Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+

Journal of Physical Chemistry B

Volumn 115, Issue 44, 2011, Pages 13051-13056

  Liu, Wei ^a,b,c,d   Fu, Yan ^e   Zheng, Bin ^a,b,c   Cheng, Sheng ^b,c,d   Li, Wei ^e   Lau, Tai Chu ^b,c   Liang, Haojun ^a,b,d  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b City University of Hong Kong Joint Advanced Research Center   (China)

^c CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^d UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^e TIANJIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM SPECTROSCOPY; DICHROISM; KINETICS; POSITIVE IONS; PYROLYSIS; STOICHIOMETRY; TITRATION;

APTAMERS; CD SPECTRA; COMPACT STRUCTURES; CONFORMATIONAL CHANGE; FOLDED STRUCTURES; G-QUADRUPLEXES; KINETIC STUDY; KINETICS AND MECHANISM; METAL CATION; SPECTRAL CHARACTERISTICS; STOPPED-FLOW TECHNIQUES; THERMAL DENATURATIONS; ULTRA-VIOLET;

DNA SEQUENCES;

EID: 80455158408     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2074489     Document Type: Article

References (52)

1. Gellert, M.; Lipsett, M. N.; Davies, D. R. Proc. Natl. Acad. Sci. U.S.A. 1962, 48, 2013-2018
2. Olaussen, K. A.; Dubrana, K.; Dornont, J.; Spano, J. P.; Sabatier, L.; Soria, J. C. Crit. Rev. Oncol. Hematol. 2006, 57, 191-214
3. Han, H. Y.; Hurley, L. H. Trends Pharmacol. Sci. 2000, 21, 136-142
4. Neidle, S.; Parkinson, G. Nat. Rev. Drug Discovery 2002, 1, 383-393
5. Muniyappa, K. Med. Chem. Res. 2010, 19, 28-29
6. Kelland, L. R.; Ireson, C. R. Mol. Cancer Ther. 2006, 5, 2957-2962
7. Marsh, T. C.; Vesenka, J.; Henderson, E. Nucleic Acids Res. 1995, 23, 696-700
8. Neidle, S.; Parkinson, G. N.; Lee, M. P. H. Nature 2002, 417, 876-880
9. Chen, F. M. Biophys. J. 1997, 73, 348-356
10. Macaya, R. F.; Schultze, P.; Smith, F. W.; Roe, J. A.; Feigon, J. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 3745-3749
11. Jing, N. J.; Hogan, M. E. J. Biol. Chem. 1998, 273, 34992-34999
12. Sugimoto, N.; Toda, T.; Ohmichi, T. Chem. Commun. 1998, 1533-1534
13. Forman, S. L.; Fettinger, J. C.; Pieraccini, S.; Gottareli, G.; Davis, J. T. J. Am. Chem. Soc. 2000, 122, 4060-4067
14. Jia, G.; Feng, Z.; Wei, C.; Zhou, J.; Wang, X.; Li, C. J. Phys. Chem. B 2009, 113, 16237-16245
15. Cheng, X. H.; Liu, X. J.; Bing, T.; Zhao, R.; Xiong, S. X.; Shangguan, D. H. Biopolymers 2009, 91, 874-883
16. Fu, Y.; Wang, X.; Zhang, J. L.; Xiao, Y.; Li, W.; Wang, J. K. Biomacromolecules 2011, 12, 747-756
17. Chowdhury, S.; Bansal, M. J. Phys. Chem. B 2001, 105, 7572-7578
18. Engelhart, A. E.; Plavec, J.; Persil, O.; Hud, N. V. Metal Ion Interactions with G-Quadruplex Structures. In Nucleic Acid-Metal Ion Interactions; Hud, N. V., Eds.; Royal Society of Chemistry: Cambridge, U.K., 2009; pp 118-147.
19. Mergny, J. L.; Phan, A. T.; Lacroix, L. FEBS Lett. 1998, 435, 74-78
20. Hong, E. S.; Yoon, H. J.; Kim, B.; Yim, Y. H.; So, H. Y.; Shin, S. K. J. Am. Soc. Mass Spectrom. 2010, 21, 1245-1255
21. Mergny, J. L.; Gros, J.; De Cian, A.; Bourdoncle, A.; Rosu, F.; Sacca, B.; Guittat, l.; Amrane, S.; Mills, M.; Alberti, P. Energetics, kinetics and dynamics of quadruplex folding. In Quadruplex Nucleic Acid; Neidle, S.; Balasubramanian, S., Eds.; Royal Society of Chemistry: Cambridge, U.K., 2006; pp 31-80.
22. Kankia, B. I.; Marky, L. A. J. Am. Chem. Soc. 2001, 123, 10799-10804
23. Vairamani, M.; Gross, M. L. J. Am. Chem. Soc. 2003, 125, 42-43
24. Mondragón-Sánchez, J. A.; Liquier, J.; Shafer, R. H.; Taillandier, E. J. Biomol. Struct. Dyn. 2004, 22, 365-373
25. Marathias, V. M.; Wang, K. Y.; Kumar, S.; Pham, T. Q.; Swaminathan, S.; Bolton, P. H. J. Mol. Biol. 1996, 260, 378-394
26. Lin, J.; Yan, Y. Y.; Ou, T. M.; Tan, J. H.; Huang, S. L.; Li, D.; Huang, Z. S.; Gu, L. Q. Biomacromolecules 2010, 11, 3384-3389
27. Huang, J. W. W.; Chen, J. J.; Berti, W. R.; Cunningham, S. D. Environ. Sci. Technol. 1997, 31, 800-805
28. Bressler, J.; Kim, K. A.; Chakraborti, T.; Goldstein, G. Neurochem. Res. 1999, 24, 595-600
29. Lasley, S. M. J. Neurochem. 2002, 81, 87-87
30. Leung, M. C.; Williams, P. L.; Benedetto, A.; Au, C.; Helmcke, K. J.; Aschner, M.; Meyer, J. N. Toxicol. Sci. 2008, 106, 5-28
31. Oliveira, S. C.; Corduneanu, O.; Oliveira-Brett, A. M. Bioelectrochemistry 2008, 72, 53-58
32. Kotch, F. W.; Fettinger, J. C.; Davis, J. T. Org. Lett. 2000, 2, 3277-3280
33. Smirnov, I.; Shafer, R. H. J. Mol. Biol. 2000, 296, 1-5
34. Li, T.; Wang, E. K.; Dong, S. J. J. Am. Chem. Soc. 2009, 131, 15082-15083
35. Smirnov, I.; Shafer, R. H. Biochemistry 2000, 39, 1462-1468
36. Smirnov, I. V.; Kotch, F. W.; Pickering, I. J.; Davis, J. T.; Shafer, R. H. Biochemistry 2002, 41, 12133-12139
37. Hud, N. V.; Plavec, J. The role of cations in determining quadruplex structure and stability. In Quadruplex Nucleic Acids; Neidle, S.; Balasubramanian, S., Eds.; Royal Society of Chemistry: Cambridge, U.K., 2006; p 100.
38. Majhi, P. R.; Qi, J.; Tang, C. F.; Shafer, R. H. Biopolymers 2008, 89, 302-309
39. Pagano, B.; Martino, L.; Randazzo, A.; Giancola, C. Biophys. J. 2008, 94, 562-569
40. Chang, T. C.; Lin, C. T.; Tseng, T. Y.; Wang, Z. F. J. Phys. Chem. B 2011, 115, 2360-2370
41. Kelly, J. A.; Feigon, J.; Yeates, T. O. J. Mol. Biol. 1996, 256, 417-422
42. Marathias, V. M.; Bolton, P. H. Nucleic Acids Res. 2000, 28, 1969-1977
43. Gray, R. D.; Chaires, J. B. Nucleic Acids Res. 2008, 36, 4191-4203
44. Gray, R. D.; Chaires, J. B.; Li, J. J. Phys. Chem. B 2009, 113, 2676-2683
45. Miyoshi, D.; Nakao, A.; Sugimoto, N. Nucleic Acids Res. 2003, 31, 1156-1163
46. Gray, D. M.; Hung, S. H.; Johnson, K. H. Methods Enzymol. 1995, 246, 19-34
47. Hatzakis, E.; Okamoto, K.; Yang, D. Biochemistry 2010, 49, 9152-9160
48. Lu, M.; Guo, Q.; Kallenbach, N. R. Biochemistry 1993, 32, 598-601
49. Williamson, J. R. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 703-730
50. Hud, N. V.; Smith, F. W.; Anet, F. A. L.; Feigon, J. Biochemistry 1996, 35, 15383-15390
51. Hud, N. V.; Schultze, P.; Sklenar, V.; Feigon, J. J. Mol. Biol. 1999, 285, 233-243
52. Sclavi, B.; Sullivan, M.; Chance, M. R.; Brenowitz, M.; Woodson, S. A. Science 1998, 279, 1940-1943