Publications on Molecular Beacons



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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.

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

  3. 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.

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

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

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

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

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




    II.   Review papers on molecular beacons

  9. 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.

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

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

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

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

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

  15. 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.

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

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

  18. Marras SAE (2006) Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes. Methods Mol Biol 335, 3-16.

  19. 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.

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

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

  22. 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.

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

  24. 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.

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

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

  27. Yang CJ, Medley CD, and Tan W (2005) Monitoring nucleic acids using molecular beacons. Curr Pharm Biotechnol 6, 445-452.
    III.   Papers on molecular beacons used for detection of DNA and RNA in living cells

  28. 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.

  29. Chen AK, Behlke MA, and Tsourkas A (2007) Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells. Nucleic Acids Res 35, e105.

  30. 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.

  31. 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.

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

  33. 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.

  34. 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.

  35. 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.

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

  37. 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

  38. 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.

  39. 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.

  40. 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.

  41. Santangelo PJ, 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.

  42. 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.

  43. Tyagi S and Alsmadi O (2004) Imaging native Beta-actin mRNA in motile fibroblasts. Biophys J 78, 4153-4163.

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

  45. 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.

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




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

  47. 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. Thromb Haemost 88, 195-199.

  48. 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.

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

  50. 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.

  51. 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.

  52. 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.

  53. 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.

  54. 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.

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

  56. 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.

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

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

  59. 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.

  60. 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.

  61. 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.

  62. 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.

  63. 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.

  64. 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.

  65. 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.

  66. 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.

  67. Täpp 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.

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




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

  69. 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.

  70. 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.

  71. Alsmadi OA, Al-Rubeaan K, Wakil SM, Imtiaz F, Mohamed G, Al-Saud H, Al-Saud NA, Aldaghri N, Mohammad S, and Meyer BF (2008) Genetic study of saudi diabetes (GSSD): significant association of the KCNJ11 E23K polymorphism with type 2 diabetes. Diabetes Metab Res Rev 24, 137-140.

  72. 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.

  73. 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.

  74. 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.

  75. 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.

  76. 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.

  77. 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.

  78. 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.

  79. 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. Eur J Plant Pathol 110, 689-702.

  80. 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.

  81. 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.

  82. 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.

  83. 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.

  84. 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.

  85. 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.

  86. 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.

  87. 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.

  88. 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.

  89. 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.

  90. 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.

  91. 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.

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

  93. 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.

  94. 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

  95. 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.

  96. 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

  97. 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.

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

  99. Gullsby K, Storm M, and Bondeson K (2008) Simultaneous detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae using molecular beacons in a duplex real-time PCR. J Clin Microbiol 46, 727-731.

  100. 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.

  101. 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.

  102. 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.

  103. 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.

  104. Henry KM, Jiang J, Rozmajzl PJ, Azad AF, Macaluso KR, and Richards AL (2007) 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.

  105. 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.

  106. 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.

  107. 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.

  108. 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.

  109. 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.

  110. 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.

  111. 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.

  112. 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.

  113. 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. Clin Diagn Lab Immunol 10, 1123-1128.

  114. 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.

  115. 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.

  116. 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.

  117. 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.

  118. 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.

  119. 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.

  120. 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.

  121. 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.

  122. 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.

  123. 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.

  124. 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.

  125. 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.

  126. 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.

  127. 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.

  128. 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.

  129. 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.

  130. Morandi L, Ferrari D, Lombardo C, Pession A, and Tallini G (2007) Monitoring HCV RNA viral load by locked nucleic acid molecular beacons real time PCR. J Virol Methods 140, 148-154.

  131. 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.

  132. 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.

  133. 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.

  134. 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.

  135. 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.

  136. 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.

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

  138. 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.

  139. 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.

  140. 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.

  141. 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.

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

  143. 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.

  144. 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.

  145. Poddar SK (1999) Detection of adenovirus using PCR and molecular beacon. J Virol Methods 82, 19-26.

  146. 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.

  147. 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.

  148. 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. Mol Cell Probes 17, 91-98.

  149. 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.

  150. 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.

  151. Rousseau S and Brunel D (2003) Use of molecular beacon for the detection of fertile male plants in batches of sterile male rapeseed. Mol Breed 12, 91-96.

  152. 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.

  153. 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.

  154. 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.

  155. Santi-Rocca J, Weber C, Guigon G, Sismeiro O, Coppee JY, and Guillen N (2008) The lysine-and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis. Cell Microbiol 10, 202-217.

  156. 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.

  157. 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.

  158. 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.

  159. 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.

  160. 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.

  161. 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.

  162. 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.

  163. 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.

  164. 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.

  165. 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.

  166. 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.

  167. 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

  168. 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.

  169. 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.

  170. 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.

  171. 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.

  172. 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.

  173. 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. Lett Appl Microbiol 37, 386-391.

  174. 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.

  175. 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.

  176. 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.

  177. 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.

  178. 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.

  179. 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.

  180. 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.

  181. 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.

  182. 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.

  183. 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.

  184. 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

  185. 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.

  186. 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.

  187. 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.

  188. 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.

  189. 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.




    VI.   Papers on molecular beacons used in NASBA

  190. 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.

  191. 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.

  192. 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.

  193. 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.

  194. 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.

  195. 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.

  196. 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. Appl Environ Microbiol 70, 4727-4732.

  197. 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.

  198. 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 117, 85-90.

  199. 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.

  200. 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.

  201. 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.

  202. 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.

  203. 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.

  204. 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.

  205. 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 55, 510-517.

  206. 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.

  207. 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.

  208. 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.

  209. Ginocchio C C, 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

  210. 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. Eur J Plant Pathol 108, 401-407.

  211. 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.

  212. 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.

  213. 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.

  214. 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.

  215. 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.

  216. 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.

  217. 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.

  218. 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.

  219. Lam HY, Chen JH, Wong KH, Chan K, Li P, Lee MP, Tsang DN, Yuen KY, and Yam WC (2007) 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.

  220. 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.

  221. 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.

  222. 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.

  223. 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.

  224. 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.

  225. 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.

  226. 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.

  227. 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.

  228. 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.

  229. 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.

  230. 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.

  231. 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.

  232. 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.

  233. 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.

  234. 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.

  235. 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.

  236. 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.

  237. 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.

  238. 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.

  239. 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.

  240. 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.

  241. 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.

  242. 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.

  243. 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.

  244. 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.

  245. 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.

  246. 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.

  247. 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.

  248. 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.

  249. 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.

  250. 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. Eur J Plant Pathol 110, 25-33.

  251. Vaskova D, Spak J, Klerks MM, Schoen CD, Thompson JR, and Jelkmann W (2004) Real-time NASBA for detection of strawberry vein banding virus. Eur J Plant Pathol 110, 213-221.

  252. 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.

  253. 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.

  254. 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.

  255. 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.




    VII.   Papers on molecular beacons used on arrays

  256. Beaucage SL (2001) Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications. Curr Med Chem 8, 1213-1244.

  257. 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.

  258. 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.

  259. 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.

  260. 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.

  261. 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.

  262. 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.

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

  264. Fang XH, Liu XJ, Schuster S, and Tan WH (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. J Am Chem Soc 121, 2921-2922.

  265. 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.

  266. 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.

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

  268. 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.

  269. Palecek E (2004) Surface-attached molecular beacons light the way for DNA sequencing. Trends Biotechnol 22, 55-58.

  270. 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.

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

  272. 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.

  273. Yao G and Tan W (2004) Molecular beacon-based array for sensitive DNA analysis. Anal Biochem 331, 216-223.

  274. 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, 3476-3483.




    VIII.   Papers on general application of molecular beacons

  275. 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.

  276. 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.

  277. 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.

  278. 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.

  279. Bang GS, Cho S, and Kim BG (2005) A novel electrochemical detection method for aptamer biosensors. Biosens Bioelectron 21, 863-870.

  280. 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.

  281. 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.

  282. 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.

  283. 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. Proc Natl Acad Sci USA 97, 13537-13542.

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

  285. 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.

  286. Browne KA (2005) Sequence-specific, self-reporting hairpin inversion probes. J Am Chem Soc 127, 1989-1994.

  287. Brunner J and Kraemer R (2004) Copper(II)-quenched oligonucleotide probes for fluorescent DNA sensing. J Am Chem Soc 126, 13626-13627.

  288. 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.

  289. Cady NC, Strickland AD, and Batt CA (2007) Optimized linkage and quenching strategies for quantum dot molecular beacons. Mol Cell Probes 21, 116-124.

  290. Cazzato A, Capobianco ML, Zambianchi M, Favaretto L, Bettini C, and Barbarella G (2007) Oligothiophene molecular beacons. Bioconjug Chem 18, 318-322.

  291. Chang E, Zhu MQ, and Drezek R (2007) Novel siRNA-based molecular beacons for dual imaging and therapy. Biotechnol J 2, 2-5.

  292. 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.

  293. 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.

  294. 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.

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

  296. 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.

  297. Deerinck TJ (2008) The application of fluorescent quantum dots to confocal, multiphoton, and electron microscopic imaging. Toxicol Pathol 36, 112-116.

  298. 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.

  299. 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.

  300. 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.

  301. 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.

  302. 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.

  303. 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.

  304. 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.

  305. 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.

  306. Frauendorf C and Jaschke A (2001) Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem 9, 2521-2524.

  307. 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.

  308. 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.

  309. 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.

  310. Ghosn B, Haselton FR, Gee KR, and Monroe WT (2005) Control of DNA hybridization with photocleavable adducts. Photochem Photobiol 81, 953-959.

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

  312. 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.

  313. 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.

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

  315. Hamaguchi N, Ellington A, and Stanton M (2001) Aptamer beacons for the direct detection of proteins. Anal Biochem 294, 126-131.

  316. 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.

  317. 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.

  318. 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.

  319. Hopkins JF and Woodson SA (2005) Molecular beacons as probes of RNA unfolding under native conditions. Nucleic Acids Res 33, 5763-5770.

  320. 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.

  321. 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 371,162-166.

  322. 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.

  323. 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.

  324. 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 USA 103, 2564-2569.

  325. 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.

  326. 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.

  327. 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.

  328. 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.

  329. 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.

  330. 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.

  331. 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.

  332. Joshi HS and Tor Y (2001) Metal-containing DNA hairpins as hybridization probes. Chemical Comm 6, 549-550.

  333. 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.

  334. 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.

  335. Kehlenbach RH (2003) In vitro analysis of nuclear mRNA export using molecular beacons for target detection. Nucleic Acids Res 31, e64.

  336. 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.

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

  338. 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.

  339. Kim Y, Yang CJ, and Tan W (2008) Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem. Nucleic Acids Res 35, 7279-7287.

  340. 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.

  341. 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.

  342. 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.

  343. 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.

  344. Krusinski T, Wietrzych M, Grad I, Ozyhar A, and Dobryszycki P (2008) 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 18, 1-10.

  345. 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.

  346. 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.

  347. 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.

  348. 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.

  349. Lagally ET, Lee SH, and Soh HT (2005) Integrated microsystem for dielectrophoretic cell concentration and genetic detection. Lab Chip 5, 1053-1058.

  350. 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.

  351. 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.

  352. 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.

  353. 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.

  354. Levy M, Cater SF, and Ellington AD (2005) Quantum-dot aptamer beacons for the detection of proteins. Chembiochem 6, 2163-2166.

  355. 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.

  356. 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.

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

  358. Li JJ and Tan W (2003) A real-time assay for DNA sticky-end pairing using molecular beacons. Anal Biochem 312, 251-254.

  359. Li JJ, Chu Y, Lee BY, and Xie XS (2008) Enzymatic signal amplification of molecular beacons for sensitive DNA detection. Nucleic Acids Res

  360. 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.

  361. 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.

  362. 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.