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. 1990 Mar 11;18(5):1271–1282. doi: 10.1093/nar/18.5.1271

Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding.

B G Feuerstein 1, N Pattabiraman 1, L J Marton 1
PMCID: PMC330444  PMID: 2320418

Abstract

We used energy minimization of a molecular mechanical force field to evaluate spermine interactions with B-form DNA oligomers with either alternating purine/pyrimidine or homopolymeric sequences. Four different positions for spermine docking--within, along, and bridging the minor groove and bridging the major groove--were assessed for each sequence. Interaction at the major groove of alternating purine/pyrimidine sequences appears to be the most favorable of all models assessed, and are associated with significant bending of DNA. Interactions at the major groove of homopolymers were less favorable than those of heteropolymers and showed little or no bending. Interactions with the minor groove were most favorable for spermine positioned near the base of the groove, and became less favorable as spermine was moved toward the top of the groove. Association along the phosphate backbone alone was the least favorable of the interactions.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arnott S., Hukins D. W. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504–1509. doi: 10.1016/0006-291X(72)90243-4. [DOI] [PubMed] [Google Scholar]
  2. Bash P. A., Pattabiraman N., Huang C., Ferrin T. E., Langridge R. Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Science. 1983 Dec 23;222(4630):1325–1327. doi: 10.1126/science.222.4630.1325. [DOI] [PubMed] [Google Scholar]
  3. Basu H. S., Feuerstein B. G., Zarling D. A., Shafer R. H., Marton L. J. Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies. J Biomol Struct Dyn. 1988 Oct;6(2):299–309. doi: 10.1080/07391102.1988.10507714. [DOI] [PubMed] [Google Scholar]
  4. Basu H. S., Shafer R. H., Marton L. J. A stopped-flow H-D exchange kinetic study of spermine-polynucleotide interactions. Nucleic Acids Res. 1987 Jul 24;15(14):5873–5886. doi: 10.1093/nar/15.14.5873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Behe M., Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623. doi: 10.1073/pnas.78.3.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chattoraj D. K., Gosule L. C., Schellman A. DNA condensation with polyamines. II. Electron microscopic studies. J Mol Biol. 1978 May 25;121(3):327–337. doi: 10.1016/0022-2836(78)90367-4. [DOI] [PubMed] [Google Scholar]
  7. Chattoraj D. K., Gosule L. C., Schellman A. DNA condensation with polyamines. II. Electron microscopic studies. J Mol Biol. 1978 May 25;121(3):327–337. doi: 10.1016/0022-2836(78)90367-4. [DOI] [PubMed] [Google Scholar]
  8. Drew H. R., Dickerson R. E. Structure of a B-DNA dodecamer. III. Geometry of hydration. J Mol Biol. 1981 Sep 25;151(3):535–556. doi: 10.1016/0022-2836(81)90009-7. [DOI] [PubMed] [Google Scholar]
  9. Drew H. R., Travers A. A. DNA bending and its relation to nucleosome positioning. J Mol Biol. 1985 Dec 20;186(4):773–790. doi: 10.1016/0022-2836(85)90396-1. [DOI] [PubMed] [Google Scholar]
  10. Feuerstein B. G., Pattabiraman N., Marton L. J. Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand. Nucleic Acids Res. 1989 Sep 12;17(17):6883–6892. doi: 10.1093/nar/17.17.6883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Feuerstein B. G., Pattabiraman N., Marton L. J. Spermine-DNA interactions: a theoretical study. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5948–5952. doi: 10.1073/pnas.83.16.5948. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fratini A. V., Kopka M. L., Drew H. R., Dickerson R. E. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem. 1982 Dec 25;257(24):14686–14707. [PubMed] [Google Scholar]
  13. Garner M. M., Felsenfeld G. Effect of Z-DNA on nucleosome placement. J Mol Biol. 1987 Aug 5;196(3):581–590. doi: 10.1016/0022-2836(87)90034-9. [DOI] [PubMed] [Google Scholar]
  14. Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 1988 Jun 30;333(6176):824–829. doi: 10.1038/333824a0. [DOI] [PubMed] [Google Scholar]
  15. Gosule L. C., Schellman J. A. Compact form of DNA induced by spermidine. Nature. 1976 Jan 29;259(5541):333–335. doi: 10.1038/259333a0. [DOI] [PubMed] [Google Scholar]
  16. IITAKA Y., HUSE Y. THE CRYSTAL STRUCTURE OF SPERMINE PHOSPHATE HEXAHYDRATE. Acta Crystallogr. 1965 Jan 10;18:110–121. doi: 10.1107/s0365110x65000191. [DOI] [PubMed] [Google Scholar]
  17. Laundon C. H., Griffith J. D. Cationic metals promote sequence-directed DNA bending. Biochemistry. 1987 Jun 30;26(13):3759–3762. doi: 10.1021/bi00387a003. [DOI] [PubMed] [Google Scholar]
  18. Marquet R., Houssier C. Different binding modes of spermine to A-T and G-C base pairs modulate the bending and stiffening of the DNA double helix. J Biomol Struct Dyn. 1988 Oct;6(2):235–246. doi: 10.1080/07391102.1988.10507710. [DOI] [PubMed] [Google Scholar]
  19. Marquet R., Wyart A., Houssier C. Influence of DNA length on spermine-induced condensation. Importance of the bending and stiffening of DNA. Biochim Biophys Acta. 1987 Aug 25;909(3):165–172. doi: 10.1016/0167-4781(87)90074-1. [DOI] [PubMed] [Google Scholar]
  20. Marx K. A., Ruben G. C. Studies of DNA organization in hydrated spermidine-condensed DNA toruses and spermidine-DNA fibres. J Biomol Struct Dyn. 1984 Mar;1(5):1109–1132. doi: 10.1080/07391102.1984.10507507. [DOI] [PubMed] [Google Scholar]
  21. Minyat E. E., Ivanov V. I., Kritzyn A. M., Minchenkova L. E., Schyolkina A. K. Spermine and spermidine-induced B to A transition of DNA in solution. J Mol Biol. 1979 Mar 5;128(3):397–409. doi: 10.1016/0022-2836(79)90094-9. [DOI] [PubMed] [Google Scholar]
  22. Pegg A. E. Recent advances in the biochemistry of polyamines in eukaryotes. Biochem J. 1986 Mar 1;234(2):249–262. doi: 10.1042/bj2340249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Quigley G. J., Teeter M. M., Rich A. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc Natl Acad Sci U S A. 1978 Jan;75(1):64–68. doi: 10.1073/pnas.75.1.64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rich A., Nordheim A., Wang A. H. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791–846. doi: 10.1146/annurev.bi.53.070184.004043. [DOI] [PubMed] [Google Scholar]
  25. Richmond T. J., Finch J. T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature. 1984 Oct 11;311(5986):532–537. doi: 10.1038/311532a0. [DOI] [PubMed] [Google Scholar]
  26. Satchwell S. C., Drew H. R., Travers A. A. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986 Oct 20;191(4):659–675. doi: 10.1016/0022-2836(86)90452-3. [DOI] [PubMed] [Google Scholar]
  27. Sen D., Crothers D. M. Condensation of chromatin: role of multivalent cations. Biochemistry. 1986 Apr 8;25(7):1495–1503. doi: 10.1021/bi00355a004. [DOI] [PubMed] [Google Scholar]
  28. Suwalsky M., Traub W., Shmueli U., Subirana J. A. An X-ray study of the interaction of DNA with spermine. J Mol Biol. 1969 Jun 14;42(2):363–373. doi: 10.1016/0022-2836(69)90049-7. [DOI] [PubMed] [Google Scholar]
  29. TABOR H. The protective effect of spermine and other polyamines against heat denaturation of deoxyribonucleic acid. Biochemistry. 1962 May 25;1:496–501. doi: 10.1021/bi00909a021. [DOI] [PubMed] [Google Scholar]
  30. Tabor C. W., Tabor H. Polyamines. Annu Rev Biochem. 1984;53:749–790. doi: 10.1146/annurev.bi.53.070184.003533. [DOI] [PubMed] [Google Scholar]
  31. Thomas T. J., Messner R. P. Structural specificity of polyamines in left-handed Z-DNA formation. Immunological and spectroscopic studies. J Mol Biol. 1988 May 20;201(2):463–467. doi: 10.1016/0022-2836(88)90155-6. [DOI] [PubMed] [Google Scholar]
  32. Vertino P. M., Bergeron R. J., Cavanaugh P. F., Jr, Porter C. W. Structural determinants of spermidine-DNA interactions. Biopolymers. 1987 May;26(5):691–703. doi: 10.1002/bip.360260510. [DOI] [PubMed] [Google Scholar]
  33. Zakrzewska K., Pullman B. Spermine-nucleic acid interactions: a theoretical study. Biopolymers. 1986 Mar;25(3):375–392. doi: 10.1002/bip.360250302. [DOI] [PubMed] [Google Scholar]
  34. Zhurkin V. B., Lysov Y. P., Ivanov V. I. Interaction of spermine with different forms of DNA. A conformational study. Biopolymers. 1980 Aug;19(8):1415–1434. doi: 10.1002/bip.1980.360190802. [DOI] [PubMed] [Google Scholar]

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