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

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

2011-07-20

arxiv.org/abs/1107.3921v1

Biology

Quantitative Biology

Biomolecules

6 pages, 3 figures

Scientific paper

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

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