SOLUTION STRUCTURE OF A DNA QUADRUPLEX CONTAINING THE FRAGILE-X SYNDROME TRIPLET REPEAT

Both X-ray and NMR structural studies have defined the polymorphic of G-quadruplexes generated through mutual stacking of G . G . G . G tetrads by guanine rich telomeric sequences. Recently the fragile X syndrome d(C-G-G)(n) triplet nucleotide repeat has been shown to form a stable quadruplex of undefined structure in monovalent cation solution. We have undertaken a structural characterization of the d(G-C-G-G-T-3-G-C-G-G) undecanucleotide to elucidate the structural alignments associated with quadruplex formation by this oligomer which contains sequence elements associated with the fragile X syndrome triplet repeat. d(G-C-G-G-T-3-G-C-G-G) in Na+ cation solution forms a quadruplex through dimerization of two symmetry related hairpins with the lateral connecting T-3 loops positioned at opposite ends of the quadruplex. This novel NMR-molecular dynamics based solution structure contains internal G . C . G . C tetrads sandwiched between terminal G . G . G . G tetrads. Watson-Crick G . C base-pairs within individual hairpins dimerize through their major groove edges using bifurcated hydrogen bonds to form internal G(anti). C(anti). G(anti). C(anti) tetrads. Adjacent strands are anti-parallel to each other around the symmetric G-quadruplex which contains two distinct narrow and two symmetric wide grooves. By contrast, the terminal G-tetrads adopt G(syn). G(anti). G(syn). G(anti) alignments. The structure of the d(G-C-G-G-T-3-G-C-G-G) quadruplex with its multi-layer arrangement of G . G . G . G and G . C . G . C tetrads greatly expands on our current knowledge of quadruplex folding topologies. Our results establish the pairing alignments that can be potentially utilized by the fragile X syndrome triplet repeat to form quadruplex structures through dimerization of hairpin stems. The formation of novel G . C . G . C tetrads through dimerization of Watson-Crick G . C base-pairs is directly relevant to the potential pairing alignments of helical sterns in genetic recombination. (C) 1995 Academic Press Limited