Nucleic acid detection using G-quadruplex amplification methodologies

Methods

Volumn 64, Issue 3, 2013, Pages 185-198

  Roembke, Benjamin T ^a   Nakayama, Shizuka ^a   Sintim, Herman O ^a  

^a UNIVERSITY OF MARYLAND   (United States)

Author keywords

Amplification; Diagnostics; Fluorescence; G quadruplex; G quadruplex hemin conjugate; Gene detection; Peroxidase; Split G quadruplex

Indexed keywords

ENDONUCLEASE; EXONUCLEASE; GUANINE QUADRUPLEX; NUCLEIC ACID; TELOMERASE;

ARTICLE; CHEMOLUMINESCENCE; COLORIMETRY; CONJUGATE; ELECTROCHEMICAL ANALYSIS; FLUORESCENCE; GENE AMPLIFICATION; MOLECULAR BEACON; PRIORITY JOURNAL;

AMPLIFICATION; DIAGNOSTICS; FLUORESCENCE; G-QUADRUPLEX; G-QUADRUPLEX-HEMIN CONJUGATE; GENE DETECTION; PEROXIDASE; SPLIT G-QUADRUPLEX;

BASE SEQUENCE; BIOSENSING TECHNIQUES; ELECTROCHEMICAL TECHNIQUES; FLUORESCENT DYES; G-QUADRUPLEXES; HEMIN; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACIDS; POLYDEOXYRIBONUCLEOTIDES;

EID: 84888305113     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.10.003     Document Type: Article

References (120)

1. Ford D., Easton D.F., Stratton M., Narod S., Goldgar D., Devilee P., Bishop D.T., Weber B., Lenoir G., Chang-Claude J., Sobol H., Teare M.D., Struewing J., Arason A., Scherneck S., Peto J., Rebbeck T.R., Tonin P., Neuhausen S., Barkardottir R., Eyfjord J., Lynch H., Ponder B.A.J., Gayther S.A., Birch J.M., Lindblom A., Stoppa-Lyonnet D., Bignon Y., Borg A., Hamann U., Haites N., Scott R.J., Maugard C.M., Vasen H., Am C. J. Hum. Genet. 1998, 62:676-689.
2. Zhao X.J., Tapec-Dytioco R., Tan W.H. J. Am. Chem. Soc. 2003, 125:11474-11475.
3. Nam J.M., Stoeva S.I., Mirkin C.A. J. Am. Chem. Soc. 2004, 126:5932-5933.
4. Lanciotti R.S., Kerst A.J., Nasci R.S., Godsey M.S., Mitchell C.J., Savage H.M., Komar N., Panella N.A., Allen B.C., Volpe K.E., Davis B.S., Roehrig J.T. J. Clin. Microbiol. 2000, 38:4066-4071.
5. Erdem A., Kerman K., Meric B., Akarca U.S., Ozsoz M. Anal. Chim. Acta 2000, 422:139-149.
6. Cai H., Wang Y.Q., He P.G., Fang Y.H. Anal. Chim. Acta 2002, 469:165-172.
7. Authier L., Grossiord C., Brossier P., Limoges B. Anal. Chem. 2001, 73:4450-4456.
8. Leary J.J., Brigati D.J., Ward D.C. Proc. Natl. Acad. Sci. USA 1983, 80:4045-4049.
9. Alfonta L., Singh A.K., Willner I. Anal. Chem. 2001, 73:91-102.
10. Burns J., Graham A.K., Frank C., Fleming K.A., Evans M.F., McGee J.O. J. Clin. Pathol. 1987, 40:858-864.
11. Kemp D.J., Smith D.B., Foote S.J., Samaras N., Peterson M.G. Proc. Natl. Acad. Sci. USA 1989, 86:2423-2427.
12. Xiang Y., Lu Y. Anal. Chem. 2012, 84:1975-1980.
13. Davis J.T. Angew. Chem. Int. Ed. Engl. 2004, 43:668-698.
14. Ren J.T., Qin H.X., Wang J.H., Luedtke N.W., Wang E.K., Wang J. Anal. Bioanal. Chem. 2011, 399:2763-2770.
15. Paramasivan S., Bolton P.H. Nucleic Acids Res. 2008, 36:e106.
16. Larsen A.F., Nielsen M.C., Ulven T. Chem. Eur. J. 2012, 18:10892-10902.
17. Alzeer J., Luedtke N.W. Biochemistry 2010, 49:4339-4348.
18. Sen D., Gilbert W. Nature 1988, 334:364-366.
19. Travascio P., Li Y.F., Sen D. Chem. Biol. 1998, 5:505-517.
20. Allentoft M.E., Collins M., Harker D., Haile J., Oskam C.L., Hale M.L., Campos P.F., Samaniego J.A., Gilbert M.T.P., Willerslev E., Zhang G., Scofield R.P., Holdaway R.N., Bunce M. Proc. Biol. Sci. 2012, 279:4724-4733.
21. Kolpashchikov D.M. J. Am. Chem. Soc. 2008, 130:2934-2935.
22. Xiao Y., Pavlov V., Gill R., Bourenko T., Willner I. ChemBioChem 2004, 5:374-379.
23. Li T., Dong S., Wang E. Chem. Commun. 2007, 41:4209-4211.
24. Nakayama S., Sintim H.O. J. Am. Chem. Soc. 2009, 131:10320-10333.
25. He H.Z., Chan D.S.H., Leung C.H., Ma D.L. Chem. Commun. 2012, 48:9462-9464.
26. Darius A.K.L., Ling N.J., Mahesh U. Mol. BioSyst. 2010, 6:792-794.
27. Deng M., Zhang D., Zhou Y., Zhou X. J. Am. Chem. Soc. 2008, 130:13095-13102.
28. Deng M., Feng S., Luo F., Wang S., Sun X., Zhou X., Zhang X.-L. J. Clin. Microbiol. 2012, 50:3443-3450.
29. Xiao Y., Pavlov V., Niazov T., Dishon A., Kotler M., Willner I. J. Am. Chem. Soc. 2004, 126:7430-7431.
30. Freeman R., Liu X.Q., Willner I. J. Am. Chem. Soc. 2011, 133:11597-11604.
31. Zhang L.B., Zhu J.B., Li T., Wang E.K. Anal. Chem. 2011, 83:8871-8876.
32. Fu R., Li T., Lee S.S., Park H.G. Anal. Chem. 2011, 83:494-500.
33. Pavlov V., Shlyahovsky B., Willner I. J. Am. Chem. Soc. 2005, 127:6522-6523.
34. Yoshida W., Sode K., Ikebukuro K. Biochem. Biophys. Res. Commun. 2006, 348:245-252.
35. Pelossof G., Tel-Vered R., Elbaz J., Willner I. Anal. Chem. 2010, 82:4396-4402.
36. Golub E., Niazov A., Freeman R., Zatsepin M., Willner I. J. Phys. Chem. C 2012, 116:13827-13834.
37. Kong D.-M., Cai L.-L., Guo J.-H., Wu J., Shen H.-X. Biopolymers 2009, 91:331-339.
38. Cheng X., Liu X., Bing T., Cao Z., Shangguan D. Biochemistry 2009, 48:7817-7823.
39. Kong D.-M., Yang W., Wu J., Li C.-X., Shen H.-X. Analyst 2010, 135:321-326.
40. Li T., Wang E., Dong S. J. Am. Chem. Soc. 2009, 131:15082-15083.
41. Nakayama S., Wang J.X., Sintim H.O. Chem. Eur. J. 2011, 17:5691-5698.
42. S. Nakayama, H. O. Sintim, unpublished.
43. Zheng Z., Han J., Pang W., Hu J. Sensors 2013, 13:1064-1075.
44. Bourdoncle A., Torres A.E., Gosse C., Lacroix L., Vekhoff P., Le Saux T., Jullien L., Mergny J.L. J. Am. Chem. Soc. 2006, 128:11094-11105.
45. Wang N., Kong D.M., Shen H.X. Chem. Commun. 2011, 47:1728-1730.
46. Cheglakov Z., Weizmann Y., Beissenhirtz M.K., Willner I. Chem. Commun. 2006, 3205-3207.
47. Du F., Tang Z. ChemBioChem 2011, 12:43-46.
48. Elbaz J., Shlyahovsky B., Willner I. Chem. Commun. 2008, 1569-1571.
49. Zhang Z., Sharon E., Freeman R., Liu X., Willner I. Anal. Chem. 2012, 84:4789-4797.
50. Li J., Fu H.-E., Wu L.-J., Zheng A.-X., Chen G.-N., Yang H.-H. Anal. Chem. 2012, 84:5309-5315.
51. Zheng D., Zou R., Lou X. Anal. Chem. 2012, 84:3554-3560.
52. Yin B.-C., Ye B.-C., Tan W., Wang H., Xie C.-C. J. Am. Chem. Soc. 2009, 131:14624-14625.
53. Neo J.L., Kamaladasan K., Uttamchandani M. Curr. Pharm. Des. 2012, 18:2048-2057.
54. Liu D.Y., Daubendiek S.L., Zillman M.A., Ryan K., Kool E.T. J. Am. Chem. Soc. 1996, 118:1587-1594.
55. Zhao W., Ali M.M., Brook M.A., Li Y. Angew. Chem. Int. Ed. Engl. 2008, 47:6330-6337.
56. Daubendiek S.L., Kool E.T. Nat. Biotechnol. 1997, 15:273-277.
57. Cheglakov Z., Weizmann Y., Basnar B., Willner I. Org. Biomol. Chem. 2007, 5:223-225.
58. Y.-p. Zeng, J. Hu, Y. Long, C.-y. Zhang, Anal. Chem. (2013) doi:10.1021/ac4011292.
59. Shimron S., Wang F., Orbach R., Willner I. Anal. Chem. 2012, 84:1042-1048.
60. Li J.W.J., Chu Y.Z., Lee B.Y.H., Xie X.L.S. Nucleic Acids Res. 2008, 36:e36.
61. Chen J.H., Zhang J., Guo Y., Li J., Fu F.F., Yang H.H., Chen G.N. Chem. Commun. 2011, 47:8004-8006.
62. Zhao C., Wu L., Ren J., Qu X. Chem. Commun. 2011, 47:5461-5463.
63. Li J., Yao Q.-H., Fu H.-E., Zhang X.-L., Yang H.-H. Talanta 2011, 85:91-96.
64. Zhao X.-H., Gong L., Zhang X.-B., Yang B., Fu T., Hu R., Tan W., Yu R. Anal. Chem. 2013, 85:3614-3620.
65. Li J., Jia Y., Zheng J., Zhong W., Shen G., Yang R., Tan W. Chem. Commun. 2013, 49:6137-6139.
66. Elbaz J., Moshe M., Shlyahovsky B., Willner I. Chem. Eur. J. 2009, 15:3411-3418.
67. Tian T., Xiao H., Zhang Z., Long Y., Peng S., Wang S., Zhou X., Liu S., Zhou X. Chem. Eur. J. 2013, 19:92-95.
68. Zhao Y., Zhou L., Tang Z. Nat. Commun. 2013, 4. 10.1038/ncomms2492.
69. Li Y., Li X., Ji X., Li X. Biosens. Bioelectron. 2011, 26:4095-4098.
70. Liu J., Lu C.-Y., Zhou H., Xu J.-J., Wang Z.-H., Chen H.-Y. Chem. Commun. 2013, 49:6602-6604.
71. Ueyama H., Takagi M., Takenaka S. J. Am. Chem. Soc. 2002, 124:14286-14287.
72. Zhang Q., Cai Y., Li H., Kong D.M., Shen H.X. Biosens. Bioelectron. 2012, 38:331-336.
73. Li T., Shi L.L., Wang E.K., Dong S.J. Chem. Eur. J. 2009, 15:3347-3350.
74. Liu J., Lu Y. Angew. Chem. Int. Ed. Engl. 2007, 46:7587-7590.
75. Li T., Wang E., Dong S. Anal. Chem. 2010, 82:1515-1520.
76. Zhang J., Gao Q.L., Chen P.P., Chen J.H., Chen G.N., Fu F.F. Biosens. Bioelectron. 2011, 26:4053-4057.
77. Jiang B.Y., Wang M., Li C., Xie J.Q. Biosens. Bioelectron. 2013, 43:289-292.
78. Wu J., Wang C., Li X.L., Song Y.L., Wang W., Li C., Hu J., Zhu Z., Li J.X., Zhang W.Y., Lu Z.X., Yang C.J. PLoS ONE 2012, 7:e46393.
79. Huang Y., Chen J., Zhao S., Shi M., Chen Z.-F., Liang H. Anal. Chem. 2013, 85:4423-4430.
80. Chen S.-J., Huang C.-C., Chang H.-T. Talanta 2010, 81:493-498.
81. Bovaird J.H., Ngo T.T., Lenhoff H.M. Clin. Chem. 1982, 28:2423-2426.
82. Boorsma D.M. Histochemistry 1984, 80:103-106.
83. Nakayama S., Sintim H.O. Mol. BioSyst. 2010, 6:95-97.
84. Gross A.J., Sizer I.W. J. Biol. Chem. 1959, 234:1611-1614.
85. Davis L., Maizels N. EMBO J. 2011, 30:3878-3879.
86. Biffi G., Tannahill D., McCafferty J., Balasubramanian S. Nat. Chem. 2013, 5:182-186.
87. Boddupally P.V.L., Hahn S., Beman C., De B., Brooks T.A., Gokhale V., Hurley L.H. J. Med. Chem. 2012, 55:6076-6086.
88. Balasubramanian S., Hurley L.H., Neidle S. Nat. Rev. Drug. Disc. 2011, 10:261-275.
89. De Cian A., DeLemos E., Mergny J.L., Teulade-Fichou M.P., Monchaud D. J. Am. Chem. Soc. 2007, 129:1856-1857.
90. Singh V., Benz A., Hartig J.S. Chem. Eur. J. 2011, 17:10838-10843.
91. Douarre C., Mergui X., Sidibe A., Gomez D., Alberti P., Mailliet P., Trentesaux C., Riou J.F. Nucleic Acids Res. 2013, 41:3588-3599.
92. Kuryavyi V., Cahoon L.A., Seifert H.S., Patel D.J. Structure 2012, 20:2090-2102.
93. Jurczyluk J., Nouwens A.S., Holien J.K., Adams T.E., Lovrecz G.O., Parker M.W., Cohen S.B., Bryan T.M. Nucleic Acids Res. 2011, 39:1774-1788.
94. Balthasart F., Plavec J., Gabelica V. J. Am. Soc. Mass Spectrom. 2013, 24:1-8.
95. Halder K., Benzler M., Hartig J.S. Methods 2012, 57:115-121.
96. Cao K.J., Ryvkin P., Johnson F.B. Methods 2012, 57:3-10.
97. Postberg J., Tsytlonok M., Sparvoli D., Rhodes D., Lipps H.J. Gene 2012, 497:147-154.
98. Dhakal S., Cui Y.X., Koirala D., Ghimire C., Kushwaha S., Yu Z.B., Yangyuoru P.M., Mao H.B. Nucleic Acids Res. 2013, 41:3915-3923.
99. Guedin A., Gros J., Alberti P., Mergny J.L. Nucleic Acids Res. 2010, 38:7858-7868.
100. Lopes J., Piazza A., Bermejo R., Kriegsman B., Colosio A., Teulade-Fichou M.P., Foiani M., Nicolas A. EMBO J. 2011, 30:4033-4046.
101. Marusic M., Sket P., Bauer L., Viglasky V., Plavec J. Nucleic Acids Res. 2012, 40:6946-6956.
102. Randazzo A., Esposito V., Ohlenschlager O., Ramachandran R., Mayol L. Nucleic Acids Res. 2004, 32:3083-3092.
103. Court R., Chapman L., Fairall L., Rhodes D. EMBO Rep. 2005, 6:39-45.
104. Xu Y., Sugiyama H. Nucleic Acids Res. 2006, 34:949-954.
105. Wang F., Tang M.L., Zeng Z.X., Wu R.Y., Xue Y., Hao Y.H., Pang D.W., Zhao Y., Tan Z. Proc. Natl. Acad. Sci. USA 2012, 109:20413-20418.
106. Xu Y., Suzuki Y., Ito K., Komiyama M. Proc. Natl. Acad. Sci. USA 2010, 107:14579-14584.
107. Mathad R.I., Hatzakis E., Dai J.X., Yang D.Z. Nucleic Acids Res. 2011, 39:9023-9033.
108. Baral A., Kumar P., Halder R., Mani P., Yadav V.K., Singh A., Das S.K., Chowdhury S. Nucleic Acids Res. 2012, 40:3800-3811.
109. Bai L.P., Ho H.M., Ma D.L., Yang H., Fu W.C., Jiang Z.H. PLoS ONE 2013, 8:e53962.
110. Iida K., Tera M., Hirokawa T., Shin-ya K., Nagasawa K. Chem. Commun. 2009, 42:6481-6483.
111. Chen M.L., Song G.T., Wang C.Y., Hu D., Ren J.S., Qu X.G. Biophys. J. 2009, 97:2014-2023.
112. Koirala D., Dhakal S., Ashbridge B., Sannohe Y., Rodriguez R., Sugiyama H., Balasubramanian S., Mao H.B. Nat. Chem. 2011, 3:782-787.
113. Nakayama S., Sintim H.O. Anal. Chim. Acta 2012, 747:1-6.
114. Kong D.-M., Xu J., Shen H.-X. Anal. Chem. 2010, 82:6148-6153.
115. Stefan L., Denat F., Monchaud D. Nucleic Acids Res. 2012, 40:8759-8772.
116. Li C., Zhu L., Zhu Z., Fu H., Jenkins G., Wang C., Zou Y., Lu X., Yang C.J. Chem. Commun. 2012, 48:8347-8349.
117. Nakayama S., Roelofs K., Lee V.T., Sintim H.O. Mol. BioSyst. 2012, 8:726-729.
118. Roembke B.T., Wang J.X., Nakayama S., Zhou J., Sintim H.O. RSC Adv. 2013, 3:6305-6310.
119. Xu H.J., Stefan L., Haudecoeur R., Vuong S., Richard P., Denat F., Barbe J.M., Gros C.P., Monchaud D. Org. Biomol. Chem. 2012, 10:5212-5218.
120. Stefan L., Xu H.-J., Gros C.P., Denat F., Monchaud D. Chem. Eur. J. 2011, 17:10857-10862.