Small-molecule binding at an abasic site of DNA: Strong binding of lumiflavin for improved recognition of thymine-related single nucleotide polymorphisms

Journal of Physical Chemistry B

Volumn 113, Issue 5, 2009, Pages 1522-1529

  Sankaran, N B ^a,b,c   Sato, Yusuke ^a   Sato, Fuyuki ^a,d   Rajendar, Burki ^a   Morita, Kotaro ^a   Seino, Takehiro ^a   Nishizawa, Seiichi ^a,b   Teramae, Norio ^a,b  

^a TOHOKU UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c MCGILL UNIVERSITY   (Canada)

^d SOPHIA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; DNA; GENES; HYDROGEN; IONIC STRENGTH; LIGANDS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; NUCLEOTIDES; POLYMORPHISM;

AP-SITES; BINDING BEHAVIORS; DNA COMPLEXATION; DNA COMPLEXES; DNA DUPLEXES; EFFICIENT DETECTIONS; FLUORESCENCE MEASUREMENTS; H NMR SPECTROSCOPIES; HYDROGEN-BOND FORMATIONS; ISOTHERMAL TITRATIONS; LIGAND BINDINGS; NUCLEOBASES; SELECTIVE LIGANDS; SINGLE NUCLEOTIDE POLYMORPHISMS; SMALL-MOLECULE BINDINGS; STACKING INTERACTIONS; STRONG BINDINGS;

BINDING SITES;

EID: 61949165909     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp808576t     Document Type: Article

References (65)

1. Meselson, M.; Stahl, F. W. Proc. Natl. Acad. Sci. U.S.A. 1958, 44, 671.
2. Kirk, J. M. Biochim. Biophys. Acta 1960, 42, 167.
3. Waring, M. J. Annu. Rev. Biochem. 1981, 50, 159.
4. Bailly, C; Chaires, J. B. Bioconjugate Chem. 1998, 9, 513.
5. Zimmer, C; Wähnert, U. Prog. Biophys. Mol. Biol. 1986, 47, 31.
6. Jenkins, T. C; Neidle, S.; Brown, D. G.; Lane, A. N. Eur. J. Biochem. 1993, 213, 1175.
7. Lane, A. N.; Jenkins, T. C; Brown, T.; Neidle, S. Biochemistry 1991, 30, 1372.
8. Haq, I.; Ladbury, J. E.; Chowdhury, B. Z.; Jenkins, T. C; Chaires, J. B. J. Mol. Biol. 1997, 277, 244.
9. Haq, I.; Jenkins, T. C; Chowdhury, B. Z.; Ren, J.; Chaires, J. B. Methods Enzymol. 2000, 323, 373.
10. Ren, J.; Jenkins, T. C; Chaires, J. B. Biochemistry 2000, 39, 8439.
11. Searle, M. S.; Lane, A. N. FEBS Lett. 1992, 297, 292.
12. Williams, H. E. L.; Searle, M. S. J. Mol. Biol. 1999, 290, 699.
13. Hopkins, H. P.; Fumero, J.; Wilson, W. D. Biopolymers 1990, 29, 449.
14. Nakatani, K.; Sando, S.; Saito, I. J. Am. Chem. Soc. 2000, 122, 2172.
15. Nakatani, K.; Sando, S.; Saito, I. Nat. Biotechnol. 2001, 19, 51.
16. Nakatani, K.; Kobori, A.; Kumasawa, H.; Goto, Y.; Saito, I. Bioorg. Med. Chem. 2004, 12, 3117.
17. Hagihara, S.; Kumasawa, H.; Goto, Y.; Hayashi, G.; Kobori, A.; Saito, I.; Nakatani, K. Nucleic Acids Res. 2004, 32, 278.
18. Kobori, A.; Horie, S.; Suda, H.; Saito, I.; Nakatani, K. J. Am. Chem. Soc. 2004, 126, 557.
19. Nakatani, K.; Hagihara, S.; Goto, Y.; Kobori, A.; Hagihara, M; Hayashi, G.; Kyo, M.; Nomura, M.; Mishima, M; Kojima, C. Nat. Chem. Biol. 2005, 1, 39.
20. Chee, M; Yang, R.; Hubbell, E.; Berno, A.; Huang, X.-C; Stern, D.; Winkler, J.; Lockhart, D. J.; Morris, M. S.; Fodor, S. P. A. Science 1996, 274, 610.
21. Chen, X.; Zehnbauer, B.; Gnirke, A.; Kwok, P.-Y Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10756.
22. Tyagi, S.; Bratu, D. P.; Kramer, F. R. Nat. Biotechnol. 1998, 16, 49.
23. Lyamichev, V.; Brow, M. A.; Varvel, V. E.; Dahlberg, J. E. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6143.
24. Piatek, A. S.; Tyagi, S.; Pol, A. C; Telenti, A.; Miller, L. P.; Kramer, F. R.; Alland, D. Nat. Biotechnol. 1998, 16, 359.
25. Yoshimoto, K.; Nishizawa, S.; Minagawa, M.; Teramae, N. J. Am. Chem. Soc. 2003, 125, 8982.
26. Lindahl, T.; Nyberg, B. Biochemistry 1972, 11, 3610.
27. Krokan, H. E.; Standal, R.; Slupphaug, G. Biochem. J. 1997, 325, 1.
28. Nishizawa, S.; Yoshimoto, K.; Seino, T.; Xu, C.-Y.; Minagawa, M.; Satake, S.; Tong, A.; Teramae, N. Talanta 2004, 63, 175.
29. Li, N.; Mei, L.; Xiang, Y.; Tong, A.; Nishizawa, S.; Teramae, N. Anal. Chim. Acta 2007, 597, 97.
30. Yoshimoto, K.; Xu, C.-Y.; Nishizawa, S.; Haga, T.; Satake, S.; Teramae, N. Chem. Commun. 2003, 2960.
31. Dai, Q.; Xu, C.-Y.; Sato, Y.; Yoshimoto, K.; Nishizawa, S.; Teramae, N. Anal. Sci. 2006, 22, 201.
32. Rajendar, B.; Sato, Y.; Nishizawa, S.; Teramae, N. Bioorg. Med. Chem. Lett. 2007, 17, 3682.
33. Zhao, C; Dai, Q.; Seino, T.; Cui, Y.-Y.; Nishizawa, S.; Teramae, N. Chem. Commun. 2006, 1185.
34. Rajendar, B.; Nishizawa, S.; Teramae, N. Org. Biomol. Chem. 2008, 6, 670.
35. Nishizawa, S.; Sankaran, N. B.; Seino, T.; Cui, Y.-Y.; Dai, Q.; Xu, C.-Y.; Yoshimoto, K.; Teramae, N. Anal. Chim. Acta 2006, 556, 133.
36. Sankaran, N. B.; Nishizawa, S.; Seino, T.; Yoshimoto, K.; Teramae, N. Angew. Chem., Int. Ed. 2006, 45, 1563.
37. Morita, K.; Sankaran, N. B.; Huang, W.; Seino, T.; Sato, Y.; Nishizawa, S.; Teramae, N. Chem. Commun. 2006, 2376.
38. Huang, W.; Morita, K.; Sankaran, N. B.; Nishizawa, S.; Teramae, N. Electrochem. Commun. 2006, 8, 395.
39. Said, H. M.; Ortiz, A.; Ma, T. Y.; McCloud, E. J. Cell. Physiol. 1998, 176, 588.
40. Said, H. M.; Ortiz, A.; Moyer, M. P.; Yanagawa, N. Am. J. Physiol. Cell Physiol. 2000, 278, C270.
41. Puglisi, J. D.; Tinoco, I., Jr. Methods Enzymol. 1989, 180, 304.
42. Piotto, M.; Saudek, V.; Sklenar, V. J. Biomol. NMR 1992, 2, 661.
43. Bhattacharya, P. K.; Cha, J.; Barton, J. K. Nucleic Acids Res. 2002, 30, 4740.
44. Cuniasse, Ph.; Fazakerly, G. V.; Guschlbauer, W.; Kaplan, B.; Sowers, L. C. J. Mol. Biol. 1990, 213, 303.
45. Stivers, J. T. Nucleic Acids Res. 1998, 26, 3837.
46. Greco, N. J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784.
47. Rachofsky, E. L.; Seibert, E.; Stivers, J. T.; Osman, R.; Ross, J. B. A. Biochemistry, 2001, 40, 957.
48. Brauns, E. B.; Madaras, M. L.; Coleman, R. S.; Murphy, C. J.; Berg, M. A. J. Am. Chem. Soc. 1999, 121, 11644.
49. Somoza, M. M.; Andreatta, D.; Murphy, C. J.; Coleman, R. S.; Berg, M. A. Nucleic Acids Res. 2004, 32, 2494.
50. Record, M. T, Jr.; Anderson, C. F.; Lohman, T. M. Q. Rev. Biophys. 1978, 11, 103.
51. Record, M. T., Jr.; Spolar, R. In The Biology of Nonspecific DNA-Protein Interactions; Revzin, A., Ed.; CRC Press: Boca Raton, FL, 1990; pp. 33-69.
52. Jelesarov, I.; Bosshard, H. R. J. Mol. Recognit. 1999, 12, 3.
53. Freire, E.; Mayorga, O. L.; Straume, M. Anal. Chem. 1990, 62, 950A.
54. Breslauer, K. J.; Freire, E.; Straume, M. Methods Enzymol. 1992, 211, 533.
55. Fisher, H. F.; Singh, N. Methods Enzymol. 1995, 259, 194.
56. Burgstaller, P.; Famulok, M. Angew. Chem., Int. Ed. Engl. 1994, 33, 1084.
57. Fan, P.; Suri, A. K.; Fiala, R.; Live, D.; Patel, D. J. J. Mol. Biol. 1996, 258, 480.
58. Heelis, P. F. Chem. Soc. Rev. 1982, 11, 15.
59. Hermann, T.; Patel, D. J. Science 2000, 287, 820.
60. Heelis, P. F. Chem. Soc. Rev. 1982, 11, 15.
61. Zhao, C; Rajendran, A.; Dai, Q.; Nishizawa, S.; Teramae, N. Anal. Sci. 2008, 24, 693.
62. Record, M. T.; Ha, J.-H.; Fisher, M. A. Methods Enzymol. 1991, 208, 291.
63. Searle, M. S.; Williams, D. H.; Gerhard, U. J. Am. Chem. Soc. 1992, 114, 10697.
64. Williams, D. H.; Searle, M. S.; Mackay, J. P.; Gerhard, U.; Maplestone, R. A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 1172.
65. Spolar, R. S.; Record, M. T. Science 1994, 263, 777.