Internal mobility of the oligonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations.

In this paper we present longitudinal relaxation times, order parameters and effective correlation times for the base and sugar carbons in both strands of the oglionucleotide duplexes d(TCGCG)2 and d(CGCGCG)2, as calculated from 400 ps molecular dynamics trajectories in aqueous solution. The model-free approach (Lipari and Szabo, 1982) was used to determine the amplitudes and time scales of the internal motion. Comparisons were made with NMR relaxation measurements (Borer et al., 1994). The order parameters could acceptably be reproduced, and the effective correlation times were found to be lower than the experimental estimates. Reasonable T1 relaxation times were obtained in comparison with experiment for the nonterminal nucleosides. The T1 relaxation times were found to depend mainly on the order parameters and overall rotational correlation time.