Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Theoretical Calculations for DNA-drug Complexes

We present the results from the continuum solvent analysis of the molecular dynamics trajectories applied to the dna-drug complexes in order to determine binding free energies. Four different complexes of the DNA fragments have been studied with : actinomycin, its phenoxazine ring system, acridine and netropsin. Besides the DNA-drug binding free energies, the intrastrand interaction free energies, dna deformation and base pairs unstacking energetical effects have been determined. The correct sequence dependent unstacking energies have been obtained for CG vs GC and TA vs AT due to intercalation of the drug.

Piotr Cieplak, Peter A.Kollman

Department of Chemistry, University of Warsaw, Pasteur 1, 02-093 Warsaw, Poland and Department of Pharm.Chem. University of California, San Francisco, USA.
Email: cieplak@tiger.chem.uw.edu.pl