Conformational studies of the duplex d-(CCAAAAATTTCC).d-(GGAAATTTTTGG) containing a (dA)5 tract using two-dimensional 1H-n.m.r. spectroscopy.

A variety of two-dimensional nuclear magnetic resonance (n.m.r.) techniques were utilized for structural studies of the dodecadeoxy-nucleotide duplex d-(CCAAAAATTTCC).d-(GGAAATTTTTGG). Overall, the duplex was found to adopt a conformation of the B-DNA type. Direct measurement of 1H-1H coupling constants of the deoxyribose rings and comparison of nuclear Overhauser effects (NOEs) involving characteristic intra- and inter-nucleotide proton-proton connectivities indicate that the sugar rings are all in predominantly C2'-endo/S-type conformation. The appearance of NOEs between adenine 2H and sugar l'H resonances indicates a narrowing of the minor groove at the 3' end of the (dA)n tracts. Several lines of evidence indicate that a conformational change in the DNA duplex is introduced by the (dA)5 tract, in support of the junction model for curved DNA. The results are compared with previous structural studies of the evidence for curvature in duplex DNA containing (dA)n tracts.