Molecular Dynamics Simulations Find That 3' Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition

摘要

We present unrestrained molecular dynamics studies on a deoxyribose dodecamer duplex d(CGCGAAT- TCGCG)_2 and its phosphoramidate (replacing o3' by NH) analog using particle mesh Ewald electrostatics and the Cornell et al. force field. The simulations were carried out beginning in both canonical A and B forms, which differ in RMS position by～6.5 A deg.