Structural and dynamic studies of a non-self-complementary dodecamer DNA duplex

Abstract

A non-self-complementary dodecamer duplex d(CCTAAATTTGCC).d(GGCAAATTTAGG) has been investigated in solution by high resolution 1H NMR. Almost complete resonance assignment of both non-exchangeable and exchangeable protons, has been achieved. The duplex is essentially B-type, with distortions apparent at the AT and TA steps. These distortions and their affects on dynamics have been probed by the measurement of base-pair lifetimes, and observation of water of hydration. Base-pair opening rates were derived from measurements of T1's and effects on linewidths of the T and G imino protons on addition of an exchange catalyst. Our results are generally in line with observations reported for other systems, but we see only a slight drop in the A.T base-pair lifetime on moving out from the central region. This observation is reinforced by the detection of DNA-water nOe's for residues distributed throughout the dodecamer sequence.