Dimeric DNA quadruplex containing major groove-aligned A center dot T center dot A center dot T and G center dot C center dot G center dot C tetrads stabilized by inter-subunit Watson-Crick A center dot T and G center dot C pairs

We report on an NMR study of unlabeled and uniformly C-13,N-15-labeled d(GA GCAGGT) sequence in I M NaCl solution, conditions under which it forms a he ad-to-head dimeric quadruplex containing sequentially stacked G . C . G . C , G . G . G . G and A . T . A . T tetrads. We have identified, for the firs t time, a slipped A - T - A - T tetrad alignment, involving recognition of Watson-Crick A - T pairs along the major groove edges of opposing adenine r esidues. Strikingly, both Watson-Crick G-C and A-T pairings within the dire ct G.C.G.C and slipped A.T.A.T tetrads, respectively, occur between rather than within hairpin subunits of the dimeric d(GAGCAGGT) quadruplex. The hai rpin turns in the head-to-head dimeric quadruplex involve single adenine re sidues and adds to our knowledge of chain reversal involving edgewise loops in DNA quadruplexes. Our structural studies, together with those from othe r laboratories, definitively establish that DNA quadruplex formation is not restricted to G, repeat sequences, with their characteristic stacked unifo rm G.G.G.G tetrad architectures. Rather, the quadruplex fold is a more vers atile and robust architecture, accessible to a range of mixed sequences, wi th the potential to facilitate G-C-G,C and A-T-A-T tetrad through major and minor groove alignment, in addition to G - G - G - G tetrad formation. The definitive experimental identification of such major groove-aligned mixed A - T. A - T and G - C - G - C tetrads within a quadruplex scaffold, has im portant implications for the potential alignment of duplex segments during homologous recombination. (C) 2001 Academic Press.