Structure of a two-G-tetrad intramolecular G-quadruplex formed by variant human telomeric sequence in K+ solution: Insights into the interconversion of human telomeric G-quadruplex structures

Nucleic Acids Research

Volumn 38, Issue 3, 2009, Pages 1009-1021

  Zhang, Zhenjiang ^a,b   Dai, Jixun ^a   Veliath, Elizabeth ^c   Jones, Roger A ^c   Yang, Danzhou ^a,d  

^a UNIVERSITY OF ARIZONA   (United States)

^b PEKING UNIVERSITY   (China)

^c RUTGERS UNIVERSITY   (United States)

^d UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POTASSIUM ION; DNA; GUANINE QUADRUPLEX; POTASSIUM; PROTON;

ARTICLE; CONFORMATIONAL TRANSITION; DNA FLANKING REGION; DNA SEQUENCE; DNA STRUCTURE; GENE CONVERSION; HUMAN GENETICS; MOLECULAR MECHANICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TELOMERE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; HUMAN; NUCLEAR MAGNETIC RESONANCE;

CIRCULAR DICHROISM; DNA; G-QUADRUPLEXES; HUMANS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; POTASSIUM; PROTONS; TELOMERE;

EID: 77950344651     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1029     Document Type: Article

References (43)

1. Blackburn, E.H. (2000) Telomere states and cell fates. Nature, 408, 53-56.
2. van Steensel, B., Smogorzewska, A. and de Lange, T. (1998) TRF2 protects human telomeres from end-to-end fusions. Cell, 92, 401-413.
3. Hackett, J.A., Feldser, D.M. and Greider, C.W. (2001) Telomere dysfunction increases mutation rate and genomic instability. Cell, 106, 275-286.
4. Mergny, J.L. and Helene, C. (1998) G-quadruplex DNA: A target for drug design. Nat. Med., 4, 1366-1367.
5. Sun, D.Y. and Hurley, L.H. (2001) Targeting telomeres and telomerase. In Chaires, J.B. and Waring, M.J. (eds), Methods in Enzymology, Drug-Nucleic Acid Interactions. Vol. 340. Academic Press Inc, San Diego, pp. 573-592.
6. Hurley, L.H. (2002) DNA and its associated processes as targets for cancer therapy. Nat. Rev. Cancer, 2, 188-200.
7. Neidle, S. and Parkinson, G. (2002) Telomere maintenance as a target for anticancer drug discovery. Nat. Rev. Drug Discov., 1, 383-393.
8. Bodnar, A.G., Ouellette, M., Frolkis, M., Holt, S.E., Chiu, C.P., Morin, G.B., Harley, C.B., Shay, J.W., Lichtsteiner, S. and Wright, W.E. (1998) Extension of life-span by introduction of telomerase into normal human cells. Science, 279, 349-352.
9. Harley, C.B. (1991) Telomere loss: mitotic clock or genetic time bomb? Mutation Res., 256, 271-282.
10. Sun, H., Karow, J.K., Hickson, I.D. and Maizels, N. (1998) The Bloom's Syndrome Helicase Unwinds G4 DNA. J. Biol. Chem., 273, 27587-27592.
11. Sun, H., Bennett, R.J. and Maizels, N. (1999) The Saccharomyces cerevisiae Sgs1 helicase efficiently unwinds G-G paired DNAs. Nucleic Acids Res., 27, 1978-1984.
12. Blackburn, E.H. and Gall, J.G. (1978) A tandemly repeated sequence at the termini of extrachromosomal ribosomal RNA genes in Tetrahymena. J. Mol. Biol., 120, 33-53.
13. Allshire, R.C., Dempster, M. and Hastie, N.D. (1989) Human Telomeres Contain at Least 3 Types of G-Rich Repeat Distributed Non-Randomly. Nucleic Acids Res., 17, 4611-4627.
14. de Lange, T., Shiue, L., Myers, R.M., Cox, D.R., Naylor, S.L., Killery, A.M. and Varmus, H.E. (1990) Structure and variability of human chromosome ends. Mol. Cell Biol., 10, 518-527.
15. Moyzis, R.K., Buckingham, J.M., Cram, L.S., Dani, M., Deaven, L.L., Jones, M.D., Meyne, J., Ratliff, R.L. and Wu, J.R. (1988) A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc. Natl Acad. Sci. USA, 85, 6622-6626.
16. Harley, C.B., Futcher, A.B. and Greider, C.W. (1990) Telomeres shorten during ageing of human fibroblasts. Nature, 345, 458-460.
17. Greider, C.W. and Blackburn, E.H. (1985) Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell, 43, 405-413.
18. Kim, N.W., Piatyszek, M.A., Prowse, K.R., Harley, C.B., West, M.D., Ho, P.L., Coviello, G.M., Wright, W.E., Weinrich, S.L. and Shay, J.W. (1994) Specific association of human telomerase activity with immortal cells and cancer. Science, 266, 2011-2015.
19. Hanahan, D. and Weinberg, R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70.
20. Zahler, A.M., Williamson, J.R., Cech, T.R. and Prescott, D.M. (1991) Inhibition of telomerase by G-quartet DNA structures. Nature, 350, 718-720.
21. Hurley, L.H. (2001) Secondary DNA structures as molecular targets for cancer therapeutics. Biochem. Soc. Trans., 29, 692-696.
22. Hurley, L.H., Wheelhouse, R.T., Sun, D., Kerwin, S.M., Salazar, M., Fedoroff, O.Y., Han, F.X., Han, H.Y., Izbicka, E. and Von Hoff, D.D. (2000) G-quadruplexes as targets for drug design. Pharmacol. Ther., 85, 141-158.
23. Neidle, S. and Read, M.A. (2000) G-quadruplexes as therapeutic targets. Biopolymers, 56, 195-208.
24. 3] G-Tetraplex. Structure, 1, 263-282.
25. Parkinson, G.N., Lee, M.P.H. and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880.
26. Ambrus, A., Chen, D., Dai, J.X., Bialis, T., Jones, R.A. and Yang, D.Z. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/ antiparallel strands in potassium solution. Nucleic Acids Res., 34, 2723-2735.
27. Dai, J.X., Carver, M., Punchihewa, C., Jones, R.A. and Yang, D.Z. (2007) Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res., 35, 4927-4940.
28. Dai, J.X., Punchihewa, C., Ambrus, A., Chen, D., Jones, R.A. and Yang, D.Z. (2007) Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation. Nucleic Acids Res., 35, 2440-2450.
29. + solution. Bioorg. Med. Chem., 14, 5584-5591.
30. + solution: An intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.
31. Phan, A.T., Luu, K.N. and Patel, D.J. (2006) Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution. Nucleic Acids Res., 34, 5715-5719.
32. Matsugami, A., Xu, Y., Noguchi, Y., Sugiyama, H. and Katahira, M. (2007) Structure of a human telomeric DNA sequence stabilized by 8-bromoguanosine substitutions, as determined by NMR in a K+ solution. FEBS J., 274, 3545-3556.
33. + solution. Nucleic Acids Res., 35, 6517-6525.
34. Dai, J.X., Carver, M. and Yang, D.Z. (2008) Polymorphism of human telomeric quadruplex structures. Biochimie, 90, 1172-1183.
35. Antonacci, C., Chaires, J.B. and Sheardy, R.D. (2007) Biophysical characterization of the human telomeric (TTAGGG)(4) repeat in a potassium solution. Biochemistry, 46, 4654-4660.
36. Gray, R.D. and Chaires, J.B. (2008) Kinetics and mechanism of K+-and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures. Nucleic Acids Res., 36, 4191-4203.
37. Lim, K.W., Amrane, S., Bouaziz, S., Xu, W.X., Mu, Y.G., Patel, D.J., Luu, K.N. and Phan, A.T. (2009) Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J. Am. Chem. Soc., 131, 4301-4309.
38. Ambrus, A., Chen, D., Dai, J.X., Jones, R.A. and Yang, D.Z. (2005) Solution structure of the biologically relevant g-quadruplex element in the human c-MYC promoter implications for g-quadruplex stabilization. Biochemistry, 44, 2048-2058.
39. Dai, J.X., Dexheimer, T.S., Chen, D., Carver, M., Ambrus, A., Jones, R.A. and Yang, D.Z. (2006) An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. J. Am. Chem. Soc., 128, 1096-1098.
40. Dai, J.X., Chen, D., Jones, R.A., Hurley, L.H. and Yang, D.Z. (2006) NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res., 34, 5133-5144.
41. Dai, J.X., Punchihewa, C., Mistry, P., Ooi, A.T. and Yang, D.Z. (2004) Novel DNA bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug. J. Biol. Chem., 279, 46096-46103.
42. Brünger, A.T. (1993) X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
43. Nicholls, A., Sharp, K.A. and Honig, B. (1991) Protein folding and association - insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-296.