Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy

J. Černý

Institute of Biotechnology, Academy of Sciences of the Czech Republic, Laboratory of Ligand Engineering, Videnska 1083, 142 00 Prague

The role of the dispersion energy and electrostatic energy on the geometry and stability of the B-DNA helix was investigated. Both molecular dynamics simulations with empirical force field and hybrid quantum mechanical/molecular mechanics molecular dynamics simulations, where the dispersion or electrostatics term is suppressed/increased, have shown that the lack of the dispersion term leads to an increase of the vertical separation of the bases as well as to a loss of helicity, thus resulting in a ladder-like structure. A decrease of the electrostatic term produces a separation of the DNA strands.