High-resolution A-DNA crystal structures of d(AGGGGCCCCT) an A-DNA model of poly(dG) · poly(dC)

European Journal of Biochemistry

Volumn 261, Issue 2, 1999, Pages 413-420

  Yi Gui, Gao ^a   Robinson, Howard ^a   Wang, Andrew H J ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b MC 123 ^*  (United States)

Author keywords

A DNA; Atomic resolution structure; DNA conformation; DNA dynamics; Metal ions; X ray diffraction

Indexed keywords

DNA A; POLYDEOXYRIBONUCLEOTIDE;

ARTICLE; CRYSTAL STRUCTURE; DNA CONFORMATION; HYDROGEN BOND; ISOMER; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; STEREOCHEMISTRY; STRUCTURE ANALYSIS; TEMPERATURE SENSITIVITY;

DNA; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; POLYDEOXYRIBONUCLEOTIDES; WATER; X-RAY DIFFRACTION;

EID: 0033561291     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1999.00270.x     Document Type: Article

References (42)

1. 1. Sinden, R.R. (1994) DNA Structure and Function. Academic Press, San Diego, USA.
2. 2. Kim, Y.C., Geiger, J.H., Hahn, S. & Sigler, P.B. (1993) Crystal structure of a yeast TBP TATA-box complex. Nature 365, 512-520.
3. 3. Kim, J.L., Nikolov, D.B. & Burley, S.K. (1993) Co-crystal of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
4. 4. Robinson, H., Gao, Y.-G., McCrary, B.S., Edmondson, S.P., Shriver, J.W. & Wang, A.H.-J. (1998) The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature 392, 202-205.
5. 5. Gao, Y.-G., Su, S.-Y., Robinson, H., Padmanabhan, S., Lim, L., McCrary, B.S., Edmondson, S.P., Shriver, J.W. & Wang, A.H.-J. (1998) The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nat. Struct. Biol. 5, 782-786.
6. 6. Gao, X.L., Mirau, P. & Patel, D.J. (1992) Structure refinement of the chromomycin dimer-DNA oligomer complex in solution. J. Mol. Biol. 223, 259-279.
7. 7. Mooers, B.H., Schroth, G.P. & Ho, P.S. (1995) Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA. J. Mol. Biol. 249, 772-784.
8. 8. Wang, A.H.-J., Fujii, S., van Boom, J.H. & Rich, A. (1982) Molecular structure of the octamer d (G-G-C-C-G-G-C-C): modified A-DNA. Proc. Natl Acad. Sci. USA. 79, 3968-3972.
9. 9. Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W.B.T., Salibury, S.A. & Viswamitra, M.A. (1983) Sequence-dependent conformation of an A-DNA double helix - the crystal structure of the octamer d (G-G-T-A-T-A-C-C). J. Mol. Biol. 166, 183-201.
10. 10. Haran, T.E., Shakked, Z., Wang, A.H.-J. & Rich, A. (1987) The crystal structure of d (CCCCGGGG): a new A-form variant with an extended backbone conformation. J. Biomol. Struct. Dyn. 5, 199-217.
11. 11. Frederick, C.A., Quigley, G.J., Teng, M.-K., Coll, M., van der Maret, G.A., van Boom, J.H., Rich, A. & Wang, A.H.-J. (1989) Molecular structure of an A-DNA decamer d (ACCGGCCGGT). Eur. J. Biochem. 181, 295-307.
12. 12. Ramakrishnan, B. & Sundaralingam, M. (1993) Evidence for crystal environment dominating base sequence effects on DNA conformation: Crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d (GCGGGCCCGC) and comparison with their isomorphous crystal structures. Biochemistry 32, 11458-11468.
13. 13. Ramakrishnan, B. & Sundaralingam, M. (1993) High resolution crystal structure of the A-DNA decamer d (CCCGGCCGGG) - novel intermolecular base paired G* (G·C) triplets. J. Mol. Biol 231, 431-444.
14. 2+ to A-DNA. Biophys. J. 69, 559-568.
15. 15. Nunn, C.M. & Neidle, S. (1996) The high resolution crystal structure of the DNA decamer d (AGGCATGCCT). J. Mol. Biol. 256, 340-351.
16. 16. Bingman, C.A., Zon, G. & Sundaralingam, M. (1992) Crystal and molecular structure of the A-DNA dodecamer d (CCGTACGTAC-GG) - Choice of fragment helical axis. J. Mol. Biol. 227, 738-756.
17. 17. Verdguer, N., Aymami, J., Fernandez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J. & Subirana, J.A. (1991) Molecular structure of a complete turn of A-DNA. J. Mol. Biol. 221, 623-635.
18. 18. Wahl, M.C. & Sundaralingam, M. (1997) Crystal structures of A-DNA duplexes. Biopolymers 44, 45-63.
19. 19. Schneider, B., Neidle, S. & Berman, H.M. (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42, 113-124.
20. 20. Robinson, H., Gao, Y.-G., Bauer, C., Roberts, C., Switzer, C.Y. & Wang, A.H.-J. (1998) 2′-Deoxy-isoguanosine adopts more than one tautomers to base pair with thymidine observed by high resolution crystal structure. Biochemistry 37, 10897-10905.
21. 21. Shui, X., McFail-Isom, L., Hu, G.G. & Williams, L.D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37, 8341-8355.
22. 22. Berger, I., Tereshko, V., Ikeda, H., Marquez, V.E. & Egli, M. (1998) Crystal structure of B-DNA with incorporated 2′-deoxy-2′-fluro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability. Nucl Acids Res. 26, 2473-2480.
23. 23. Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R.E. (1980) Crystal structure analysis of a complete turn of DNA. Nature 287, 755-758.
24. 24. Wang, A.H.-J. & Gao, Y.-G. (1990) Crystallization of oligonucleotides and their complexes with antitumor drugs. Methods. A Companion to Methods in Enzymology 1, 91-99.
25. 25. Brünger, A. (1993) XPLOR (Version 3.1) The Howard Hughes Medical Institute and Yale University, New Haven, CT, USA.
26. 26. Sheldrick, G.M. (1997) SHELX-97, crystallographic refinement program. University of Gottingen, Germany.
27. 27. Moews, P.C. & Kretsinger, R.H. (1975) Refinement of the structure of carp muscle calcium binding parvalbumin by model building and difference Fourier analysis. J. Mol. Biol. 91, 201-228.
28. 28. Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A.T. & Berman, H.M. (1996) New parameters of nucleic acid-containing structures. Acta Crystallogr. D52, 57-64.
29. 29. Rosenberg, J.M., Seeman, N.C., Day, R.O. & Rich, A. (1976) RNA double helical fragment at atomic resolution. II. The crystal and molecular structure of sodium guanynyl-3′,5′-cytidine nonahydrate. J. Mol. Biol. 104, 145-167.
30. 30. Gessner, R.V., Frederick, C.A., Quigley, G.J., Rich, A. & Wang, A.H.-J. (1989) The molecular structure of the left-handed Z-DNA double helix at 1.0 Å atomic resolution: geometry, conformation and ionic interactions of d (CGCGCG). J. Biol. Chem. 264, 7921-7935.
31. 31. Eisenstein, M. & Shakked, Z. (1995) Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248, 662-678.
32. 32. Benevides, J.M., Wang, A.H.-J., Rich, A., Kyogoku, Y., van der Marel, G.A., van Boom, J.H. & Thomas, G.J. Jr (1986) Raman spectra of single crystals of r (GCG) d (CGC) and d (CCCCGGGG) and models for A-DNA, their structure transitions in aqueous solution, and comparison with double-helical poly (dG).poly (dC). Biochemistry 25, 41-50.
33. 33. Prive, G.G., Heinemann, U., Chandrasegaran, S., Kan, L.-S., Kopka, M.L. & Dickerson, R.E. (1987) Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science 238, 498-504.
34. 34. Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., van der Marel, G.A., van Boom, J.H. & Rich, A. (1981) Left-handed double helical DNA: Variations in the backbone conformation. Science 211, 171-176.
35. 35. Ban, C., Ramakrishnan, B. & Sundaralingam, M. (1994) Crystal structure of the highly distorted chimeric decamer r (C) d (CGGCGCCG) r (G).spermine binding to phosphate only and minor groove tertiary base-paring. Nucl Acids Res. 22, 5466-5476.
36. 36. Gessner, R.G., Quigley, G.J., Wang, A.H.-J., van der Marel, G.A., van Boom, J.H. & Rich, A. (1985) Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesiun cations. Biochemistry 24, 237-250.
37. 37. Robinson, H. & Wang, A.H.-J. (1996) Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B-to A-DNA. Nucl Acids Res. 24, 676-682.
38. 38. Xu, Q., Schoemaker, R.K. & Braunlin, W.H. (1993) Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution. Biophys. J. 65, 1039-1049.
39. 2 in the presence of hexaamminecoblt (III). Structure 5, 1297-1311.
40. 40. Bauer, C. & Wang, A.H.-J. (1997) Bridged cobalt amine complexes induce DNA conformational changes effectively. J. Inorg. Biochem. 68, 129-135.
41. 41. EMBO Workshop. (1989) Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4.
42. 42. Chandrasekaran, R. & Arnott, S. (1989) The structures of DNA and RNA in oriented fibres. In Landolt-Bornstein, New Series, Group VII, Vol. 1b (Saenger, W., ed.), pp. 31-170. Springer-Verlag, Berlin, Germany.