The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages

Nucleic Acids Research

Volumn 40, Issue 12, 2012, Pages 5731-5738

  Clark, George R ^a   Pytel, Patrycja D ^a   Squire, Christopher J ^b  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

DAUNORUBICIN;

ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA DRUG COMPLEX; DNA SEQUENCE; DRUG STRUCTURE; GENE INSERTION; LIGAND BINDING; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; DAUNORUBICIN; DNA; G-QUADRUPLEXES; LIGANDS; MODELS, MOLECULAR; SODIUM; TELOMERE;

EID: 84863191355     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks193     Document Type: Article

References (36)

1. n, present at the telomeres of human chromosomes. Proc. Natl. Acad. Sci., USA, 85, 6622-6626.
2. Bibby,M.C. (2002) Introduction to telomeres and telomerase. Methods Mol. Biol., 191, 1-12.
3. Gardano,L. and Harrington,L. (2010) Telomere biology and biochemistry. Cellular senescence and tumor suppression, Part 1, 3-43.
4. Burge,S., Parkinson,G.N., Hazel,P., Todd,A.K. and Neidle,S. (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res., 34, 5402-5415. (Pubitemid 44742430)
5. Morin,G.B. (1989) The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesises TTAGGG repeats. Cell, 59, 521-529.
6. Greider,C.W. and Blackburn,E.H. (1985) Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell, 43, 405-413. (Pubitemid 16213265)
7. 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.
8. Neidle,S. (2009) Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS J., 277, 1118-1125.
9. Gunaratnam,M. and Neidle,S. (2010) An evaluation cascade for G-quadruplex telomere targeting agents in human cancer cells. Methods Mol. Biol., 613, 303-313.
10. Campbell,N.H., Parkinson,G.N., Reszka,A.P. and Neidle,S. (2008) Structural basis of DNA quadruplex recognition by an acridine drug. J. Am. Chem. Soc., 130, 6722-6724. (Pubitemid 351748405)
11. Collie,G., Reszka,A.P., Haider,S.M., Gabelica,V., Parkinson,G.N. and Neidle,S. (2009) Selectivity in small molecule binding to human RNA and DNA quadruplexes. Chem. Commun., 7482-7484.
12. Neidle,S. (2009) The structures of quadruplex nucleic acids and their drug complexes. Curr. Opin. Struct. Biol., 19, 239-250.
13. Cang,X., Šponer,J. and Cheatham,T.E. III (2011) Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis. J. Am. Chem. Soc., 133, 14270-14279.
14. Kaushik,M., Kaushik,S., Bansal,A., Saxena,S. and Kukreti,S. (2011) Structural diversity and specific recognition of four stranded G-quadruplex DNA. Curr. Mol. Med., 11, 744-769.
15. Collie,G.W., Haider,S.M., Neidle,S. and Parkinson,G.N. (2010) A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Res., 38, 5569-5580.
16. Collie,G.W., Sparapani,S., Parkinson,G.N. and Neidle,S. (2011) Structural basis of telomeric RNA quadruplex-acridine ligand recognition. J. Am. Chem. Soc., 133, 2721-2728.
17. Garner,T.P., Williams,H.E.L., Gluszyk,K.I., Roe,S., Oldham,N.J., Stevens,M.F.G., Moses,J.E. and Searle,M.S. (2009) Selectivity of small molecule ligands for parallel and anti-parallel DNA G-quadruplex structures. Org. Biomol. Chem., 7, 4194-4200.
18. Phillips,K., Dauter,Z., Murchie,A.I.H., Lilley,D.M.J. and Luisi,B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol., 273, 171-182. (Pubitemid 27460223)
19. Gill,M.L., Strobel,S.A. and Loria,J.P. (2006) Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex. Nucleic Acids Res., 34, 4506-4514. (Pubitemid 44567050)
20. + Ions. Nucleic Acids Res., 32, 1097-1102.
21. Creze,C., Rinaldi,B., Haser,R., Bouvet,P. and Gouet,P. (2007) Structure of a d(TGGGGT) quadruplex crystallised in the presence of Li+ ions. Acta Crystallogr., D63, 682-688. (Pubitemid 46787693)
22. Haider,S., Parkinson,G.N. and Neidle,S. (2002) Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. J. Mol. Biol., 320, 189-200. (Pubitemid 34722211)
23. + solution: an intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.
24. Lee,M.P.H., Parkinson,G.N., Hazel,P. and Neidle,S. (2007) Observation of the coexistence of sodium and calcium ions in a DNA quadruplex ion channel. J. Am. Chem. Soc., 129, 10106-10107. (Pubitemid 47312948)
25. Clark,G.R., Pytel,P.D., Squire,C.J. and Neidle,S. (2003) Structure of the first parallel DNA quadruplex-drug complex. J. Am. Chem. Soc., 125, 4066-4067. (Pubitemid 36512298)
26. Haider,S., Parkinson,G.N. and Neidle,S. (2003) Structure of a G-quadruplex-ligand complex. J. Mol. Biol., 326, 117-125. (Pubitemid 36279362)
27. 4. J. Am. Chem. Soc., 129, 16048-16056.
28. Parkinson,G.N., Cuenca,F. and Neidle,S. (2008) Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes. J. Mol. Biol., 381, 1145-1156.
29. Campbell,N.H., Patel,M., Tofa,A.B., Ghosh,R., Parkinson,G.N. and Neidle,S. (2009) Selectivity in ligand recognition of G-quadruplex loops. Biochemistry, 48, 1675-1680.
30. Hampel,S.M., Sidibe,A., Genaratnam,M., Riou,J.-F. and Neidle,S. (2010) Tetrasubstituted naphthalene diimide ligands with selectivity for telomeric G-quadruplexes and cancer cells. Bioorg. Med. Chem. Lett., 20, 6459-6463.
31. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326. (Pubitemid 27085611)
32. Navaza,J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr., A50, 157-163.
33. Sheldrick,G.M. (2008) A short history of SHELX. Acta Crystallogr., A64, 112-122.
34. Tong,X., Lan,W., Zhang,X., Wu,H., Liu,M. and Cao,C. (2011) Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence. Nucleic Acids Res., 39, 6753-6763.
35. Cang,X., Šponer,J. and Cheatham,T.E. III (2011) Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic. Acids Res., 39, 4499-4512.
36. Tran,P.L.T., Virgilo,A., Esposito,V., Citarella,G., Mergny,J.-L. and Galeone,A. (2011) Effects of 8-methylguanine on structure, stability and kinetics of formation of tetramolecular quadruplexes. Biochimie, 93, 399-408.