Structural properties of hybrid triplex of polycation deoxyribonucleic s-methylthiourea (dnmt) strands with a complementary dna strand, probed by nanosecond molecular dynamics

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 4, 2000, Pages 629-643

  Luo, Jia ^a   Bruice, Thomas C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; POLYCATION;

ARTICLE; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA STRAND; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; TRIPLE HELIX;

EID: 0033970274     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2000.10506554     Document Type: Article

References (42)

1. Uhlmann, E., and Peyman, A., 1990. Chem. Rev., 90:543
2. Crooke, S. T., 1992. Annu. Rev. Pharmacol. Toxicol., 32:329
3. Crooke, S. T., 1993. FASEB J., 7:533
4. Cook, P. D., 1993. In Antisense Research and Applications. Edited by:Crooke, S. T., and Lebleu, B., 149–187. Boca Raton, FL:CRC.
5. Sanghvi, Y. S., and Cook, P. D., 1993. In Nucleosides and Nucleotides as Antitumor and Antiviral Agents. Edited by:Chu, C. K., and Baker, D. C., 311–324. New York):Plenum.
6. Dempcy, R. O., Almarsson, O., and Bruice, T. C., 1994. Proc. Natl. Acad. Sci. USA, 91:7864
7. Dempcy, R. O., Browne, K. A., and Bruice, T. C., 1995. J. Am. Chem. Soc., 117:6140
8. Dempcy, R. O., Browne, K. A., and Bruice, T. C., 1995. Proc. Natl. Acad. Sci. USA, 92:6097
9. Browne, K. A., Dempcy, R. O., and Bruice, T. C., 1995. Proc. Natl. Acad. Sci. USA, 92:7051
10. Dempcy, R. O., Luo, J., and Bruice, T. C., 1996. Proc. Natl. Acad. Sci. USA, 93:4326 (a)
11. Blaskó, A., Dempcy, R. O., Minyat, E. E., and Bruice, T. C., 1996. J. Am. Chem. Soc., 118:7892 (a); (b) Blaskó, A., Minyat, E.E., Dempcy, R.O. & Bruice, T.C., Biochemistry 36, 7821 (1997)
12. Arya, D. P., and Bruice, T. C., 1998. J. Am. Chem. Soc., 120:12419–12427.
13. Arya, D. P., and Bruice, T. C., 1998. J. Am. Chem. Soc., 120:6619–6620.
14. Arya, D. P., and Bruice, T. C., 1999. Proc. Natl. Acad. Sci. USA, 96:4384–4389.
15. Beveridge, D. L., Swaminathan, S., Ravishanker, G., Withka, J. M., Srinivasan, J., Prevost, C., Louise-May, S., Langley, D. R., DiCapua, F. M., and Bolton, P. H., 1993. Water and Biological Molecules Edited by:Westhof, E., 165–225. Macmillan Press. (a), In(b) Beveridge, D.L. & Ravishanker, G., Curr. Opin. Struct. Biol. 4, 246 (1994)
16. Weerasinghe, S., Smith, P. E., Mohan, V., Cheng, Y.-K., and Pettitt, B. M., 1995. J. Am. Chem. Soc., 117:2147 (a); (b) Cheatham, T.E. III and Kollman, P.A. J. Mol. Biol. 259, 434 (1996); (c) Cheatham, T.E. III and Kollman, P.A. J. Am. Chem. Soc. 119, 4805 (1997)
17. Luo, J., and Bruice, T. C., 1997. J. Am. Chem. Soc., 119:6693–6701. (b) Luo, J & Bruice, T.C., J. Am. Chem. Soc. 120, 1115–1123 (1998)
18. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983. J. Comput. Chem., 4:187 (a); (b) MacKerell, Jr. A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. J. Am. Chem. Soc. 117, 11946 (1995); (c) Raghunathan, G., Miles, H.T. & Sasisekharan, V. Biochemistry, 32, 455 (1993); (d) Jorgensen, W.L., Chandrasekhar, J., & Madura, J.D., J. Comput. Chem. 14, 89 (1983)
19. Harvey, S. C., Tan, RKZ, and Cheatham, T. E., 1998. J. Comput. Chem., 19:726
20. York, D. M., Darden, T. A., and Petersen, L. G., 1993. J. Chem. Phys., 99:8345 (a); (b) Schreiber, H. and Steinhauser, O. Biochemistry 31, 5856 (1992); (c) Steinbach, P.J. and Brooks, B.R., J. Comput. Chem. 15, 667 (1994); (d) De Leeuw, S. W., Perram, J.W., and Smith, E.R., Proc. R. Soc. London, Ser. A 373, 27 (1980); (e) Ewald, P. Ann. Phys. (Leipzig) 64 253264 (1921)
21. VanGunsteren, W. F., and Berendsen, H., 1977. J. C. Mol. Phys., 34:1311
22. Luo, J., Sarma, M. H., Gupta, G., and Sarma, R. H., 1991. International J. Quantum Chemistry:Quantam Biology Symposium, 18:213
23. Nelson, H. C.M., Finch, J. T., Luisi, B. F., and Klug, A., 1987. Nature, 330:221 (a); (b) Coll, M., Frederick, C.A. Wang, H.-J. and Rich, A., Proc. Natl. Acad. Sci. USA, 84, 8385 (1987)
24. Conner, B. N., Takano, T., Tanaka, S., Itakura, K., and Dickerson, R. E., 1982. Nature, 295:294 (a); (b) Dickerson, R.E., Scientific American 249 (6), 94 (1983); (c) Minor groove width was defined (24a, b) as the centered atom distance less the van de Waals radius van de Waals radius is taken as 5.8Å (24a, b) for the two centered atoms, phosphate-P and guanidinium-C. (d) Prive, G.G., Yanagi, K. and Dickerson, R.E., J. Mol. Biol. 217, 177 (1991); (e) Prive, G.G. and Dickerson, R.E., et. al., in Structure & Expression, Vol. 2, DNA & Its Drug Complexes, Eds., M.H. Sarma and R.H. Sarma, Adenine Press, (1988)
25. Liepinsh, E., Otting, G., and Wuthrich, K., 1992. Nucleic Acids Research, 25 (24):6549 (a); (b) Otting, G. and Liepinsh, E. Acc. Chem. Res. 28, 171 (1995); (c) Sigler, P.B. “Proceedings of the Robert A. Welch Foundation 37th Conference on Chemical research”, Houston (Chapter 5) (1993)
26. Saenger, W., 1983. “Principles of Nucleic Acid Structure”. New York:Springer Verlag. (a); (b) McCammon, J.A. and Harvey, S.C., “Dynamics of Proteins and Nucleic Acids”, Cambridge University, Cambridge and New York, (1988); (c) Harvey, C.H. and Prabhakaran, M., J. Am. Chem. Soc, 108, 20, 6128 (1986)
27. Levitt, M., and Warshel, A., 1978. J. Amer. Chem. Soc., 100:2607–2613.
28. Sarma, R. H., 1988. J. Biomol. Struct. & Dyn. Vol., 6 (3) (a) 391; (b) Lavery, R. and Sklenar, H., J. Biomol. Struct. & Dyn. Vol. 6, 4, 655 (1989)
29. Liberles, D. A., and Dervan, P. B., 1996. Proc. Natl. Acad. Sci. USA, 93:9510
30. Thompson, J. F., and Landy, A., 1988. Nucleic Acids Res., 16:9687
31. Goodman, S. D., Nicholson, S. C., and Nash, H. A., 1992. Proc. Natl. Acad. Sci. USA, 89:11910
32. Hallet, B., Rezsohazy, R., Mahillon, J., and Delcour, J., 1994. Mol. Microbiol., 14:131
33. Goryshin, I. Y., Kil, Y. V., and Reznikoff, W. S., 1994. Proc. Natl. Acad. Sci. USA, 91:10834
34. Henriquez, V., Milisavljevic, V., Kahn, J. D., and Gennaro, M. L., 1993. Gene, 134:93
35. Nakajima, M., Sheikh, Q. I., Yamaoka, K., Yui, Y., Kajiwara, S., and Shishido, K., 1993. Mol. Gen. Genet., 237:1
36. Muller, H. P., and Varmus, H. E., 1994. EMBO J., 13:4704
37. Milot, E., Belmaaza, A., Rassart, E., and Chartrand, P., 1994. Virlogy, 201:408
38. Natesan, S., and Gilman, M. Z., 1993. Genes Dev., 7:2497
39. Meacock, S., Pescini-Gobert, R., DeLamarter, J. F., and vanHuijsduijen, R. H., 1994. J. Biol. Chem., 269:31756
40. Kim, J., Klooster, S., and Shapiro, D. J., 1995. J. Biol. Chem., 270:1282
41. Perez-Martin, J., Rojo, F., and DeLorenzo, V., 1994. Microbiol. Rev., 58:268
42. Strauss, J. K., Roberts, C., Nelson, M. G., Switzer, C., and Maher, L. J., III. 1996. Proc. Natl. Acad. Sci. USA, 93:9515