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The 3'-monofunctional adduct of cisplatin and d(CTCTG*G*TCTC)2 duplex DNA insolvent with explicit counter ions and water molecules were subjected to MD-simulation with AMBER force field on a nanosecond time scale. In order tosimulate the closure of the bond between the Pt and 5'-guanine-N7 atoms, theforces acting between them were gradually increased during MD. After 500-800 psthe transformation of the mono-adduct (straight DNA with the cisplatin residuelinked to one guanine-N7) to the bus-adduct (bent DNA where Pt atom isconnected through the N7 atoms of neighboring guanines) was observed. A cavitybetween palatinate guanines is formed and filled with solvent molecules. Therapid inclination of the center base pairs initiates a slow transition of thewhole molecule from the linear to the bent conformation. After about 1000-1300ps a stable structure was reached, which is very similar to the one describedexperimentally. The attractive force between the Pt- atom and the N7 of thesecond guanine plays the main role in the large conformational changes inducedby formation of the adduct-adduct. X-N-Pt-N-torsions accelerate the bending buta torsion force constant greater than 0.2 Kcal/mol lead to the breaking of theH-bonds within the base pairs. The present study is the first dynamicalsimulation that demonstrates in real time scale such a large conformationalperturbation of DNA.

Molecular Dynamics Studies of Changes in the DNA- Structure as Result of Interactions with Cisplatin