STRUCTURAL AND DYNAMIC STUDIES OF A NON-SELF-COMPLEMENTARY DODECAMER DNA DUPLEX

A non-self-complementary dodecamer duplex d(CCTAAATTTGCC).d(GGCAAATTTA GG) has been investigated in solution by high resolution H-1 NMR. Almo st complete resonance assignment of both non-exchangeable and exchange able protons, has been achieved. The duplex is essentially B-type, wit h distortions apparent at the AT and TA steps. These distortions and t heir affects on dynamics have been probed by the measurement of base-p air lifetimes, and observation of water of hydration. Base-pair openin g rates were derived from measurements of T1's and effects on linewidt hs of the T and G imino protons on addition of an exchange catalyst. O ur 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 o n moving out from the central region. This observation is reinforced b y the detection of DNA-water nOe's for residues distributed throughout the dodecamer sequence.