The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution

Journal of Molecular Biology

Volumn 273, Issue 1, 1997, Pages 171-182

  Phillips, Kathryn ^a   Dauter, Zbyszek ^b   Murchie, Alastair I H ^c   Lilley, David M J ^c   Luisi, Ben ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF YORK   (United Kingdom)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Base stacking; Guanine tetraplex; Hydration structure; Metal coordination; X ray crystallography

Indexed keywords

CALCIUM ION; DNA; GUANINE; PHOSPHATE; POTASSIUM ION; RNA; SODIUM ION; THYMINE;

ARTICLE; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA RECOMBINATION; DNA STRUCTURE; HYDROGEN BOND; IMMUNOGLOBULIN GENE; PRIORITY JOURNAL; RNA STRUCTURE; TELOMERE;

EID: 0031576353     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1292     Document Type: Article

References (41)

1. 4. Nature. 360:1992;280-282.
2. 4. J. Mol. Biol. 243:1994;458-471.
3. Arnott S., Chandrasekaran R., Marttila C. M. Structures for polyinosinic acid and polyguanylic acid. Biochem. J. 141:1974;537-543.
4. Beaucage S. L., Caruthers M. H. Deoxynucleoside phosphoramidites - a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Letters, 22:1981;1859-1862.
5. Berman H. M. Hydration of DNA. Curr. Opin. Struct. Biol. 1:1991;423-427.
6. Berman H. M. Hydration of DNA: take 2. Curr. Opin. Struct. Biol. 4:1994;345-350.
7. Blackburn E. H. Structure and function of telomeres. Nature. 350:1991;569-573.
8. Bouquiere J. P., Finney J. L., Savage H. F. J. High-resolution neutron study of vitamin B12 coenzyme at 15 K: solvent structure. Acta Crystallog. sect. B. 50:1994;566-578.
9. Cheong C., Moore P. B. Solution structure of an unusually stable RNA tetraplex containing G and U-quartet structures. Biochemistry. 31:1992;8406-8414.
10. Fang G., Cech T. R. The β subunit ofOxytricha. Cell. 74:1993;875-885.
11. Gellert M., Lipsett M. N., Davies D. R. Helix formation by guanylic acid. Proc. Natl Acad. Sci. USA. 48:1962;21013-22018.
12. Kang C., Zhang X., Ratliff R., Moyzis R., Rich A. Crystal structure of four-strandedOxytricha. Nature. 356:1992;126-131.
13. Lamzin V. S., Wilson K. S. Automated refinement of protein models. Acta Crystallog. sect. D. 49:1993;129-147.
14. Laughlan G., Murchie A. I. H., Norman D. G., Moore M. H., Moody P. C. E., Lilley D. M. J., Luisi B. The high-resolution crystal structure of a parallel-stranded guanine tetraplex. Science. 265:1994;520-524.
15. Liu Z., Gilbert W. The yeast KEM1 gene encodes a nuclease specific for G4 tetraplex DNA: implications ofin vivo. Cell. 77:1994;1083-1092.
16. Liu Z., Lee A., Gilbert W. Gene disruption of a G4-DNA-dependent nuclease in yeast leads to cellular senescence and telomere shortening. Proc. Natl Acad. Sci. USA. 92:1995;6002-6006.
17. MacKerell A. D., Wiorkiewicz-Kuczera J., Karplus M. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:1995;11946-11975.
18. McCall M., Brown T., Kennard O. The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG)-poly(dC). J. Mol. Biol. 183:1985;385-396.
19. Moodie S. L., Thorton J. M. A study into the effects of protein binding on nucleotide conformation. Nucl. Acids Res. 21:1993;1369-1380.
20. Neidle S. DNA Structure and Recognition. 1994;IRL Press, Oxford.
21. Otwinowski, Z. 1993, Oscillation data reduction program, Proceedings of the CCP4 Study Weekend, SERC Daresbury, UK.
22. Parkinson G., Vojtechovsky J., Clowney L., Brünger A. T., Berman H. M. New parameters for the refinement of nucleic acid containing structures. Acta Crystallog. sect. D. 52:1996;57-64.
23. Rhodes D., Giraldo R. Telomere structure and function. Curr. Opin. Struct. Biol. 5:1995;311-322.
24. Saenger W. Principles of Nucleic Acid Structure. 1984;Springer-Verlag Inc. New York.
25. Saenger W., Hunter W. N., Kennard O. DNA conformation is determined by economics in the hydration of phosphate groups. Nature. 324:1986;385-388.
26. Schneider B., Cohen D. M., Schleifer L., Srinivasan A. R., Olson W. K., Berman H. M. A systematic method for studying the spatial distributions of water-molecules around nucleic acid bases. Biophys. J. 65:1993;2291-2303.
27. Schultze P., Smith F. W., Feigon J. Refined solution strcture of the dimeric quadruplex formed from theOxytricha. Structure. 2:1994;221-233.
28. Sen D., Gilbert W. Formation of parallel-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 334:1988;364-366.
29. Sheldrick, G. M. 1993, SHELXL-93, Göttingen.
30. Sinha N. D., Biernat J., McManus J., Koster H. Polymer support oligonucleotides synthesis XVIII: Use of β-cyanoethyl-NNN. Nucl. Acids Res. 12:1984;4539-4557.
31. 444. Biochemistry, 32:1993;8682-8692.
32. Sundquist W. I., Klug A. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 342:1989;825-829.
33. Teeter M. M., Roe S. M., Heo N. H. Atomic resolution (0.83 Å) crystal structure of the hydrophobic protein crambin at 130 K. J. Mol. Biol. 230:1993;292-311.
34. Tougard P., Chantot J.-F., Guschlbauer W. Nucleoside conformations X. An X-ray fibre diffraction study of the gels of guanine dinucleosides. Biochim. Biophys. Acta. 308:1973;9-16.
35. 2324anti. Biochemistry, 31:1992;8112-8119.
36. Wang Y., Patel D. J. Solution structure of a parallel-stranded G-quadruplex DNA. J. Mol. Biol. 234:1993;1171-1183.
37. Wang Y., de los Santos C., Gao X., Greene K., Live D., Patel D. J. Multinuclear nuclear magnetic resonance studies of Na cation-stabilised complex formed by d(G-G-T-T-T-T-C-G-G) in solution. J. Mol. Biol. 222:1991;819-832.
38. Wang K. Y., Kumar S., Pham T. Q., Marathias V. M., Swaminathan S., Bolton P. H. Determination of the number and location of the manganese binding sites of DNA quadruplexes in solution by EPR and NMR in the presence and absence of thrombin. J. Mol. Biol. 260:1996;378-394.
39. Williamson J. R., Raghuraman M. K., Cech T. R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell. 59:1989;871-880.
40. Zimmerman S. B. X-ray study by fiber diffraction methods of a self-aggregate of guanosine-5′-phosphate with the same helical parameters as poly(rG). J. Mol. Biol. 106:1976;663-672.
41. Zimmerman S. B., Cohen G. H., Davies D. R. X-ray fibre diffraction and model building studies of polyguanylic acid and polyinosinic acid. J. Mol. Biol. 92:1975;181-192.