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Nucleic Acids Research, 1989, Vol. 17, No. 17 6883-6892
© 1989

MOLECULAR BIOLOGY

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

Burt G. Feuerstein1,2,3,*, Nagarajan Pattabiraman4,+ and Laurence J. Marton1,3

1Department of Laboratory Medicine, The University of California San Francisco, CA 94143, USA 2Department of Pediatrics, The University of California San Francisco, CA 94143, USA 3Brain Tumor Research Center of the Department of Nuerological Surgery, School of Medicine, The University of California San Francisco, CA 94143, USA 4Department of Pharmaceutical Chemistry, School of Pharmacy, The University of California San Francisco, CA 94143, USA

*To whom correspondence should be addressed at The Editorial Office, 1360 Ninth Avenue, Suite 210, San Francisco, CA 94122, USA

Received June 15, 1989. Accepted August 3, 1989.

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.

+Present address: Code 6030, Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375 USA


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