MPD and DNA bending in crystals and in solution

Journal of Molecular Biology

Volumn 256, Issue 1, 1996, Pages 108-125

  Dickerson, Richard E ^a   Goodsell, David ^b   Kopka, Mary L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

A tract; DNA bending; Junction; MPD; Wedge

Indexed keywords

ADENINE; CURVED DNA; GUANINE; HEXYLENE GLYCOL;

ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DNA CONFORMATION; DNA DENATURATION; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR MODEL; PRIORITY JOURNAL;

EID: 0029978007     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0071     Document Type: Article

References (85)

1. 2 system. Biochemistry, 29, 1914-1923.
2. Arakawa, T., Bhat, R. & Timasheff, S. N. (1990b). Why preferential hydration does not always stabilize the native structure of globular proteins. Biochemistry, 29, 1924-1931.
3. Aymami, J., Coll, M., van der Marel, G. A., van Boom, J. H., Wang, A. H.-J. & Rich, A. (1990). Molecular structure of nicked DNA - A substrate for DNA repair enzymes. Proc. Natl Acad. Sci. USA, 87, 2526-2530.
4. 6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn. J. Mol. Biol. 231, 768-784.
5. 2 tracts. J. Biomol. Struct. Dynam. 9, 511-516.
6. Balendiran, K., Rao, S. T., Sekharudu, C. Y., Zon, G. & Sundaralingam, M. (1995). X-ray structures of the B-DNA dodecamer d(C-G-C-G-T-T-A-A-C-G-C-G) with an inverted central tetranucleotide and its netropsin complex. Acta Crystallog. sect. D, 51, 190-198.
7. Bolshoy A., McNamara, P., Harrington, R.E. & Trifonov, E. N. (1991). Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl Acad. Sci. USA, 88, 2312-2316.
8. Brukner, I., Susic, S., Dlakic, M., Savic, A. & Pongor, S. (1994). Physiological concentration of magnesium ions induces a strong macroscopic curvature in G-G-G-C-C-C-containing DNA. J. Mol. Biol. 236, 26-32.
9. Brukner, I., Sánchez, R., Suck, D. & Pongor, S. (1995). Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J. 14, 1812-1818.
10. Cacchione, S., De Santis, P., Foti, D. P., Palleschi, A. & Savino, M. (1989). Periodical polydeoxynucleotides and DNA curvature. Biochemistry, 23, 8706-8713.
11. Calladine, C. R., Drew, H. R. & McCall, M. J. (1988). The intrinsic curvature of DNA in solution. J. Mol. Biol. 201, 127-137.
12. Chan, S. S., Breslauer, K. J., Hogan, M. E., Kessler, D. J., Austin, R. N., Ojemann, J., Passner, J. M. & Wiles, N. C. (1990). Physical studies of DNA premelting equilibria in duplexes with and without homo dA·dT tracts: correlations with DNA bending. Biochemistry, 29, 6161-6171.
13. 5 tracts. Biochemistry, 32, 11776-11784.
14. Crothers, D. M. & Drak, J. (1992). Global features of DNA structures by comparative gel electrophoresis. Methods Enzymol. 212B, 46-71.
15. Crothers, D. M., Haran, T. E. & Nadeau, J. G. (1990). Intrinsically bent DNA. J. Biol. Chem. 165, 7093-7096.
16. Dickerson, R. E. (1992). DNA structure from A to Z. In Methods in Enzymology (Lilley, D. M. J. & Dahlberg, J. E., eds), vol. 211, pp. 67-111, Academic Press, Orlando, FL.
17. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C.-S., Wang, A. H.-J. & Zhurkin, V. B. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4; J. Biomol. Struct. Dynam. 6, 627-634; Nucl. Acids Res. 17, 1797-1803; J. Mol. Biol. 205, 787-791.
18. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C.-S., Wang, A. H.-J. & Zhurkin, V. B. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4; J. Biomol. Struct. Dynam. 6, 627-634; Nucl. Acids Res. 17, 1797-1803; J. Mol. Biol. 205, 787-791.
19. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C.-S., Wang, A. H.-J. & Zhurkin, V. B. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4; J. Biomol. Struct. Dynam. 6, 627-634; Nucl. Acids Res. 17, 1797-1803; J. Mol. Biol. 205, 787-791.
20. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C.-S., Wang, A. H.-J. & Zhurkin, V. B. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4; J. Biomol. Struct. Dynam. 6, 627-634; Nucl. Acids Res. 17, 1797-1803; J. Mol. Biol. 205, 787-791.
21. Dickerson, R. E., Goodsell, D. S. & Neidle, S. (1994). . . . the tyranny of the lattice . . . . Proc. Natl Acad. Sci. USA, 91, 3579-3583.
22. Diekmann, S. (1987). Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucl. Acids Res. 15, 247-285.
23. Diekmann, S., von Kitzing, E., McLaughlin, L. W., Ott, J. & Eckstein, F. (1987). The influence of exocyclic substituents of purine bases on DNA curvature. Proc. Natl Acad. Sci. USA, 84, 8257-8261.
24. Diekmann, S., Mazzarelli, J. M., McLaughlin, L. W., von Kitzing, E. & Travers, A. A. (1992). DNA curvature does not require bifurcated hydrogen bonds or pyrimidine methyl groups. J. Mol. Biol. 225, 729-738.
25. Di Gabriele, A. D. & Steitz, T. A. (1993). A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. J. Mol. Biol. 231, 1024-1029.
26. Di Gabriele, A. D., Sanderson, M. R., & Steitz, T. A. (1989). Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl Acad. Sci. USA, 86, 1816-1820.
27. Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: Conformation and dynamics. Proc. Natl Acad. Sci. USA, 78, 2179-2183.
28. Drew, H. R., Samson, S. & Dickerson, R. E. (1982). Structure of a B-DNA dodecamer at 16 K. Proc. Natl Acad. Sci. USA, 79, 4040-4044.
29. 2: an examination of propeller twist and minor-groove water structure at 2.2 Å resolution. J. Mol. Biol. 226, 1161-1173.
30. brC-G-C-G. J. Biol. Chem. 257, 14686-14707.
31. m6A-T-T-C-G-C-G) at 2.0 Å resolution. J. Biol. Chem. 263, 17872-17879.
32. Gekko, K. & Timasheff, S. N. (1981a). Mechanism of protein stabilization by glycerol: preferential hydration in glycerol-water mixtures. Biochemistry, 20, 4667-4676.
33. Gekko, K. & Timasheff, S. N. (1981b). Thermodynamic and kinetic examination of protein stabilization by glycerol. Biochemistry, 20, 4677-4686.
34. Goodsell, D. S. & Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucl. Acids Res. 22, 5497-5503.
35. Goodsell, D. S., Kopka, M. L., Cascio, D. & Dickerson, R. E. (1993). Crystal structure of C-A-T-G-G-C-C-A-T-G and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA, 90, 2930-2934.
36. Goodsell, D. S., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1994). The crystal structure of C-C-A-T-T-A-AT-G-G: implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79-96.
37. Griffith, J., Bleyman, M., Rauch, C. A., Kitchin, P. A. & Englund, P. T. (1986). Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell, 46, 717-724.
38. Grzeskowiak, K., Yanagi, K., Privé, G. G. & Dickerson, R. E. (1991). The structure of B-helical C-G-A-T-C-GA-T-C-G, and comparison with C-C-A-A-C-G-T-T-GG: the effect of base-pair reversals. J. Biol. Chem. 266, 8861-8883.
39. Grzeskowiak, K., Goodsell, D. S., Kaczor-Grzeskowiak, M., Cascio, D. & Dickerson, R. E. (1993). Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA. Biochemistry, 32, 8923-8931.
40. Hagerman, P. J. (1984). Evidence for the existence of stable curvature of DNA in solution. Proc. Natl Acad. Sci. USA, 81, 4632-4636.
41. Hagerman, P. J. (1986). Sequence-directed curvature of DNA. Biochemistry, 24, 7033-7037.
42. Hagerman, P. J. (1990). Sequence-directed curvature of DNA. Annu. Rev. Biochem. 59, 755-781.
43. Haran, T. E., Kahn, J. D. & Crothers, D. M. (1994). Sequence elements responsible for DNA curvature. J. Mol. Biol. 244, 135-143.
44. Harvey, S. C., Dlakic, M., Griffith, J., Harrington, R., Park, K., Sprous, D. & Zacharias, W. (1995). What is the basis of sequence-directed curvature in DNAs containing A tracts? J. Biomol. Struct. Dynam. 13, 301-307.
45. Heinemann, U. & Alings, C. (1989). Crystallographic study of one turn of G/C-rich B-DNA. J. Mol. Biol. 210, 369-381.
46. Heinemann, U. & Alings, C. (1991). The conformation of a B-DNA decamer is mainly determined by its sequence and not by crystal environment. EMBO J. 10, 35-43.
47. m5C-TG-G: helical fine structure, hydration, and comparison with C-G-A-G-G-C-C-T-G-G. J. Biol. Chem. 267, 7332-7341.
48. Herrera, J. E. & Chaires, J. B. (1989). A premelting transition in poly(dA)·poly(dT) coupled to daunomycin binding. Biochemistry, 28, 1993-2000.
49. Hunter, W. N., Brown, T., Kneale, G., Anand, N. N., Rabinovich, D. & Kennard, O. (1987). The structure of guanosine-thymidine mismatches in B-DNA at 2.5-Å resolution. J. Biol. Chem. 21, 9962-9970.
50. Kitchin, P. A., Klein, V. A., Ryan, K. A., Gann, K. L., Rauch, C. A., Kang, D. S., Wells, R. D. & Englund, P. T. (1986). A highly bent fragment of Crithidia fasciculata kinetoplast DNA. J. Biol. Chem. 261, 11301-11309.
51. Koo, H.-S. & Crothers, D. M. (1988). Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl Acad. Sci. USA, 85, 1763-1767.
52. Koo, H.-S., Wu, H.-M. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature, 320, 501-506.
53. Larsen, T. A., Kopka, M. L. & Dickerson, R. E. (1990). Crystal structure analysis of the B-DNA dodecamer C-G-T-G-A-A-T-T-C-A-C-G. Biochemistry, 30, 4443-4449.
54. Lee, J. C. & Timasheff, S. N. (1981). The stabilization of proteins by sucrose. J. Biol. Chem. 256, 7093-7201.
55. Leonard, G. A. & Hunter, W. N. (1993). Crystal and molecular structure of d(C-G-T-A-G-A-T-C-T-A-C-G) at 2.5 Å resolution. J. Mol. Biol. 234, 198-208.
56. Lipanov, A., Kopka, M. L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R. E. (1993). Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA. Biochemistry, 32, 1373-1389.
57. Marini, J. C., Levene, S. D., Crothers, D. M. & Englund, P. T. (1982). Bent helical structure in kinetoplast DNA. Proc. Natl Acad. Sci. USA, 79, 7664-7668. (See also sequence correction in: (1983) Proc. Natl Acad. Sci. USA, 80, 7678.)
58. Marini, J. C., Effron, P. N., Goodman, T. C., Singleton, C. K., Wells, R. D., Wartell, R. M. & Englund, P. T. (1984). Physical characterization of a kinetoplast DNA fragment with unusual properties. J. Biol. Chem. 259, 8974-8979.
59. Maroun, R. C. & Olson, W. K. (1988). Base sequence effects in double-helical DNA: III. Average properties of curved DNA. Biopolymers, 27, 585-603.
60. Narayana, N., Ginell, S. L., Russu, I. M. & Berman, H. M. (1990). Crystal and molecular structure of a DNA fragment: d(C-G-T-G-A-A-T-T-C-A-C-G). Biochemistry, 30, 4450-4455.
61. Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987). The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature, 330, 221-226.
62. Park, Y. W. & Breslauer, K. J. (1991). A spectroscopic and calorimetric study of the melting behavior of a "bent" and a "normal" DNA duplex. Proc. Natl Acad. Sci. USA, 88, 1551-1555.
63. Pennings, S., Meersseman, G. & Bradbury, E. M. (1992). Effect of glycerol on the separation of nucleosomes and bent DNA in low ionic strength polyacrylamide gel electrophoresis. Nucl. Acids Res. 20, 6667-6672.
64. Pittz, E. P., & Timasheff, S. N. (1978). Interaction of ribonuclase A with aqueous 2-methyl-2,4-pentanediol at pH 5.8. Biochemistry, 17, 615-623.
65. Popper, K. R. (1980). The Logic of Scientific Discovery. Hutchinson, London.
66. Privé, G. G., Heinemann, U., Chandrasegaran, S.-S., Kan, L., Kopka, M. L. & Dickerson, R. E. (1987). Helix geometry hydration, and G·A mismatch in a B-DNA decamer. Science, 238, 498-504.
67. Privé, G. G., Yanagi, K. & Dickerson, R. E. (1991). The structure of the B-DNA decamer C-C-A-A-C-G-T-TG-G, and comparison with the isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-CC-T-G-G. J. Mol. Biol. 217, 177-199.
68. Quintana, J. R., Grzeskowiak, K., Yanagi, K. & Dickerson, R. E. (1992). Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J. Mol. Biol. 225, 379-395.
69. Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659-675.
70. Sprous, D., Zacharias, W., Wood, Z. A. & Harvey S. C. (1995). Dehydrating agents sharply reduce curvature in DNAs containing A tracts. Nucl. Acids Res. 23, 1816-1821.
71. Timasheff, S. N. (1993). The control of protein stability and association by weak interactions with water. Annu. Rev. Biophys. Biomol. Struct. 22, 67-97.
72. Trifonov, E. N. (1985). Curved DNA. CRC Crit. Rev. Biochem. 19, 89-106.
73. Trifonov, E. N. (1991). DNA in profile. Trends Biochem. Sci. 16, 467-470.
74. Ulanovsky L., Bodner, M., Trifonov, E. N. & Choder, M. (1986). Curved DNA: design, synthesis, and circularization. Proc. Natl Acad. Sci. USA, 83, 862-866.
75. Webster, G. D., Sanderson, M. R., Skelly, J. V., Neidle, S., Swann, P. F., Li, B. F. & Tickle, I. J. (1990). Crystal structure and sequence-dependent conformation of the A·G mis-paired oligonucleotide d(C-G-C-A-A-GC-T-G-G-C-G). Proc. Natl Acad. Sci. USA, 87, 6693-6697.
76. Wing, R. M., Drew, H. R., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature, 287, 755-758.
77. Wolfe, S. A., Ferentz, A. E., Grantcharova, V., Churchill, M. E. A. & Verdine, G. L. (1995). Modifying the helical structure of DNA by design: recruitment of an architecture-specific protein to an enforced DNA bend. Chem. Biol. 2, 213-221.
78. Wu, H.-M. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature, 308, 509-513.
79. Yanagi, K., Privé, G. G. & Dickerson, R. E. (1991). An analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 217, 201-214.
80. m2I-A-A-T-T-C-G-C-G). Biochemistry, 32, 8672-8681.
81. Yoon, C., Privé, G. G., Goodsell, D. S. & Dickerson, R. E. (1988). Structure of an alternating-B DNA helix and its relationship to A-tract DNA. Proc. Natl Acad. Sci. USA, 85, 6332-6336.
82. Young, M. A., Ravishanker, G., Beveridge, D. L. & Berman, H. M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68, 2454-2468.
83. Yuan, H., Quintana, J. R. & Dickerson, R. E. (1992). Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G. Biochemistry, 31, 8009-8021.
84. Zhurkin, V. B., Lysov, Y. P. & Ivanov, V. I. (1979). Anisotropic flexibility of DNA and the nucleosomal structure. Nucl. Acids Res. 6, 1081-1096.
85. Zinkel, S. S. & Crothers, D. M. (1987). DNA bend direction by phase sensitive detection. Nature, 328, 178-181.