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. 1989 Sep 12;17(17):6883–6892. doi: 10.1093/nar/17.17.6883

Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand.

B G Feuerstein 1, N Pattabiraman 1, L J Marton 1
PMCID: PMC318419  PMID: 2780313

Abstract

We used molecular dynamics to model interactions between the physiologically important polyamine spermine and two B-DNA oligomers, the homopolymer (dG)10-(dC)10 and the heteropolymer (dGdC)5-(dGdC)5. Water and counterions were included in the simulation. Starting coordinates for spermine-DNA complexes were structures obtained by molecular mechanics modeling of spermine with the two oligomers; in these models, spermine binding induced a bend in the heteropolymer but not in the homopolymer. During approximately 40 psec of molecular dynamics simulation, spermine moves away from the floor of the major groove and interacts nospecifically with d(G)10-d(C)10. In contrast, a spermine-induced bend in the helix of (dGdC)5-(dGdC)5 is maintained throughout the simulation and spermine remains closely associated with the major groove. These results provide further evidence that the binding of spermine to nucleic acids can be sequence specific and that bending of alternating purine-pyrimidine sequences may be a physiologically important result of spermine binding.

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Selected References

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

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