Structural and dynamic studies of a non-selfcomplementary 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 nonexchangeable 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 th 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 basepair 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. © 1993 Oxford University Press.