Structural and dynamic studies of the central segments in the self-complementary decamer DNA duplexes d(ACGTATACGT)(2) and d(ACGTTAACGT)(2)

Abstract

The structures of the self-complementary decamer duplexes, d(ACGTATACGT)(2) (TATA-duplex) and d(ACGTTAACGT)(2), (TTAA-duplex) has been obtained in solution by proton NMR spectroscopy and restrained molecular dynamics. The duplexes are essentially B-type, with distortions apparent at the TATA and TTAA steps, These distortions and their effects on dynamics have been investigated by the measurement of imino proton exchange time of the base-pairs, The unusual opening kinetics of central A.T base-pairs could be correlated to the abnormal structural properties of the corresponding sequences.