G (2003) Hybridization of 2'-O-methyl and 2'-deoxy molecular beacons to RNA and DNA targets. Nucleic Acids Res 30: 5168-5174. PMI: 12669716: PubMed Link

  760. Tsourkas A, Behlke MA, Rose SD, and Bao G (2003) Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res 31: 1319-1330. PMI: 12582252: PubMed Link

  761. Tsourkas A, Behlke MA, Xu Y, and Bao G (2003) Spectroscopic features of dual fluorescence/luminescence resonance energy-transfer molecular beacons. Anal Chem 75: 3697-3703. PMI: 14572032: PubMed Link

  762. Tung CH, Mahmood U, Bredow S, and Weissleder R (2000) In vivo imaging of proteolytic enzyme activity using a novel molecular reporter. Cancer Res 60: 4953-4958. PMI: 10987312: PubMed Link

  763. Tyagi S and Kramer FR (2012) Molecular beacons in diagnostics. F1000 Med Rep 4: 10. PMI: 22619695: PubMed Link

  764. Uddayasankar U and Krull UJ (2013) Analytical performance of molecular beacons on surface immobilized gold nanoparticles of varying size and density. Anal Chim Acta 803: 113-122. PMI: 24216204: PubMed Link

  765. Ueno Y, Kawamura A, Kato T, and Kitade Y (2007) Synthesis and properties of a novel molecular beacon containing a benzene-phosphate backbone at a stem moiety. Nucleic Acids Symp Ser (Oxf): 293-294. PMI: 18029702: PubMed Link

  766. Ueno Y, Kawamura A, Takasu K, Komatsuzaki S, Kato T, Kuboe S, Kitamura Y, and Kitade Y (2009) Synthesis and properties of a novel molecular beacon containing a benzene-phosphate backbone at its stem moiety. Org Biomol Chem 7: 2761-2769. PMI: 19532993: PubMed Link

  767. Urata H, Tamaki C, Matsuno M, Wada S, and Akagi M (2007) Monitoring of Eco RI-catalyzed cleavage reaction of fluorescent-labeled heterochiral DNA. Nucleic Acids Symp Ser (Oxf): 453-454. PMI: 18029782: PubMed Link

  768. Vallee-Belisle A, Ricci F, and Plaxco KW (2009) Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors. Proc Natl Acad Sci U S A 106: 13802-13807. PMI: 19666496: PubMed Link

  769. Varghese R and Wagenknecht HA (2009) Red-white-blue emission switching molecular beacons: ratiometric multicolour DNA hybridization probes. Org Biomol Chem 8: 526-528. PMI: 20090965: PubMed Link

  770. Venkatesan N, Jun Seo Y, and Hyean Kim B (2008) Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis. Chem Soc Rev 37: 648-663. PMI: 18362974: PubMed Link

  771. Verhille M, Benachour H, Ibrahim A, Achard M, Arnoux P, Barberi-Heyob M, Andre JC, Allonas X, Baros F, Vanderesse R, and Frochot C (2012) Photodynamic molecular beacons triggered by MMP-2 and MMP-9: influence of the distance between photosensitizer and quencher onto photophysical properties and enzymatic activation. Curr Med Chem 19: 5580-5594. PMI: 22978328: PubMed Link

  772. Vet JA and Marras SAE (2004) Design and optimization of molecular beacon real-time polymerase chain reaction assays. Methods Mol Biol 288: 273-290. PMI: 15333910: PubMed Link

  773. Vicens MC, Sen A, Vanderlaan A, Drake TJ, and Tan W (2005) Investigation of molecular beacon aptamer-based bioassay for platelet-derived growth factor detection. Chembiochem 6: 900-907. PMI: 15812865: PubMed Link

  774. Vijayanathan V, Thomas T, Sigal LH, and Thomas TJ (2002) Direct measurement of the association constant of HER2/neu antisense oligonucleotide to its target RNA sequence using a molecular beacon. Antisense Nucleic Acid Drug Dev 12: 225-233. PMI: 12238811: PubMed Link

  775. Vitko J, Rujan I, Androga LA, Mukerji I, and Bolton PH (2007) Molecular beacon-equilibrium cyclization detection of DNA-protein complexes. Biophys J 93: 3210-3217. PMI: 17631534: PubMed Link

  776. Wabuyele MB, Farquar H, Stryjewski W, Hammer RP, Soper SA, Cheng YW, and Barany F (2003) Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes. J Am Chem Soc 125: 6937-6945. PMI: 12783546: PubMed Link

  777. Wahba AS, Esmaeili A, Damha MJ, and Hudson RH (2010) A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity. Nucleic Acids Res 38: 1048-1056. PMI: 19933258: PubMed Link

  778. Wang C, Wu R, Li FD, Liu L, Zhang XL, Zhao CL, Diao XL, and Guan HW (2011) Expression patterns of prion protein gene in differential genotypes sheep: quantification using molecular beacon real-time RT-PCR. Virus Genes 42: 457-462. PMI: 21318242: PubMed Link

  779. Wang C, Zhu Z, Song Y, Lin H, Yang CJ, and Tan W (2011) Caged molecular beacons: controlling nucleic acid hybridization with light. Chem Commun (Camb) 47: 5708-5710. PMI: 21499630: PubMed Link

  780. Wang G, Becker E, and Mesa C (2007) Optimization of 6-carboxy-X-rhodamine concentration for real-time polymerase chain reaction using molecular beacon chemistry. Can J Microbiol 53: 391-397. PMI: 17538648: PubMed Link

  781. Wang G, Zhu Y, Chen L, and Zhang X (2014) Dual hairpin-like molecular beacon based on coralyne-adenosine interaction for sensing melamine in dairy products. Talanta 129: 398-403. PMI: 25127611: PubMed Link

  782. Wang J, Onoshima D, Aki M, Okamoto Y, Kaji N, Tokeshi M, and Baba Y (2011) Label-free detection of DNA-binding proteins based on microfluidic solid-state molecular beacon sensor. Anal Chem 83: 3528-3532. PMI: 21476599: PubMed Link

  783. Wang J, Wang W, Liu Y, Duo L, Huang L, and Jiang X (2008) The method of single-nucleotide variations detection using capillary electrophoresis and molecular beacons. Mol Biol Rep. PMI: 18989751: PubMed Link

  784. Wang L, Blasic JR, Jr., Holden MJ, and Pires R (2005) Sensitivity comparison of real-time PCR probe designs on a model DNA plasmid. Anal Biochem 344: 257-265. PMI: 16091278: PubMed Link

  785. Wang L, Yang CJ, Medley CD, Benner SA, and Tan W (2005) Locked nucleic acid molecular beacons. J Am Chem Soc 127: 15664-15665. PMI: 16277483: PubMed Link

  786. Wang Q, Chen L, Long Y, Tian H, and Wu J (2013) Molecular beacons of xeno-nucleic acid for detecting nucleic acid. Theranostics 3: 395-408. PMI: 23781286: PubMed Link

  787. Wang TH, Peng Y, Zhang C, Wong PK, and Ho CM (2005) Single-molecule tracing on a fluidic microchip for quantitative detection of low-abundance nucleic acids. J Am Chem Soc 127: 5354-5359. PMI: 15826173: PubMed Link

  788. Wang X, Dong P, Yun W, Xu Y, He P, and Fang Y (2009) A solid-state electrochemiluminescence biosensing switch for detection of thrombin based on ferrocene-labeled molecular beacon aptamer. Biosens Bioelectron. PMI: 19442509: PubMed Link

  789. Wang X, Dong P, Yun W, Xu Y, He P, and Fang Y (2010) Detection of T4 DNA ligase using a solid-state electrochemiluminescence biosensing switch based on ferrocene-labeled molecular beacon. Talanta 80: 1643-1647. PMI: 20152390: PubMed Link

  790. Wang X, Yun W, Dong P, Zhou J, He P, and Fang Y (2008) A controllable solid-state Ru(bpy)(3)(2+) electrochemiluminescence film based on conformation change of ferrocene-labeled DNA molecular beacon. Langmuir. PMI: 18225925: PubMed Link

  791. Wang Y, He X, Wang K, and Ni X (2010) A sensitive ligase-based ATP electrochemical assay using molecular beacon-like DNA. Biosens Bioelectron 25: 2101-2106. PMI: 20299199: PubMed Link

  792. Wang Y, Li J, Jin J, Wang H, Tang H, Yang R, and Wang K (2009) Strategy for molecular beacon binding readout: separating molecular recognition element and signal reporter. Anal Chem. PMI: 19899746: PubMed Link

  793. Wang Y, Wang H, Gao L, Liu H, Lu Z, and He N (2005) Polyacrylamide gel film immobilized molecular beacon array for single nucleotide mismatch detection. J Nanosci Nanotechnol 5: 653-658. PMI: 16004134: PubMed Link

  794. Wang ZQ, Zhao J, Zeng J, Wu KJ, Chen YL, Wang XY, Chang LS, and He DL (2011) Specific survivin dual fluorescence resonance energy transfer molecular beacons for detection of human bladder cancer cells. Acta Pharmacol Sin 32: 1522-1528. PMI: 22019956: PubMed Link

  795. Watanabe S, Hagihara K, Tsukagoshi K, and Hashimoto M (2014) Microbead-based ligase detection reaction assay using a molecular beacon probe for the detection of low-abundance point mutations. Anal Chem 86: 900-906. PMI: 24328157: PubMed Link

  796. Wei X, Su S, Guo Y, Jiang X, Zhong Y, Su Y, Fan C, Lee ST, and He Y (2013) A molecular beacon-based signal-off surface-enhanced Raman scattering strategy for highly sensitive, reproducible, and multiplexed DNA detection. Small 9: 2493-2499, 2652. PMI: 23359560: PubMed Link

  797. Whitcombe D, Theaker J, Guy SP, Brown T, and Little S (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 17: 804-807. PMI: 10429248: PubMed Link

  798. Wilson R and Johansson MK (2003) Photoluminescence and electrochemiluminescence of a Ru(II)(bpy)(3)-quencher dual-labeled oligonucleotide probe. Chem Commun (Camb): 2710-2711. PMI: ISI:000186492000032: PubMed Link

  799. Wolfrum C and Josten A (2005) Oligonucleotides as coding molecules in an anti-counterfeiting system. Nucleosides Nucleotides Nucleic Acids 24: 1069-1074. PMI: 16248094: PubMed Link

  800. Wu AH, Sun JJ, Zheng RJ, Yang HH, and Chen GN (2010) A reagentless DNA biosensor based on cathodic electrochemiluminescence at a C/C(x)O(1-x) electrode. Talanta 81: 934-940. PMI: 20298875: PubMed Link

  801. Wu CS, Oo MK, Cupps JM, and Fan X (2011) Robust silica-coated quantum dot-molecular beacon for highly sensitive DNA detection. Biosens Bioelectron. PMI: 21458980: PubMed Link

  802. Wu CS, Peng L, You M, Han D, Chen T, Williams KR, Yang CJ, and Tan W (2012) Engineering molecular beacons for intracellular imaging. Int J Mol Imaging 2012: 501579. PMI: 23209893: PubMed Link

  803. Wu J, Zou Y, Li C, Sicking W, Piantanida I, Yi T, and Schmuck C (2012) A molecular peptide beacon for the ratiometric sensing of nucleic acids. J Am Chem Soc 134: 1958-1961. PMI: 22242714: PubMed Link

  804. Wu S, Duan N, Li X, Tan G, Ma X, Xia Y, Wang Z, and Wang H (2013) Homogenous detection of fumonisin B(1) with a molecular beacon based on fluorescence resonance energy transfer between NaYF4: Yb, Ho upconversion nanoparticles and gold nanoparticles. Talanta 116: 611-618. PMI: 24148452: PubMed Link

  805. Wu SM, Tian ZQ, Zhang ZL, Huang BH, Jiang P, Xie ZX, and Pang DW (2010) Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon. Biosens Bioelectron 26: 491-496. PMI: 20729070: PubMed Link

  806. Wu X, Chen J, and Zhao JX (2013) A reversible fluorescent logic gate for sensing mercury and iodide ions based on a molecular beacon. Analyst 138: 5281-5287. PMI: 23865088: PubMed Link

  807. Wu X, Chen J, and Zhao JX (2014) Ultrasensitive detection of 3'-5' exonuclease enzymatic activity using molecular beacons. Analyst 139: 1081-1087. PMI: 24404561: PubMed Link

  808. Wu Y, Kwak KJ, Agarwal K, Marras A, Wang C, Mao Y, Huang X, Ma J, Yu B, Lee R, Vachani A, Marcucci G, Byrd JC, Muthusamy N, Otterson G, Huang K, Castro CE, Paulaitis M, Nana-Sinkam SP, and Lee LJ (2013) Detection of extracellular RNAs in cancer and viral infection via tethered cationic lipoplex nanoparticles containing molecular beacons. Anal Chem 85: 11265-11274. PMI: 24102152: PubMed Link

  809. Wu ZS, Jiang JH, Shen GL, and Yu RQ (2007) Highly sensitive DNA detection and point mutation identification: an electrochemical approach based on the combined use of ligase and reverse molecular beacon. Hum Mutat 0: 1-8. PMI: 17309058: PubMed Link

  810. Xi C, Balberg M, Boppart SA, and Raskin L (2003) Use of DNA and peptide nucleic acid molecular beacons for detection and quantification of rRNA in solution and in whole cells. Appl Environ Microbiol 69: 5673-5678. PMI: 12957960: PubMed Link

  811. Xi C, Raskin L, and Boppart SA (2005) Evaluation of microfluidic biosensor development using microscopic analysis of molecular beacon hybridization kinetics. Biomed Microdevices 7: 7-12. PMI: 15834515: PubMed Link

  812. Xi D, Wang X, Ai S, and Zhang S (2014) Detection of cancer cells using triplex DNA molecular beacons based on expression of enhanced green fluorescent protein (eGFP). Chem Commun (Camb) 50: 9547-9549. PMI: 25012879: PubMed Link

  813. Xiang D, Zhai K, Xiang W, and Wang L (2014) Highly sensitive fluorescence quantitative detection of specific DNA sequences with molecular beacons and nucleic acid dye SYBR Green I. Talanta 129: 249-253. PMI: 25127591: PubMed Link

  814. Xiang D, Zhang C, Chen L, Ji X, and He Z (2012) Tricolour fluorescence detection of sequence-specific DNA with a new molecular beacon and a nucleic acid dye TOTO-3. Analyst 137: 5898-5905. PMI: 23113317: PubMed Link

  815. Xiang DS, Zhai K, and Wang LZ (2013) Multiplexed DNA detection with a composite molecular beacon based on guanine-quenching. Analyst 138: 5318-5324. PMI: 23869386: PubMed Link

  816. Xiang DS, Zhou GH, Luo M, Ji XH, and He ZK (2012) Dual color fluorescence quantitative detection of specific single-stranded DNA with molecular beacons and nucleic acid dye SYBR Green I. Analyst 137: 3787-3793. PMI: 22763945: PubMed Link

  817. Xiao Y, Pavlov V, Niazov T, Dishon A, Kotler M, and Willner I (2004) Catalytic beacons for the detection of DNA and telomerase activity. J Am Chem Soc 126: 7430-7431. PMI: 15198576: PubMed Link

  818. Xiao Z, Guo X, and Ling L (2013) Sequence-specific recognition of double-stranded DNA with molecular beacon with the aid of Ag(+) under neutral pH environment. Chem Commun (Camb) 49: 3573-3575. PMI: 23525117: PubMed Link

  819. Xing X, Zhou Y, Liu X, Pang D, and Tang H (2014) Graphene Oxide and Metal-Mediated Base Pairs Based "Molecular Beacon" Integrating with Exonuclease I for Fluorescence Turn-on Detection of Biothiols. Small 10: 3412-3420. PMI: 24788855: PubMed Link

  820. Xiong Y, Wei M, Wei W, Yin L, Pu Y, and Liu S (2014) Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction. Spectrochim Acta A Mol Biomol Spectrosc 118: 806-810. PMI: 24152865: PubMed Link

  821. Xu H and Hepel M (2011) "Molecular beacon"-based fluorescent assay for selective detection of glutathione and cysteine. Anal Chem 83: 813-819. PMI: 21210683: PubMed Link

  822. Xu H, Zhu X, Ye H, Yu L, Liu X, and Chen G (2011) A simple "molecular beacon"-based fluorescent sensing strategy for sensitive and selective detection of mercury (II). Chem Commun (Camb) 47: 12158-12160. PMI: 21986702: PubMed Link

  823. Xu YJ, Zhou ZR, Lin L, Liu Q, and Liu HC (2008) [Development of a molecular beacon real-time PCR for the rapid detection of Mycobacterium tuberculosis]. Sichuan Da Xue Xue Bao Yi Xue Ban 39: 661-663. PMI: 18798520: PubMed Link

  824. Xuan F, Luo X, and Hsing IM (2012) Ultrasensitive solution-phase electrochemical molecular beacon-based DNA detection with signal amplification by exonuclease III-assisted target recycling. Anal Chem 84: 5216-5220. PMI: 22721426: PubMed Link

  825. Xue Y, An R, Zhang D, Zhao J, Wang X, Yang L, and He D (2011) Detection of survivin expression in cervical cancer cells using molecular beacon imaging: new strategy for the diagnosis of cervical cancer. Eur J Obstet Gynecol Reprod Biol 159: 204-208. PMI: 21752529: PubMed Link

  826. Yamamoto R, Baba T, and Kumar PK (2000) Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes Cells 5: 389-396. PMI: 10886366: PubMed Link

  827. Yamana K, Ohshita Y, Fukunaga Y, Nakamura M, and Maruyama A (2007) Bis-pyrene-labeled molecular beacon: A monomer-excimer switching probe for the detection of DNA base alteration. Bioorg Med Chem. PMI: 17499510: PubMed Link

  828. Yang CJ, Cui L, Huang J, Yan L, Lin X, Wang C, Zhang WY, and Kang H (2011) Linear molecular beacons for highly sensitive bioanalysis based on cyclic Exo III enzymatic amplification. Biosens Bioelectron 27: 119-124. PMI: 21764287: PubMed Link

  829. Yang CJ, Li JJ, and Tan W (2006) Using molecular beacons for sensitive fluorescence assays of the enzymatic cleavage of nucleic acids. Methods Mol Biol 335: 71-81. PMI: 16785621: PubMed Link

  830. Yang CJ, Lin H, and Tan W (2005) Molecular assembly of superquenchers in signaling molecular interactions. J Am Chem Soc 127: 12772-12773. PMI: 16159250: PubMed Link

  831. Yang CJ, Wang L, Wu Y, Kim Y, Medley CD, Lin H, and Tan W (2007) Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons. Nucleic Acids Res 35: 4030-4041. PMI: 17557813: PubMed Link

  832. Yang CN, Hsu CY, and Chuang YC (2012) Molecular beacon-based half-adder and half-subtractor. Chem Commun (Camb) 48: 112-114. PMI: 22056975: PubMed Link

  833. Yang L, Cao Z, Lin Y, Wood WC, and Staley CA (2005) Molecular beacon imaging of tumor marker gene expression in pancreatic cancer cells. Cancer Biol Ther 4: 561-570. PMI: 15917666: PubMed Link

  834. Yang R, Jin J, Chen Y, Shao N, Kang H, Xiao Z, Tang Z, Wu Y, Zhu Z, and Tan W (2008) Carbon nanotube-quenched fluorescent oligonucleotides: probes that fluoresce upon hybridization. J Am Chem Soc 130: 8351-8358. PMI: 18528999: PubMed Link

  835. Yang R, Jin J, Long L, Wang Y, Wang H, and Tan W (2009) Reversible molecular switching of molecular beacon: controlling DNA hybridization kinetics and thermodynamics using mercury(ii) ions. Chem Commun (Camb): 322-324. PMI: 19209316: PubMed Link

  836. Yang X, Tong C, Long Y, and Liu B (2011) A rapid fluorescence assay for hSMUG1 activity based on modified molecular beacon. Mol Cell Probes 25: 219-221. PMI: 21933706: PubMed Link

  837. Yao G, Fang X, Yokota H, Yanagida T, and Tan W (2003) Monitoring molecular beacon DNA probe hybridization at the single-molecule level. Chemistry 9: 5686-5692. PMI: 14639652: PubMed Link

  838. Yao Q, Sun JG, Ma H, Zhang AM, Lin S, Zhu CH, Zhang T, and Chen ZT (2014) Monitoring microRNAs using a molecular beacon in CD133+/ CD338+ human lung adenocarcinoma-initiating A549 cells. Asian Pac J Cancer Prev 15: 161-166. PMI: 24528019: PubMed Link

  839. Yao Q, Zhang AM, Ma H, Lin S, Wang XX, Sun JG, and Chen ZT (2012) Novel molecular beacons to monitor microRNAs in non-small-cell lung cancer. Mol Cell Probes 26: 182-187. PMI: 22796123: PubMed Link

  840. Ye Q, Zhuang H, and Zhou C (2008) Detection of naphthalene by real-time immuno-PCR using molecular beacon. Mol Cell Probes. PMI: 19028563: PubMed Link

  841. Ye Q, Zhuang H, Zhou C, and Wang Q (2010) Real-time fluorescent quantitative immuno-PCR method for determination of fluoranthene in water samples with a molecular beacon. J Environ Sci (China) 22: 796-800. PMI: 20608519: PubMed Link

  842. Ye QY, Zhuang HS, and Zhou C (2009) Detection of trace anthracene in soil samples with real-time fluorescence quantitative immuno-PCR using a molecular beacon probe. Environ Toxicol Pharmacol 28: 386-391. PMI: 21784031: PubMed Link

  843. Ye T, Liu Y, Luo M, Xiang X, Ji X, Zhou G, and He Z (2014) Metal-organic framework-based molecular beacons for multiplexed DNA detection by synchronous fluorescence analysis. Analyst 139: 1721-1725. PMI: 24524118: PubMed Link

  844. Yeh HY, Yates MV, Mulchandani A, and Chen W (2010) Molecular beacon-quantum dot-Au nanoparticle hybrid nanoprobes for visualizing virus replication in living cells. Chem Commun (Camb). PMI: 20419176: PubMed Link

  845. Yi JW, Park J, Singh NJ, Lee IJ, Kim KS, and Kim BH (2011) Quencher-free molecular beacon: Enhancement of the signal-to-background ratio with graphene oxide. Bioorg Med Chem Lett 21: 704-706. PMI: 21194937: PubMed Link

  846. Yin H, Zhou Y, Zhang H, Meng X, and Ai S (2012) Electrochemical determination of microRNA-21 based on graphene, LNA integrated molecular beacon, AuNPs and biotin multifunctional bio bar codes and enzymatic assay system. Biosens Bioelectron 33: 247-253. PMI: 22317835: PubMed Link

  847. Ying L, Wallace MI, and Klenerman D (2001) Two-state model of conformational fluctuation in a DNA hairpin-loop. Chem Phys Lett 334: 145-150. PMI: PubMed Link

  848. Yoshinaga H, Nakano K, Soh N, and Imato T (2012) AFM-imaging diagnosis method for single nucleotide polymorphism using molecular beacon DNA as an intramolecular ligation template of target DNA and a viewable indicator. Anal Sci 28: 939-945. PMI: 23059988: PubMed Link

  849. Yu CX, Zhao ZY, Lv JX, and Zhu L (2013) A dual molecular beacon approach for fast detection of Mycobacterium tuberculosis. Mol Biol Rep 40: 1883-1892. PMI: 23104475: PubMed Link

  850. Zanoli LM, Licciardello M, D'Agata R, Lantano C, Calabretta A, Corradini R, Marchelli R, and Spoto G (2013) Peptide nucleic acid molecular beacons for the detection of PCR amplicons in droplet-based microfluidic devices. Anal Bioanal Chem 405: 615-624. PMI: 22212864: PubMed Link

  851. Zeng J, Liu Q, Xu H, Wang H, Wang J, and Cai R (2005) Detection of DNA with catalytic beacons based on peroxidase-oxidase oscillating reaction. Conf Proc IEEE Eng Med Biol Soc 5: 4658-4661. PMI: 17281279: PubMed Link

  852. Zeng X, Zhang X, Yang W, Jia H, and Li Y (2012) Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe. Anal Biochem 424: 8-11. PMI: 22369893: PubMed Link

  853. Zepeda A, Arias C, Flores-Jasso F, and Vaca L (2013) RNA imaging: tracking in real-time RNA transport in neurons using molecular beacons and confocal microscopy. Methods Cell Biol 113: 361-389. PMI: 23317911: PubMed Link

  854. Zhang C, Su X, Liang Y, Zhu X, Song C, and Zhao M (2011) A transformer of molecular beacon for sensitive and real-time detection of phosphatases with effective inhibition of the false positive signals. Biosens Bioelectron 28: 13-16. PMI: 21821409: PubMed Link

  855. Zhang C, Wu L, Yang J, Liu S, and Xu J (2013) A molecular logical switching beacon controlled by thiolated DNA signals. Chem Commun (Camb) 49: 11308-11310. PMI: 24158378: PubMed Link

  856. Zhang CY, Chao SY, and Wang TH (2005) Comparative quantification of nucleic acids using single-molecule detection and molecular beacons. Analyst 130: 483-488. PMI: 15776157: PubMed Link

  857. Zhang DW, Zhao MM, He HQ, and Guo SX (2013) Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon. Anal Biochem 440: 120-122. PMI: 23747532: PubMed Link

  858. Zhang K, Wang K, Xie M, Zhu X, Xu L, Yang R, Huang B, and Zhu X (2014) DNA-templated silver nanoclusters based label-free fluorescent molecular beacon for the detection of adenosine deaminase. Biosens Bioelectron 52: 124-128. PMI: 24035856: PubMed Link

  859. Zhang L, Zhu J, Li T, and Wang E (2011) Bifunctional colorimetric oligonucleotide probe based on a G-quadruplex DNAzyme molecular beacon. Anal Chem 83: 8871-8876. PMI: 22017597: PubMed Link

  860. Zhang M, Guo SM, Li YR, Zuo P, and Ye BC (2012) A label-free fluorescent molecular beacon based on DNA-templated silver nanoclusters for detection of adenosine and adenosine deaminase. Chem Commun (Camb) 48: 5488-5490. PMI: 22543727: PubMed Link

  861. Zhang M, Le HN, Jiang XQ, and Ye BC (2013) "Molecular beacon"-directed fluorescence of Hoechst dyes for visual detection of Hg(II) and biothiols and its application for a logic gate. Chem Commun (Camb) 49: 2133-2135. PMI: 23389052: PubMed Link

  862. Zhang M, Le HN, Wang P, and Ye BC (2012) A versatile molecular beacon-like probe for multiplexed detection based on fluorescence polarization and its application for a resettable logic gate. Chem Commun (Camb) 48: 10004-10006. PMI: 22936344: PubMed Link

  863. Zhang M, Le HN, and Ye BC (2013) Graphene oxide-based fluorescent "on/off" switch for visual bioassay using "molecular beacon"-hosted Hoechst dyes. ACS Appl Mater Interfaces 5: 8278-8282. PMI: 23968374: PubMed Link

  864. Zhang P, Beck T, and Tan W (2001) Design of a molecular beacon DNA probe with two fluorophores. Angew Chem Int Ed Engl 40: 402-405. PMI: 11180338: PubMed Link

  865. Zhang S, Yan Y, and Bi S (2009) Design of molecular beacons as signaling probes for adenosine triphosphate detection in cancer cells based on chemiluminescence resonance energy transfer. Anal Chem. PMI: 19788280: PubMed Link

  866. Zhang W, Cohenford M, Lentrichia B, Isenberg HD, Simson E, Li H, Yi J, and Zhang DY (2002) Detection of Chlamydia trachomatis by isothermal ramification amplification method: a feasibility study. J Clin Microbiol 40: 128-132. PMI: 11773105: PubMed Link

  867. Zhang XB, Wang Z, Xing H, Xiang Y, and Lu Y (2010) Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity. Anal Chem 82: 5005-5011. PMI: 20481627: PubMed Link

  868. Zhang Z, Guo L, Tang J, Guo X, and Xie J (2009) An aptameric molecular beacon-based "Signal-on" approach for rapid determination of rHuEPO-alpha. Talanta 80: 985-990. PMI: 19836583: PubMed Link

  869. Zhao J, He D, He H, Li L, Zhang LL, and Wang XY (2007) Primary application study in early diagnosis of bladder cancer by survivin molecular beacons. Urology 70: 60-64. PMI: 17656209: PubMed Link

  870. Zhao J, Wang ZQ, Wang XY, Yang XJ, and He D (2010) Preliminary Study of Diagnostic Utility of Molecular Beacons in Bladder Cancer. Urology. PMI: 20579701: PubMed Link

  871. Zheleznaya LA, Kopein DS, Rogulin EA, Gubanov SI, and Matvienko NI (2006) Significant enhancement of fluorescence on hybridization of a molecular beacon to a target DNA in the presence of a site-specific DNA nickase. Anal Biochem 348: 123-126. PMI: 16298321: PubMed Link

  872. Zheleznaya LA, Perevyazova TA, Zheleznyakova EN, and Matvienko NI (2002) Some properties of site-specific nickase BspD6I and the possibility of its use in hybridization analysis of DNA. Biochemistry (Mosc) 67: 498-502. PMI: 11996665: PubMed Link

  873. Zhen SJ, Chen LQ, Xiao SJ, Li YF, Hu PP, Zhan L, Peng L, Song EQ, and Huang CZ (2010) Carbon nanotubes as a low background signal platform for a molecular aptamer beacon on the basis of long-range resonance energy transfer. Anal Chem 82: 8432-8437. PMI: 20853851: PubMed Link

  874. Zheng G, Chen J, Stefflova K, Jarvi M, Li H, and Wilson BC (2007) Photodynamic molecular beacon as an activatable photosensitizer based on protease-controlled singlet oxygen quenching and activation. Proc Natl Acad Sci U S A 104: 8989-8994. PMI: 17502620: PubMed Link

  875. Zheng Z, Han J, Pang W, and Hu J (2013) G-quadruplex DNAzyme molecular beacon for amplified colorimetric biosensing of Pseudostellaria heterophylla. Sensors (Basel) 13: 1064-1075. PMI: 23325167: PubMed Link

  876. Zhou H, Xie SJ, Li JS, Wu ZS, and Shen GL (2012) Intermolecular G-quadruplex-based universal quencher free molecular beacon. Chem Commun (Camb) 48: 10760-10762. PMI: 23011465: PubMed Link

  877. Zhou J, Lu Q, Tong Y, Wei W, and Liu S (2012) Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide. Talanta 99: 625-630. PMI: 22967603: PubMed Link

  878. Zhou L, Wang Y, and Wittwer CT (2011) Rare allele enrichment and detection by allele-specific PCR, competitive probe blocking, and melting analysis. BioTechniques 50: 311-315. PMI: PubMed Link

  879. Zhou Z, Huang H, Chen Y, Liu F, Huang CZ, and Li N (2014) A distance-dependent metal-enhanced fluorescence sensing platform based on molecular beacon design. Biosens Bioelectron 52: 367-373. PMI: 24080216: PubMed Link

  880. Zhu J, Li T, Zhang L, Dong S, and Wang E (2011) G-quadruplex DNAzyme based molecular catalytic beacon for label-free colorimetric logic gates. Biomaterials 32: 7318-7324. PMI: 21784509: PubMed Link

  881. Zhu J, Zhang L, Zhou Z, Dong S, and Wang E (2014) Molecular aptamer beacon tuned DNA strand displacement to transform small molecules into DNA logic outputs. Chem Commun (Camb) 50: 3321-3323. PMI: 24531570: PubMed Link

  882. Zoraida BS, Arock M, Ronald BS, and Ponalagusamy R (2009) A novel generalized design methodology and realization of Boolean operations using DNA. Biosystems. PMI: 19505531: PubMed Link

  883. Zou Z, Qing Z, He X, Wang K, He D, Shi H, Yang X, Qing T, and Yang X (2014) Ligation-rolling circle amplification combined with gamma-cyclodextrin mediated stemless molecular beacon for sensitive and specific genotyping of single-nucleotide polymorphism. Talanta 125: 306-312. PMI: 24840448: PubMed Link

  884. Zuo X, Yang X, Wang K, Tan W, and Wen J (2007) A novel sandwich assay with molecular beacon as report probe for nucleic acids detection on one-dimensional microfluidic beads array. Anal Chim Acta 587: 9-13. PMI: 17386747: PubMed Link


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