Interaction and organization of DNA in condensed phases.

Abstract

In this research, we studied the interaction and organization of DNA through experimental and computational approaches, with a special focus on the interpretation of new and existing experimental results by full-atom molecular dynamics (MD) simulation. This research can be divided into three projects. First, in MD simulations we observed that multivalent ion mediated DNA-DNA attraction is related to the formation of ion bridges, i.e. multivalent ions which are simultaneously bound to the two opposing DNA molecules. Second, the structure of a 5 base-pair B-DNA duplex under sharp bending conditions was systematically investigated by MD simulations. The DNA duplex exhibited the formation of a kink or bubble under certain bending curvatures. Third, the counterion distribution in DNA liquid crystal was measured by small angle neutron scattering and interpreted with the help of molecular dynamics (MD) simulation. The research findings demonstrated that the molecular details of DNA molecules are sometimes essential to understand DNA interaction and organization