1a6h

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DNA QUADRUPLEX CONTAINING GCGC TETRAD, NMR, 4 STRUCTURES

Overview

Both X-ray and NMR structural studies have defined the polymorphic nature, 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-T3-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-T3-G-C-G-G) in Na+ cation solution forms a quadruplex through, dimerization of two symmetry related hairpins with the lateral connecting, T3 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-T3-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 stems in genetic recombination.

About this Structure

1A6H is a Protein complex structure of sequences from [1]. This structure superseeds the now removed PDB entry 228D. Full crystallographic information is available from OCA.

Reference

Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat., Kettani A, Kumar RA, Patel DJ, J Mol Biol. 1995 Dec 8;254(4):638-56. PMID:7500339

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