Molecular dynamics of spermine-DNA 1nteractioas sequence specificity and DNA bending for a simple ligand

Burt G. Feuerstein, Nagarajan Pattabiraman, Laurence J. Marton

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

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 the 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 nonspecifically 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.

Original languageEnglish (US)
Pages (from-to)6883-6892
Number of pages10
JournalNucleic acids research
Volume17
Issue number17
DOIs
StatePublished - Sep 11 1989
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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