A Study of the Hydrogen-bonded Network Around the Left-handed and Right-handed DNA in an Ionic Solution

Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ∼1.4 A rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 A around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R 6 /R 5 ).