A thymine tetrad in d(TGGGGT) quadruplexes stabilized with TI+/Na+ ions

Nucleic Acids Research

Volumn 32, Issue 3, 2004, Pages 1097-1102

  Cáceres, Carmen ^c   Wright, Glenford ^c   Gouyette, Catherine ^a   Parkinson, Gary ^b   Subirana, Juan A ^c  

^a INSTITUT PASTEUR   (France)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^c UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; SODIUM ION; THALLIUM; THYMINE; CATION; DNA; QUADRUPLEX DNA; SODIUM;

ARTICLE; CONTROLLED STUDY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROGEN BOND; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN STABILITY; TELOMERE; X RAY DIFFRACTION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; BINDING SITES; CATIONS; CRYSTALLOGRAPHY, X-RAY; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SODIUM; THALLIUM; THYMINE;

EID: 2342570222     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh269     Document Type: Article

References (31)

1. Blackburn,E.H. (2001) Switching and signalling at the telomere. Cell, 106, 661-673.
2. Phillips,K., Dauter,Z., Murchie,A.I.H., Lilley,D.M. and Luisi,B.(1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95Å resolution. J. Mol. Biol., 273, 171-182.
3. 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.
4. Parkinson,G.N., Lee,M.P.H. and Neidle,S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880.
5. Guschlbauer,W., Chantot,J.-F. and Thiele,D.(1990) Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomere DNA. J. Biomol. Struct. Dyn., 8, 491-511.
6. Miyoshi,D., Nakao,A., Toda,T. and Sugimoto,N. (2001) Effect of divalent cations on antiparallel G-quartet structure of d(G4T4G4). FEBS Lett., 496, 128-133.
7. Miyoshi,D., Matsumura,S., Li,W. and Sugimoto,N. (2003) Structural polymorphism of telomeric DNA regulated by pH and divalent cation. Nucl. Nucl., 22, 203-221.
8. Aboul-ela,F., Murchie,A.I.H., Norman,D.G. and Lilley,D.M.J. (1994) Solution structure of a parallel-stranded tetraplex formed by d(TG4T) in the presence of sodium ions by nuclear magnetic resonance spectroscopy. J. Mol. Biol., 243, 458-471.
9. Deng,J., Xiong,Y. and Sundaralingam,M. (2001) X-ray analysis of an RNA tetraplex (UGGGGU)4 with divalent Sr2+ ions at subatomic resolution (0.61Å). Proc. Natl Acad. Sci. USA, 98, 13665-13670.
10. Cheong,C. and Moore,P.B. (1992) Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures. Biochemistry, 31, 8406-8414.
11. Padmanabhan,K. and Tulinsky,A. (1996) An ambigous structure of a DNA 15-mer thrombin complex. Acta Crystallogr., D52, 272-282.
12. Horvath,M.P. and Schultz,S.C. (2001) DNA G-quartets in a 1.86Å resolution structure of an Oxytricha nova telomeric protein-DNA complex. J. Mol. Biol., 310, 367-377.
13. Crnugelj,M., Hud,N.V. and Plavec,J. (2002) The solution structure of d(G4T4G3)2: a bimolecular G-quadruplex with a novel fold. J. Mol. Biol., 320, 911-924.
14. 2+. Nucleic Acids Res., 31, 1156-1163.
15. Wang,Y. and Patel,D.J. (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure, 1, 263-282.
16. Basu,S., Szewczak,A.A., Cocco,M. and Strobel,S.A. (2000) Direct detection of monovalent metal ion binding to a DNA G-quartet by 205T1 NMR. J. Am. Chem. Soc., 122, 3240-3241.
17. 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.
18. Otwinowski,Z.M. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
19. Navaza,J. (1994) An automated package for molecular replacement. Acta Crystallogr., A50, 157-163.
20. Brünger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P. and Grosse-Kunstleve,R.W. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., D54, 905-921.
21. Sheldrick,G.M. and Schneider,T.R. (1997) SHELX-97: high-resolution refinement. Methods Enzymol., 276, 319-343.
22. Tereshko,V., Wilds,C.J., Minasov,G., Prakash,T.P., Maier,M.A., Howard,A., Wawrzak,Z., Manoharan,M. and Egli,M. (2001) Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res., 29, 1208-1215.
23. Kissinger,C.R., Gehlhaar,K. and Fogel,D.B. (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr., D55, 484-491.
24. Howerton,S.B., Sines,C.C., VanDerveer,D. and Williams,L.D. (2001) Locating monovalent cations in the grooves of B-DNA. Biochemistry, 40, 10023-10031.
25. Patel,P.K. and Hosur,R.V. (1999) NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats. Nucleic Acids Res., 27, 2457-2464.
26. Haider,S.M., Parkinson,G.N. and Neidle,S. (2003) Structure of a G-quadruplex-ligand complex. J. Mol. Biol., 326, 117-125.
27. Zakian,V.A.(1996) Structure, function, and replication of Saccharomyces cerevisiae telomeres. Annu. Rev. Genet., 30, 141-172.
28. Gaillard,C. and Strauss,F. (1994) Association of Poly(CA)·Poly(TG) DNA fragments into four-stranded complexes bound by HMG1 and 2. Science, 264, 433-436.
29. Borisova,O.F., Shchyolkina,A.K., Il'icheva,I.A. and Pozmogova,G.E. (2001) Conformational polymorphism and extensibility of DNA quadruplexes formed by d(GT)n repeats. Mol. Biol., 35, 732-739.
30. 3GCG). Biochemistry, 31, 833-841.
31. Dong,X. (2003) X-ray crystallographic study of the possible binding sites of the monovalent cations in the Z-DNA structure. Acta Crystallogr., D59, 1336-1338.