TY - JOUR
T1 - Molecular dynamics of spermine-DNA 1nteractioas sequence specificity and DNA bending for a simple ligand
AU - Feuerstein, Burt G.
AU - Pattabiraman, Nagarajan
AU - Marton, Laurence J.
N1 - Funding Information:
We thank Robert Langridge for the use of the MIDAS program and the facilities of the Computer Graphics Laboratory, UCSF (supported in part by NIH Grant RR-1081), the San Diego Supercomputer Center for granting us time on the Cray XMP, Peter Kollman for use of the AMBER program and for comments on the manuscript, and Richard H. Shafer, Hirak S. Basu and Neil Buckley for comments on the manuscript. Supported in part by NIH Grants CA-41757 (B.G.F.), National Cooperative Drug Discovery Group Grant CA-37606 (L.J.M.), and Program Project Grant CA-13525 (L.J.M.). The Computer Graphics Laboratory is supported in part by NIH Grant RR-1081.
PY - 1989/9/11
Y1 - 1989/9/11
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/17.17.6883
DO - 10.1093/nar/17.17.6883
M3 - Article
C2 - 2780313
AN - SCOPUS:0024451743
SN - 0305-1048
VL - 17
SP - 6883
EP - 6892
JO - Nucleic acids research
JF - Nucleic acids research
IS - 17
ER -