Structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4 containing the human telomeric repeat: Evidence for A-tetrad formation from NMR and molecular dynamics simulations

Organic and Biomolecular Chemistry

Volumn 1, Issue 10, 2003, Pages 1650-1656

  Gavathiotis, Evripidis ^a   Searle, Mark S ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; DNA SEQUENCES; HYDROGEN BONDS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POSITIVE IONS; PROTONS;

HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; PARALLEL-STRANDED DNA QUADRUPLEX STRUCTURE;

DNA;

DNA; OLIGODEOXYRIBONUCLEOTIDE; POTASSIUM;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; GENETICS; HUMAN; HYDROGEN BOND; METABOLISM; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; SOLUTION AND SOLUBILITY; TELOMERE; THERMODYNAMICS;

BASE SEQUENCE; COMPUTER SIMULATION; DNA; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; POTASSIUM; REPETITIVE SEQUENCES, NUCLEIC ACID; SOLUTIONS; TELOMERE; THERMODYNAMICS;

EID: 0141905867     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/b300845m     Document Type: Article

References (44)

1. S. Neidle, Oxford Handbook of Nucleic Acid Structure, 1998, Oxford University Press, New York.
2. E. H. Blackburn, Nature, 1991, 350, 569-573.
3. V. A. Zakian, Science, 1995, 270, 1601-1607.
4. C. W. Greider and E. H. Blackburn, Sci. Am., 1996, 274, 92-97.
5. D. E. Shippen, Curr. Opin. Genet. Dev., 1993, 3, 759-763.
6. T. Simonsson, P. Pecinka and M. Kubista, Nucleic Acids Res., 1998, 26, 1167-1172.
7. K. J. Woodford, R. M. Howell and K. Usdin, J. Biol. Chem., 1994, 269, 27029-27035.
8. A. Shimizu and T. Honjo, Cell, 1984, 36, 801-803.
9. J. Feigon, K. M. Koshlap and F. W. Smith, Nuclear Magn. Reson. Nucleic Acids, 1995, 261, 225-255.
10. R. H. Shafer, Prog. Nucleic Acid Res. Mol. Biol., 1998, 59, 55-94.
11. D. J. Patel, S. Bouaziz, A. Kettani, Y. Wang, 1998 Oxford Handbook of Nucleic Acid Structure, p. 389-453, Oxford University Press, New York.
12. K. Walsh and A. Gualberto, J. Biol. Chem., 1992, 267, 13714-13718.
13. R. Erlitzki and M. Fry, J. Biol. Chem., 1997, 272, 15881-15890.
14. W. I. Sundquist and S. Heaphy, Proc. Natl. Acad. Sci. U. S. A., 1993, 90, 3393-3397.
15. E. Raymond, J. C. Soria, E. Izbicka, F. Boussin, L. Hurley and D. D. Von Hoff, Invest. New Drugs, 2000, 18, 123-137.
16. H. Han, R. J. Bennett and L. H. Hurley, Clin. Cancer Res., 1999, 5, 607.
17. J. R. Williamson, Curr. Opin. Struct. Biol., 1993, 3, 357-362.
18. K. Phillips, Z. Dauter, A. I. H. Murchie, D. M. J. Lilley and B. Luisi, J. Mol. Biol., 1997, 273, 171-182.
19. N. V. Hud, V. Sklenar and J. Feigon, J. Mol. Biol., 1999, 286, 651-660.
20. Y. Wang and D. J. Patel, Structure, 1993, 1, 263-282.
21. G. Parkinson, M. P. H. Lee and S. Neidle, Nature, 2002, 417, 876-880.
22. Y. Wang and D. J. Patel, Structure, 1994, 2, 1141-1156.
23. Y. Wang and D. J. Patel, J. Mol. Biol., 1993, 234, 1171-1183.
24. V. M. Marathias and P. H. Bolton, Nucleic Acids. Res., 2000, 28, 1967-1977.
25. G. Gupta, A. E. Garcia, Q. Guo, M. Lu and N. R. Kallenbach, Biochemistry, 1993, 32, 7098-7103.
26. F. Aboulela, A. I. H. Murchie, D. G. Norman and D. M. J. Lilley, J. Mol. Biol., 1994, 243, 458-471.
27. P. K. Patel and R. V. Hosur, Nucleic Acids Res., 1999, 27, 2457-2464.
28. N. Zhang, A. Gorin, A. Majumdar, A. Kettani, N. Chernichenko, E. Skripkin and D. J. Patel, J. Mol. Biol., 2001, 312, 1073-1088.
29. A. Kettani, A. Kumar and D. J. Patel, J. Mol. Biol., 1995, 254, 638-656.
30. P. K. Patel, A. S. R. Koti and R. V. Hosur, Nucleic Acids Res., 1999, 27, 3836-3843.
31. Y. Wang and D. J. Patel, Biochemistry, 1992, 31, 8112-8119.
32. Y. Wang, C. Delossantos, X. L. Gao, K. Greene, D. Live and D. J. Patel, J. Mol. Biol., 1991, 222, 819-832.
33. R. F. Macaya, P. Schultze, F. W. Smith, J. W. Roe and J. Feigon, Proc. Natl. Acad. Sci, U. S. A., 1993, 90, 3745-3749.
34. P. Schultze, F. W. Smith, J. A. Roe and J. Feigon, Structure, 1994, 2, 221-233.
35. V. J. Wijk, B. D. Huckriede, J. H. Ippel and C. Altona, Methods Enzymol., 1992, 211, 286-306.
36. R. Z. Jin, B. L. Gaffney, C. Wang, R. A. Jones and K. J. Breslauer, Proc. Natl. Acad. Sci. U. S. A., 1992, 89, 8832-8836.
37. R. Lavery and H. Sklenar, J. Biomol. Struct. Dyn., 1989, 6, 655-667.
38. E. Gavathiotis, R. Heald, M. F. G. Stevens and M. S. Searle, Angew. Chem., 2001, 40, 4749-4751.
39. M. Piotto, V. Saudek and V. Sklenar, J. Biomol. NMR, 1992, 2, 661-665.
40. J. D. Baleja, J. Moult and B. D. Sykes, J. Magn. Res., 1990, 87, 375-384.
41. R. Koradi, M. Billeter and K. Wuthrich, J. Mol. Graphics, 1996, 14, 51-55.
42. D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, W. S. Ross, C. L. Simmerling, T. L. Darden, K. M. Marz, R. V. Stanton, A. L. Cheng, J.J. Vincent, M. Crowley, V. Tsui, R. J. Radmer, Y. Duan, J. Pitera, I. Massova, G. L. Seibel, U. C. Dingh, P. K. Weinerand, P. A. Kollman, 1999, AMBER 6, University of California, San Francisco.
43. T. E. Cheatham, P. Cieplak and P. A. Kollman, J. Biomol. Struct. Dyn., 1999, 16, 845-862.
44. T. E. Cheatham, J. L. Miller, T. Fox, T. A. Darden and P. A. Kollman, J. Am. Chem. Soc., 1995, 117, 4193-4194.