Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA

Journal of Molecular Biology

Volumn 274, Issue 3, 1997, Pages 421-435

  Suzuki, Masashi ^a,b   Amano, Naoki ^a   Kakinuma, Jun ^a,b   Tateno, Masaru ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

Author keywords

Crystal structure; DNA bending; DNA conformation; DNA protein interaction; TATA box

Indexed keywords

DINUCLEOTIDE; DNA; PURINE; PYRIMIDINE;

ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; DATA BASE; DNA CONFORMATION; DNA SEQUENCE; PRIORITY JOURNAL; STEREOCHEMISTRY;

EID: 0031555483     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1406     Document Type: Article

References (55)

1. Babcock, M. S., Pednault, E. P. D. & Olson, W. K. (1994). Nucleic acid structure analysis: mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237, 125-156.
2. Barber, A. M. & Zhurkin, V. B. (1990). CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending. J. Biomol. Struct. Dynam. 8, 213-232.
3. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992). The nucleic acid data base: a comprehensive relational data base of three-dimensional structures of nucleic acids. Biophys. J. 63, 751-759.
4. Bhattacharyya, D. & Bansal, M. (1992). Groove width and depth of B-DNA structures depend on local variation in slide. J. Biomol. Struct. Dynam. 10, 213-226.
5. Calladine, C. R. (1982). Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161, 343-352.
6. Calladine, C. R. & Drew, H. R. (1984). A base-centred explanation of the B-to-A transition in DNA. J. Mol. Biol. 178, 773-782.
7. Calladine, C. R. & Drew, H. R. (1992). Understanding DNA: The Molecule & How it Works, Academic Press, London.
8. Claverie, P., Pullman, B. & Caillet, J. (1996). Van der Waals-London interactions between stacked purines and pyrimidines. J. Theoret. Biol. 12, 419-434.
9. Dickerson, R. E. (1989). Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205, 787-791.
10. Dickerson, R. E. (1992). DNA structure from A to Z. Methods Enzymol. 211, 67-111.
11. Dickerson, R. E. (1997). Helix structure and molecular recognition by DNA. In Oxford Handbook of Nucleic Acid Structure (Neidle, S., ed.), Oxford University Press, in the press.
12. Dickerson, R. E., Goodsell, D. S. & Neidle, S. (1994). "...the tyranny of the lattice...". Proc. Natl Acad. Sci. USA, 91, 3579-3583.
13. EL Hassan, M. A. & Calladine, C. R. (1996). Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol. 259, 95-103.
14. EL Hassan, M. A. & Calladine, C. R. (1997). Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. Roy. Soc. ser. A, 355, 43-100.
15. Friedman, R. A. & Honig, B. (1995). A free energy analysis of nucleic acid base-stacking in aqueous solution. Biophys. J. 69, 1528-1535.
16. Gorin, A. A., Zhurkin, V. B. & Olson, W. K. (1995). B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247, 34-48.
17. Grzeskowiak, K. (1996). Sequence-dependent structural variation in B-DNA. Chem. Biol. 3, 785-790.
18. Guckian, K. M., Schweitzer, B. A., Ren, R. X.-F., Sheils, L. J., Paris, P. L., Tahmassebi, D. C. & Kool, E. T. (1996). Experimental measurement of aromatic stacking affinities in the context of duplex DNA. J. Am. Chem. Soc. 118, 8182-8183.
19. Guzikevich-Guerstein, G. G. & Shakked, Z. (1996). A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nature Struct. Biol. 3, 32-37.
20. Hegde, R. S., Grossman, S. R., Laimins, L. A. & Sigler, P. B. (1992). Crystal structure at 1.7 Å of the bovine papilomavirus-1 E2 DNA-binding domains bound to its DNA target. Nature, 359, 505-512.
21. Heinemann, U., Alings, C. & Bansal, M. (1992). Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA. EMBO. J. 5, 1931-1939.
22. Hunter, C. A. (1993). Sequence-dependent DNA structure: the role of base stacking interactions. J. Mol. Biol. 230, 1025-1054.
23. Hunter, C. A. & Lu, X.-J. (1997). DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265, 603-619.
24. Hunter, C. A. & Sanders, J. K. M. (1990). The nature of π-π: interactions. J. Am. Chem. Soc. 112, 5525-5537.
25. Juo, Z. S., Chiu, T. K., Leiberman, P. M., Baikalor, I., Berks, A. J. & Dickerson, R. E. (1996). How proteins recognize the TATA box. J. Mol. Biol. 261, 239-254.
26. Kim, J. L., Nikolov, D. B. & Burley, S. K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
27. Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
28. Klug, A., Jack, A., Viswamitra, M. A., Kennard, O., Shakked, Z. & Steitz, T. A. (1979). A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. Mol. Biol. 131, 669-680.
29. Kollman, P. A., Weiner, P. K. & Dearing, A. (1981). Studies on nucleotide conformations and interactions: the relative stabilities of double-helical B-DNA sequence isomers. Biopolymers, 20, 2583-2621.
30. Lebrun, A., Shakked, Z. & Lavery, R. (1997). Local DNA stretching mimics the distortion caused by the TATA box-binding protein. Proc. Natl Acad. Sci. USA, 94, 2993-2998.
31. Mahalanobis, P. C. (1936). On the generalised distance in statistics. Proc. Nat. Inst. Sci. India, 2, 49-55.
32. Mazur, J., Sarai, A. & Jernigan, R. L. (1989). Sequence dependence of the B-A conformational transition of DNA. Biopolymers, 28, 1223-1233.
33. Olson, W. K. (1996). Simulating DNA at low resolution. Struct. Biol. 6, 242-256.
34. Olson, W. K. & Zhurkin, V. B. (1996). Twenty years of DNA bending. Biol. Struct. Dynam., 341-370.
35. Ornstein, R. L., Rein, R., Breen, D. L. & MacElroy, R. D. (1978). An optimised potential function for the calculation of nucleic acid interaction energies I : base stacking. Biopolymers, 17, 2341-2360.
36. Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y. W., Ebright, R. E. & Berman, H. (1996a). Structure of the CAP-DNA complex at 2.5 Å resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 260, 395-408.
37. Parkinson, G., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T. A., Berman, H. & Ebright, R. H. (1996b). Aromatic hydrogen bond in sequence-specific protein-DNA recognition. Nature Struct. Biol. 3, 837-841.
38. Pearlman, D. A. & Kim, S.-H. (1990). Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211, 171-187.
39. Poltev, V. I., Milova, L. A., Zhorov, B. S. & Govyrin, V. A. (1981). Simulation of conformational possibilities of DNA via calculation of non-bonded interactions of complementary dinucleotide phosphate complexes. Biopolymers, 20, 1-15.
40. Sarai, A., Mazur, J., Nussinov, R. & Jernigan, R. L. (1988). Origin of DNA helical structure and its sequence dependence. Biochemistry, 27, 8498-8502.
41. Schultz, S. C., Shields, G. C. & Steitz, T. A. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science, 253, 1001-1007.
42. Sponer, J. & Kypr, J. (1993). Relationships among rise, cup, roll and stagger in DNA suggested by empirical potential studies of base stacking. J. Biomol. Struct. Dynam. 11, 027-041.
43. Sponer, J., Leszcynski, J. & Hobza, P. (1996a). Hydrogen bonding and stacking of DNA bases: A review of quantum-chemical ab initia studies. J. Biomol. Struct. Dynam. 14, 117-135.
44. Sponer, J., Leszczynnski, J. & Hobza, P. (1996b). Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers: comparison of stacked and H-bonded base pairs. J. Phys. Chem. 100, 5590-5596.
45. Stewart, R. F. (1970). Valence structure from X-ray diffraction daba: an L-shell protection method. J. Chem. Phys. 53, 205-213.
46. Suzuki, M. & Gerstein, M. (1995). Binding geometry of α-helices that recognize DNA. Proteins: Struct. Funct. Genet. 23, 525-535.
47. Suzuki, M. & Yagi, N. (1995). Stereochemical basis of DNA bending by transcription factors. Nucl. Acids Res. 23, 2083-2091.
48. Suzuki, M., Yagi, N. & Gerstein, M. (1995). DNA recognition and superstructure formation by helix-turn-helix proteins. Protein Eng. 8, 329-338.
49. Suzuki, M., Yagi, N. & Finch, J. T. (1996a). Role of base-backbone and base-base interactions in alternating DNA conformations. FEBS Letters, 379, 148-152.
50. Suzuki, M., Allen, M. D., Yagi, N. & Finch, J. T. (1996b). Analysis of co-crystal structures to identify the determinants of the orientation of TBP on the TATA box. Nucl. Acids Res. 24, 2767-2773.
51. Timsit, Y. & Moras, D. (1995). Self-fitting and self-modifying properties of the B-DNA molecule. J. Mol. Biol. 251, 629-647.
52. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., Jr & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
53. Yanagi, K., Prive, G. G. & Dickerson, R. E. (1991). Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 217, 201-214.
54. Young, M. A., Ravishanker, G., Breridge, D. L. & Berman, H. M. (1995). Analysis of local helix bending in crystal structures of DNA oigonucleotides and DNA-protein complexes. Biophys. J. 68, 2454-2468.
55. Zhurkin, V. B., Poltev, V. I. & Florentev, V. L. (1980). Atom-atom potential functions for conformational calculations of nucleic acids. J. MoI. Biol. 14, 882-895.