Molecular dynamics (MD) simulation of DNA dodecamer with 5-hydroxy-6-cytosinyl radical

Molecular dynamics (MD) simulation of DNA dodecamer d (CGCGAATTC*GCG)2 with a primary radiation damage represented by 5-hydroxy-6-cytosinyl radical (C*) in position 9 was performed with AMBER 4.0 force field with periodic boundary conditions for the solvent. The temperature, potential energy of the system, energetic contributions from groups and RMS deviation from original positions were examined throughout the course of the simulation up to 140 ps. The stabilized structure (after 100 ps) was distorted and bent near the damaged site, which is similar to that observed in the MD of DNA with thymine glycol (Miaskiewicz, K. et al (1994) Radiat. Protection Dosimetry, 52, 149-153). The results suggest that a small and local damage in DNA may cause a large and global conformational change in DNA. Water molecules form two layers at distance 2.5 A and 5.5 A around the DNA. The MD simulation is a new approach to study radiation damages in molecular level.