Sequence preference for bi/bii conformations in dna: Md and crystal structure data analysis

Journal of Biomolecular Structure and Dynamics

Volumn 23, Issue 1, 2005, Pages 13-27

  Madhumalar, A ^a   Bansal, Manju ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

BII conformation; Ciystal structure analysis; DNA molecular dynamics; Phosphate backbone

Indexed keywords

DINUCLEOTIDE;

ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DATA ANALYSIS; DNA CONFORMATION; DNA SEQUENCE; DNA STRAND; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

EID: 20944449840     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2005.10507043     Document Type: Article

References (62)

1. Mandel-Gutfreund, Y., Schueler, O., and Margalit, H., 1995. J. Mol. Biol., 253:370–382.
2. Otwinowski, Z., Schevitz, R. W., Zhang, R. G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., and Sigler, P. B., 1988. Nature, 335:321–329.
3. Smith, S. A., and McLaughlin, L. W., 1997. Biochemistry, 36:6046–6058.
4. Wellenzohn, B., Flader, W., Winger, R. H., Hallbrucker, A., Mayer, E., and Liedl, K. R., 2002. Biochemistry, 41:4088–4095.
5. Beamer, L. J., and Pabo, C. O., 1992. J. Mol. Biol., 227:177–96.
6. Botuyan, M. V., Keire, D. A., Kroen, C., and Gorenstein, D. G., 1993. Biochemistry, 32:6863–6874.
7. Karslake, C., Botuyan, M. V., and Gorenstein, D. G., 1992. Biochemistry, 31:1849–1858.
8. Hartmann, B., Sullivan, M. R., and Harris, L. F., 2003. Biopolymers, 68:250–264.
9. Flader, W., Wellenzohn, B., Winger, R. H., Hallbrucker, A., Mayer, E., and Liedl, K. R., 2003. Biopolymers, 68:139–149.
10. Wenz, C., Jeltsch, A., and Pingoud, A., 1996. J. Biol. Chem., 271:5565–5573.
11. Thorogood, H., Waters, T. R., Parker, A. W., Wharton, C. W., and Connolly, B. A., 1996. Biochemistry, 35:8723–8733.
12. Varnai, P., Djuranovic, D., Lavery, R., and Hartmann, B., 2002. Nucleic Acids Res., 30:5398–5406.
13. Gupta, G., Bansal, M., and Sasisekharan, V., 1980. Proc. Natl. Acad. Sci. USA, 77:6486–6490.
14. Fratini, A. V., Kopka, M. L., Drew, H. R., and Dickerson, R. E., 1982. J. Biol. Chem., 257:14686–14707.
15. Prive, G. G., Heinemann, U., Chandrasegaran, S., Kan, L. S., Kopka, M. L., and Dickerson, R. E., 1987. Science, 238:498–504.
16. Cruse, W. B., Salisbury, S. A., Brown, T., Cosstick, R., Eckstein, F., and Kennard, O., 1986. J. Mol. Biol., 192:891–905.
17. Sklenar, V., and Bax, A., 1987. J. Am. Chem. Soc., 109:7525–7526.
18. Pichler, A., Rudisser, S., Winger, H. R., Liedl, K. R., Hallbrucker, A., and Mayer, E., 2000. Chem. Phys., 258:391–404.
19. Rudisser, S., Pichler, A., Winger, R. H., Liedl, K. R., Hallbrucker, A., and Mayer, E., 2000. J. Molecular Liquids, 86:137–149.
20. Hartmann, B., Piazzola, D., and Lavery, R., 1993. Nucleic Acids Res., 21:561–568.
21. Bertrand, H., Ha-Duong, T., Fermandjian, S., and Hartmann, B., 1998. Nucleic Acids Res., 26:1261–1267.
22. Beckers, M. L. M., and Buydens, L. M. C., 1998. J. Comput. Chem., 19:695–715.
23. Winger, R. H., Liedl, K. R., Ruisser, S., Pichler, A., Hallbrucker, A., and Mayer, E., 1998. J. Phys. Chem. B, 102:8934–8940.
24. Winger, R. H., Liedl, K. R., Pichler, A., Hallbrucker, A., and Mayer, E., 1999. J. Biomol Struct Dyn., 17:223–235.
25. Flader, W., Wellenzohn, B., Winger, R. H., Hallbrucker, A., Mayer, E., and Liedl, K. R., 2001. J. Phys. Chem. B., 105:10379–10387.
26. Mocci, F., and Saba, G., 2003. Biopolymers, 68:471–485.
27. Djuranovic, D., and Hartmann, B., 2004. Biopolymers, 73:356–368.
28. Djuranovic, D., and Hartmann, B., 2003. J. Biomol Struct Dyn., 20:771–788.
29. Tisne, C., Hantz, E., Hartmann, B., and Delepierre, M., 1998. J. Mol. Biol., 279:127–142.
30. Tisne, C., Hartmann, B., and Delepierre, M., 1999. Biochemistry, 38:3883–94.
31. Tisne, C., Delepierre, M., and Hartmann, B., 1999. J. Mol. Biol., 293:139–150.
32. Van Dam, L., Korolev, N., and Nordenskiold, L., 2002. Nucleic Acids Res., 30:419–28.
33. Wellenzohn, B., Flader, W., Winger, R. H., Hallbrucker, A., Mayer, E., and Liedl, K. R., 2001. J. Am. Chem. Soc., 123:5044–9.
34. Shah, N., Thomas, T., Shirahata, A., Sigal, L. H., and Thomas, T. J., 1999. Biochemistry, 38:14763–14774.
35. Lefebvre, A., Mauffret, O., Lescot, E., Hartmann, B., and Fermandjian, S., 1996. Biochemistry, 35:12560–12569.
36. Lefebvre, A., Mauffret, O., El Antri, S., Monnot, M., Lescot, E., and Fermandjian, S., 1995. Eur. J. Biochem., 229:445–454.
37. Derreumaux, S., Chaoui, M., Tevanian, G., and Fermandjian, S., 2001. Nucleic Acids Res., 29:2314–2326.
38. Banyay, M., and Graslund, A., 2002. J. Mol. Biol., 324:667–76.
39. Geahigan, K. B., Meints, G. A., Hatcher, M. E., Orban, J., and Drobny, G. P., 2000. Biochemistry, 39:4939–4946.
40. Djuranovic, D., Oguey, C., and Hartmann, B., 2004. J. Mol. Biol., 339:785–96.
41. Reddy, S. Y., Obika, S., and Bruice, T. C., 2003. Proc. Natl. Acad. Sci. USA, 100:15475–15480.
42. Van Dam, L., and Levitt, M. H., 2000. J. Mol. Biol., 304:541–561.
43. Shindo, H., Fujiwara, T., Akutsu, H., and Matsumoto, U., 1984. J. Mol. Biol., 174:221–229. Shimidzu
44. Gorenstein, D. G., 1992. Methods Enzymol., 211:254–86.
45. Szyperski, T., Ono, A., Fernandez, C., Iwai, H., Tate, S., Wüthrich, K., and Kainosho, M., 1997. J. Am. Chem. Soc., 119:9901–9902.
46. Hogan, M. E., and Jardetzky, O., 1979. Proc. Natl. Acad. Sci. USA, 76:6341–6345.
47. Roongta, V. A., Jones, C. R., and Gorenstein, D. G., 1990. Biochemistry, 29:5245–5258.
48. Cheatham, T. E., III, Cieplak, P., and Kollman, P. A., 1999. J. Biomol. Struct. Dyn., 16:845–862.
49. Chandrasekaran, R., and Arnott, S., 1996. J. Biomol. Struct. Dyn., 13:1015–1027.
50. Madhumalar, A., and Bansal, M., 2003. Biophys. J., 85:1805–1816.
51. Berendsen, H. J.C., Postma, J. P. M., Van Gunsteren, W. F., DiNola, A., and Haak, J. R., 1984. J. Chem. Phys., 81:3684–3690.
52. Darden, T., York, D., and Pedersen, L., 1993. J. Chem. Phys., 98:10089–10092.
53. Bhattacharyya, D., and Bansal, M., 1989. J. Biomol. Struct. Dyn., 6:635–653.
54. Bansal, M., Bhattacharyya, D., and Ravi, B., 1995. CABIOS., 11:281–287.
55. Edwards, K. J., Brown, D. G., Spink, N., Skelly, J. V., and Neidle, S., 1992. J. Mol. Biol., 226:1161–1173.
56. Yoon, C., Prive, G. G., Goodsell, D. S., and Dickerson, R. E., 1988. Proc. Nat. Acad. Sci. USA, 85:6332–6336.
57. Ponomarev, S. Y., Thayer, K. M., and Beveridge, D. L., 2004. Proc. Nat. Acad. Sci. USA, 101:14771–14775.
58. Drew, H. R., and Dickerson, R. E., 1981. J. Mol. Biol., 151:535–556.
59. Isaacs, R. J., and Spielmann, H. P., 2001. J. Mol. Biol., 311:149–160.
60. Madhumalar, A., and Bansal, M., 2003. Recent Trends in Biophysical Research Edited by:Maiti, M., (Ed.). 10–16
61. Lankas, F., Sponer, J., Langowski, J., and Cheatham, T. E., III. 2003. Biophys. J., 85:2872–2883.
62. Bevan, D. R., Li, L., Pedersen, L. G., and Darden, T. A., 2000. Biophys. J., 78:668–82.