Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids

Chemistry - A European Journal

Volumn 17, Issue 46, 2011, Pages 13052-13058

  Nguyen, Camha ^a   Grimes, Jeffrey ^a   Gerasimova, Yulia V ^a   Kolpashchikov, Dmitry M ^a  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

Author keywords

DNA; fluorescent probe; hybridization; real time assay; RNA; sensors

Indexed keywords

AMBIENT TEMPERATURES; ANALYTES; BASE PAIRS; DIRECT ANALYSIS; DNA HAIRPIN; DNA MICRO-ARRAY; DNA STRANDS; FLUORESCENT PROBES; GENOTYPING; HAIRPIN STRUCTURES; HIGH AFFINITY; HYBRIDIZATION; HYBRIDIZATION PROBE; IN-VIVO; LIMIT OF DETECTION; LOOP REGIONS; MOLECULAR BEACON; NANOMOLAR RANGE; NUCLEIC ACID ANALYSIS; REAL TIME; REAL TIME ANALYSIS; REAL-TIME ASSAY; RNA SEQUENCES; ROOM TEMPERATURE; SECONDARY STRUCTURES; SINGLE-NUCLEOTIDE POLYMORPHISMS; SINGLE-STRANDED DNA; STABLE COMPLEXES;

BIOASSAY; BIOCHIPS; BIOMOLECULES; DNA; DNA SEQUENCES; OLIGONUCLEOTIDES; RNA; TEMPERATURE;

PROBES;

DNA; FLUORESCENT DYE; RNA;

ARTICLE; CHEMISTRY; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBE; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA; FLUORESCENT DYES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA;

EID: 80555144145     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.201101987     Document Type: Article

References (63)

1. H. Zhang, P. Parameswaran, J. Badalamenti, B. E. Rittmann, R. Krajmalnik-Brown, Methods Mol. Biol. 2011, 733, 107-128
2. C. J. Smith, A. M. Osborn, FEMS Microbiol. Ecol. 2009, 67, 6-20
3. Y. Hou, Q. Luo, C. Chen, M. Zhou, Pest Manag. Sci. 2011, 67, 1124- 1128
4. M. Mortarino, I. Garagiola, L. A. Lotta, S. M. Siboni, A. E. Semprini, F. Peyvandi, Haemophilia, DOI
5. J. Tong, C. Liu, P. Summanen, H. Xu, S. M. Finegold, Anaerobe 2011, 17, 64-68.
6. J. Song, W. J. Mooi, V. Petronic-Rosic, C. R. Shea, T. Stricker, T. Krausz, Adv. Supramol. Chem. Adv. Anat. Pathol. 2011, 18, 229-234
7. S. Kumar, S. S. Dagar, A. K. Mohanty, S. K. Sirohi, M. Puniya, R. C. Kuhad, K. P. Sangu, G. W. Griffith, A. K. Puniya, Naturwissenschaften 2011, 98, 457-472
8. J. R. Sotelo-Silveira, A. Calliari, A. Kun, V. Elizondo, L. Canclini, J. R. Sotelo, Methods Mol. Biol. 2011, 714, 125-138
9. J. Uniacke, D. Colõn-Ramos, W. Zerges, Methods Mol. Biol. 2011, 714, 15-29.
10. A. Huyghe, P. Francois, J. Schrenzel, Infect. Genet. Evol. 2009, 9, 987-995
11. K. B. Barken, J. A. Haagensen, T. Tolker-Nielsen, Clin. Chim. Acta 2007, 384, 1-11
12. E. Hong-Geller, S. N. Micheva-Viteva, Curr. Drug Discov. Technol. 2010, 7, 86-94
13. C. A. Barker, M. A. Farha, E. D. Brown, Chem. Biol. 2010, 17, 624-632.
14. M. Valencia-Burton, R. M. McCullough, C. R. Cantor, N. E. Broude, Nat. Methods 2007, 4, 421-427
15. P. J. Santangelo, A. W. Lifland, P. Curt, Y. Sasaki, G. J. Bassell, M. E. Lindquist, J. E. Crowe Jr., Nat. Methods 2009, 6, 347-349
16. H. Y. Park, A. R. Buxbaum, R. H. Singer, Methods Enzymol. 2010, 472, 387-406.
17. D. P. Chandler, G. J. Newton, J. A. Small, D. S. Daly, Appl. Environ. Microbiol. 2003, 69, 2950-2958
18. S. Lane, J. Evermann, F. Loge, D. R. Call, Biosens. Bioelectron. 2004, 20, 728-735.
19. J. C. Tan, J. J. Patel, A. Tan, J. C. Blain, T. J. Albert, N. F. Lobo, M. T. Ferdig, Genomics 2009, 93, 543-550
20. C. Chen, W. Wang, Z. Wang, F. Wei, X. S. Zhao, Nucleic Acids Res. 2007, 35, 2875-2884.
21. S. A. Kushon, J. P. Jordan, J. L. Seifert, H. Nielsen, P. E. Nielsen, B. A. Armitage, J. Am. Chem. Soc. 2001, 123, 10805-10813
22. B. A. Armitage, Drug Discovery Today 2003, 8, 222-228
23. Y. Gao, L. K. Wolf, R. M. Georgiadis, Nucleic Acids Res. 2006, 34, 3370-3377
24. M. M. Sekar, W. Bloch, P. M. St John, Nucleic Acids Res. 2005, 33, 366-375.
25. G. Lahoud, V. Timoshchuk, A. Lebedev, M. de Vega, M. Salas, K. Arar, Y. M. Hou, H. Gamper, Nucleic Acids Res. 2008, 36, 3409-3419.
26. E. Kierzek, A. Ciesielska, K. Pasternak, D. H. Mathews, D. H. Turner, R. Kierzek, Nucleic Acids Res. 2005, 33, 5082-5093
27. K. Kubota, A. Ohashi, H. Imachi, H. Harada, Appl. Environ. Microbiol. 2006, 72, 5311-5317
28. H. Kuhn, V. V. Demidov, J. M. Coull, M. J. Fiandaca, B. D. Gildea, M. D. Frank-Kamenetskii, J. Am. Chem. Soc. 2002, 124, 1097-1103
29. I. V. Smolina, V. V. Demidov, V. A. Soldatenkov, S. G. Chasovskikh, M. D. Frank-Kamenetskii, Nucleic Acids Res. 2005, 33, e 146
30. I. V. Smolina, H. Kuhn, C. Lee, M. D. Frank-Kamenetskii, Bioorg. Med. Chem. 2008, 16, 84-93
31. S. A. Wilks, C. W. Keevil, Appl. Environ. Microbiol. 2006, 72, 5453-5462.
32. V. V. Demidov, M. D. Frank-Kamenetskii, Trends Biochem. Sci. 2004, 29, 62-71.
33. J. Grimes, Y. V. Gerasimova, D. M. Kolpashchikov, Angew. Chem. 2010, 122, 9134-9137
34. Angew. Chem. Int. Ed. 2010, 49, 8950-8953.
35. S. A. Marras, S. Tyagi, F. R. Kramer, Clin. Chim. Acta 2006, 363, 48-60
36. K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, Z. Cao, J. Li, P. Colon, H. Lin, W. Tan, Angew. Chem. 2009, 121, 870-885
37. Angew. Chem. Int. Ed. 2009, 48, 856-870
38. Y. Li, X. Zhou, D. Ye, Biochem. Biophys. Res. Commun. 2008, 373, 457-461
39. N. Venkatesan, Y. J. Seo, B. H. Kim, Chem. Soc. Rev. 2008, 37, 648-663.
40. D. M. Kolpashchikov, J. Am. Chem. Soc. 2006, 128, 10625-10628
41. Y. V. Gerasimova, A. Hayson, J. Ballantyne, D. M. Kolpashchikov, ChemBioChem 2010, 11, 1762-1768
42. Y. V. Gerasimova, S. Peck, D. M. Kolpashchikov, Chem. Commun. 2010, 46, 8761-8763.
43. M. E. Churchill, T. D. Tullius, N. R. Kallenbach, N. C. Seeman, Proc. Natl. Acad. Sci. USA 1988, 85, 4653-4656
44. D. M. J. Lilley, Rev. Biophys. 2000, 33, 109-159.
45. G. Bao, W. J. Rhee, A. Tsourkas, Annu. Rev. Biomed. Eng. 2009, 11, 25-47
46. S. Tyagi, Nat. Methods 2009, 6, 331-338.
47. K. A. Browne, J. Am. Chem. Soc. 2005, 127, 1989-1994
48. Y. Kim, C. J. Yang, W. Tan, Nucleic Acids Res. 2007, 35, 7279-7287.
49. D. M. Kolpashchikov, Chem. Rev. 2010, 110, 4709-4723
50. R. A. Cardullo, S. Agrawal, C. Flores, P. C. Zamecnik, D. E. Wolf, Proc. Natl. Acad. Sci. USA 1988, 85, 8790-8794
51. J. L. Mergny, A. S. Boutorine, T. Garestier, F. Belloc, M. Rougée, N. V. Bulychev, A. A. Koshkin, J. Bourson, A. V. Lebedev, B. Valeur, N. T. Thuong, C. Helene, Nucleic Acids Res. 1994, 22, 920-928
52. A. Oser, G. Valet, Angew. Chem. 1990, 102, 1197-1200
53. Angew. Chem. Int. Ed. Engl. 1990, 29, 1167-1169
54. K. Ebata, M. Masuko, H. Ohtani, M. Kashiwasake-Jibu, Photochem. Photobiol. 1995, 62, 836-839
55. A. P. Silverman, E. T. Kool, Chem. Rev. 2006, 106, 3775-3789
56. D. M. Kolpashchikov, J. Am. Chem. Soc. 2005, 127, 12442-12443
57. D. M. Kolpashchikov, ChemBioChem 2007, 8, 2039-2042
58. D. M. Kolpashchikov, J. Am. Chem. Soc. 2008, 130, 2934-2935
59. Y. V. Gerasimova, E. Cornett, D. M. Kolpashchikov, ChemBioChem 2010, 11, 811-817
60. E. Mokany, S. M. Bone, P. E. Young, T. B. Doan, A. V. Todd, J. Am. Chem. Soc. 2010, 132, 1051-1059
61. Y. Taniguchi, A. Nitta, S. M. Park, A. Kohara, T. Uzu, S. Sasaki, Bioorg. Med. Chem. 2010, 18, 8614-8617
62. A. K. Darius, N. J. Ling, U. Mahesh, Mol. Biosyst. 2010, 6, 792-794
63. J. T. Ren, H. X. Qin, J. H. Wang, N. W. Luedtke, E. Wang, J. Wang, Anal. Bioanal. Chem. 2011, 399, 2763- 2770.