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 Å 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 (R6/R5).
Bibliographical noteFunding Information:
This work was supported in part by the Korea Research Center for Theoretical Physics and Chemistry. N.S. Kang would like to thank the Department of Chemistry of Soong Sil University for the financial support of the BK program.
All Science Journal Classification (ASJC) codes
- Information Systems
- Modelling and Simulation
- Chemical Engineering(all)
- Materials Science(all)
- Condensed Matter Physics