Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions an conformation and packing

Journal of Molecular Biology

Volumn 291, Issue 1, 1999, Pages 83-99

  Minasov, George ^a   Tereshko, Valentina ^a   Egli, Martin ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Crystal packing; DNA bending; Hydration; Metal ions; X ray crystallography

Indexed keywords

CALCIUM ION; DIVALENT CATION; DNA B; DOUBLE STRANDED DNA; MAGNESIUM ION; METAL ION; OLIGONUCLEOTIDE; PHOSPHATE; REPETITIVE DNA;

ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA HELIX; HYDROGEN BOND; PRIORITY JOURNAL;

EID: 0345363149     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2934     Document Type: Article

References (56)

1. Allemann R., Egli M. DNA bending and recognition. Chem. Biol. 4:1997;643-650.
2. Baikalov I., Grzeskowiak K., Yanagi K., Qunitana J., Dickerson R. E. The crystal structure of the trigonal decamer C-G-A-T-C-G-(6Me)A-T-C-G - a B -DNA helix with 10.6 base-pairs per turn. J. Mol. Biol. 231:1993;768-784.
3. Bancroft D., Williams L. D., Rich A., Egli M. The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove. Biochemistry. 33:1994;1073-1086.
4. Berger I., Egli M., Rich A. Inter-strand C-H···O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4′ in cytosine-rich DNA. Proc. Natl Acad. Sci. USA. 93:1996;12116-12121.
5. Berger I., Tereshko V., Ikeda H., Marquez V. E., Egli M. Crystal structures of B-DNA with incorporated 2′-deoxy-2′-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability. Nucl. Acids Res. 26:1998;2473-2480.
6. Berman H. M., Olson W. K., Beveridge D. L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A. R., Schneider B. The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
7. Brünger A. T. The free R value: a novel statistical quantity for accessing the accuracy of crystal structures. Nature. 355:1992;472-475.
8. Brünger A. T. Crystallography & NMR System (CNS). 1998;Yale University, New Haven.
9. 4). Biochemistry. 33:1994;13540-13546.
10. Cowan J. A. Introduction to the biological role of magnesium ion. Cowan J. A. The Biological Chemistry of Magnesium. 1995;1-23 VCH Publishers Inc. New York.
11. Dickerson R. E. DNA structure from A to Z. Methods Enzymol. 211:1992;67-111.
12. Dickerson R. E., Kopka M. L., Drew H. R. Structural correlations in B -DNA. Srinivasan R., Sarma R. H. Conformation in Biology. 1982;227-257 Adenine Press, New York.
13. Dickerson R. E., Goodsell D. S., Neidle S. "... the tyranny of the lattice ..." Proc. Natl Acad. Sci. USA. 91:1994;3579-3583.
14. Dickerson R. E., Goodsell D., Kopka M. L. MPD and DNA bending in crystals and in solution. J. Mol. Biol. 256:1996;108-125.
15. Drew H. R., Dickerson R. E. Structure of a B -DNA dodecamer. III. Geometry of hydration. J. Mol. Biol. 151:1981;535-556.
16. Egli M. Structural patterns in nucleic acids. Bürgi H.-B., Dunitz J. D. Structure Correlation. 1994;705-749 VCH Publishers Inc. Weinheim.
17. Egli M. Structural aspects of nucleic acid analogues and antisense oligonucleotides. Angew. Chem. Int. Ed. Engl. 35:1996;1894-1909.
18. Gehring K., Leroy J.-L., Guéron M. A tetrameric DNA structure with protonated cytosine·cytosine base pairs. Nature. 363:1993;561-565.
19. Gessner R. V., Frederick C. A., Quigley G. J., Rich A., Wang A. H.-J. 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. 264:1989;7921-7935.
20. Gessner R. V., Quigley G. J., Egli M. Comparative studies of high resolution Z-DNA crystal structures. I. Comparative hydration patterns of alternating dC-dG. J. Mol. Biol. 236:1994;1154-1168.
21. Grzeskowiak K. Sequence-dependent structural variation in B -DNA. Chem. Biol. 3:1996;785-790.
22. Grzeskowiak K., Yanagi K., Privé G. G., Dickerson R. E. The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G - the effect of base pair reversals. J. Biol. Chem. 266:1991;8861-8883.
23. Heinemann U., Alings C. Crystallographic study of one turn of G-C-rich B -DNA. J. Mol. Biol. 210:1989;369-381.
24. Heinemann U., Alings C. The conformation of a B -DNA decamer is mainly determined by its sequence and not by crystal environment. EMBO J. 10:1991;35-43.
25. Heinemann U., Hahn M. C-C-A-G-G-C-M5C-T-G-G - helical fine-structure, hydration and comparison with C-C-A-G-G-C-C-T-G-G. J. Biol. Chem. 267:1992;7312-7341.
26. Kang C. H., Zhang X., Ratliff R., Moyzis R., Rich A. Crystal structure of four-stranded Oxytricha telomeric DNA. Nature. 356:1992;126-131.
27. Kennard O., Hunter W. N. Single crystal X-ray diffraction studies of oligonucleotides and oligonucleotide-drug complexes. Angew. Chem. Int. Ed. Engl. 30:1991;1254-1277.
28. Kim Y., Grable J. C., Love R., Greene P. J., Rosenberg J. M. Refinement of Eco RI endonuclease crystal structure: a revised chain tracing. Science. 249:1990;1307-1309.
29. Klimasauskas S., Kumar S., Roberts R. J., Cheng X. Hha I methyltransferase flips its target base out of the DNA helix. Cell. 76:1994;357-369.
30. Kopka M. L., Fratini A. V., Drew H. R., Dickerson R. E. Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol. 163:1983;129-146.
31. Laughlan G., Murchie A. I. H., Norman D., 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.
32. Lavery R., Sklenar H. J. Defining the structure of irregular nucleic acids - conventions and principles. J. Biomol. Struct. Dyn. 6:1989;655-667.
33. Lipanov A., Kopka M. L., Kaczor-Grzeskowiak M., Quintana J., Dickerson R. E. Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility ofB -DNA. Biochemistry. 32:1993;1373-1389.
34. Liu J., Malinina L., Huynh-Dinh T., Subirana J. A. The structure of the most studied DNA fragment changes under the influence of ions: a new packing of d(CGCGAATTCGCG). FEBS Letters. 438:1998;211-214.
35. Luger K., Mader A. W., Richmond R. K., Sargent D. F., Richmond T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
36. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
37. Nunn C. M., Garman E., Neidle S. Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin. Biochemistry. 36:1997;4792-4799.
38. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
39. 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.
40. Portmann S., Altmann K.-H., Reynes N., Egli M. Crystal structures of oligodeoxyribonucleotides containing 6′-α-methyl and 6′-α-hydroxy carbocyclic thymidines. J. Am. Chem. Soc. 119:1997;2396-2403.
41. Privé G. G., Yanagi K., Dickerson R. E. Structure of the B -DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J. Mol. Biol. 217:1991;177-199.
42. Schneider B., Cohen D., Berman H. M. Hydration of DNA bases: analysis of crystallographic data. Biopolymers. 32:1992;725-750.
43. Schneider B., Cohen D. M., Schleifer L., Srinivasan A. R., Olson W. K., Berman H. M. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J. 65:1993;2291-2303.
44. Sheldrick G. M., Schneider T. R. SHELX-97: high-resolution refinement. Methods Enzymol. 276:1997;319-343.
45. Shui X., McFail-Isom L., Hu G. H., Williams L. D. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry. 37:1998;8341-8355.
46. Sklenar V., Feigon J. Formation of a stable triplex from a single strand. Nature. 345:1990;836-838.
47. Spink N., Nunn C. M., Vojtechovsky J., Berman H. M., Neidle S. Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction. Proc. Natl Acad. Sci. USA. 92:1995;10767-10771.
48. Steitz T. A. Structural Studies of Protein-Nucleic Acid Interaction: The Sources of Sequence-specific Binding. 1993;Cambridge University Press, Cambridge.
49. Takahara P. M., Frederick C. A., Lippard S. J. Crystal structure of the anticancer drug cisplatin bound to duplex DNA. J. Am. Chem. Soc. 118:1996;12309-12321.
50. Tereshko V., Minasov G., Egli M. The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc. 121:1999a;470-471.
51. Tereshko V., Minasov G., Egli M. A "hydrat-ion spine" in a B -DNA minor groove. J. Am. Chem. Soc. 121:1999b;3590-3595.
52. Van Meervelt L., Vlieghe D., Dautant A., Gallois B., Précigoux G., Kennard O. High-resolution structure of a DNA helix forming (C·G)*G base triplets. Nature. 374:1995;742-744.
53. 2triple helix fragments in a crystal structure. Science. 273:1996;1702-1705.
54. Wing R., Drew H., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Crystal structure analysis of a complete turn of B -DNA. Nature. 287:1980;755-758.
55. Winkler F. K., Banner D. W., Oefner C., Tsernoglou D., Brown R. S., Heathman S. P., Bryan R. K., Martin P. D., Petratos K., Wilson K. S. The crystal structure of Eco RV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-1795.
56. Wood A. A., Nunn C. M., Trent J. O., Neidle S. Sequence-dependent crossed helix packing in the crystal structure of a B -DNA decamer yields a detailed model for the Holliday junction. J. Mol. Biol. 269:1997;827-841.