molecular beacons


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. Marras SAE, Tyagi S, Antson D, and Kramer FR (2019) Color-coded molecular beacons for multiplex PCR screening assays. PLoS One 14: e0213906

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

  7. 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

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

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

  10. 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

  11. 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

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

  13. 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

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

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

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

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

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

  19. 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

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

  21. 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

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

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

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

  25. 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

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

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

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

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

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

  31. 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

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

  33. 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

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

  35. 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

  36. 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

  37. 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

  38. 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

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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

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

  54. 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

  55. 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

  56. 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

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

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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

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

  66. 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

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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

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

  74. 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

  75. 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

  76. 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

  77. 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.

  78. 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

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

  80. 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

  81. 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

  82. 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

  83. 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

  84. 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

  85. 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

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

  87. 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

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

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

  90. 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

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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.

  113. 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

  114. 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

  115. 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

  116. 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

  117. 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

  118. 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

  119. 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

  120. 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

  121. 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

  122. 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

  123. 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

  124. 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

  125. 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

  126. 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

  127. 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

  128. 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.

  129. 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

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  131. 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

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  243. 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

  244. 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.

  245. 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

  246. 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

  247. 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

  248. 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

  249. 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

  250. 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

  251. 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

  252. 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

  253. 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

  254. 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

  255. 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

  256. 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

  257. 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

  258. 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

  259. 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

  260. 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

  261. 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

  262. 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

  263. 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

  264. 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

  265. 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

  266. 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

  267. 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

  268. 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

  269. 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

  270. 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

  271. 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

  272. 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

  273. 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

  274. 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

  275. 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

  276. 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

  277. 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

  278. 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

  279. 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

  280. 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.

  281. 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

  282. 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

  283. 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

  284. 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

  285. 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

  286. 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

  287. 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

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

  289. 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

  290. 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

  291. 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

  292. 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.

  293. 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

  294. 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

  295. 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

  296. 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

  297. 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

  298. 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

  299. 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

  300. 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

  301. 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

  302. 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

  303. 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

  304. 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

  305. 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

  306. 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

  307. 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

  308. 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

  309. 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

  310. 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

  311. 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

  312. 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

  313. 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

  314. 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

  315. 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

  316. 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

  317. 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

  318. 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

  319. 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

  320. 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

  321. 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

  322. 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

  323. 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

  324. 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.

  325. 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

  326. 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

  327. 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

  328. 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

  329. 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

  330. 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

  331. 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

  332. 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

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

  334. 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

  335. 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.

  336. 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

  337. 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

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

  339. 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

  340. 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

  341. 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

  342. 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.

  343. 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

  344. 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

  345. 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

  346. 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

  347. 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

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

  349. 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

  350. 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

  351. 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

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

  353. 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

  354. 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

  355. 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

  356. 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

  357. 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

  358. 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

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Recent Publications from our group

Marras SAE, Bushkin Y, and Tyagi S (2019) High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules. Proceedings of the National Academy of Sciences USA, 128, 13921-13926

Marras SAE, Tyagi S, Antson D, and Kramer FR (2019) Color-coded molecular beacons for multiplex PCR screening assays. PLoS One 14: e0213906

Vargas DY, Marras SAE, Tyagi S, and Kramer FR (2018) Suppression of Wild-Type Amplification by Selectivity Enhancing Agents in PCR Assays That Utilize SuperSelective Primers for the Detection of Rare Somatic Mutations. The Journal of Molecular Diagnostics, 20, 415-427