Molecular dynamics study and electronic structure evolution of a DNA duplex d(CCCGATCGGG)2.

The molecular dynamics simulations and electronic structure evolution of a A-DNA decamer, d(CCCGATCGGG)(2), in the presence and absence of Co(NH(3))(6) ions have been investigated. In both cases, the results of 2.5 ns MD simulation indicate a A-DNA→B-DNA transition. Ab initio DFT calculations were performed on a series of conformations representing the A→B transitions to reveal the dynamical behavior of the electronic structure of the decamer. The results suggest that the conformational parameters as well as the surrounding environment have no direct correlation with the electronic structures. Instead, the thermal fluctuations play an important role in the electronic structure of the present DNA system.