1A6H

DNA QUADRUPLEX CONTAINING GCGC TETRAD, NMR, 4 STRUCTURES

Replaces:  228D

Summary for 1A6H

• Entry DOI: 10.2210/pdb1a6h/pdb
• Descriptor: DNA (5'-D(GP*CP*GP*GP*TP*TP*TP*GP*CP*GP*G)-3') (1 entity in total)
• Functional Keywords: deoxyribonucleic acid, dna quadruplex, fragile x syndrome, d(cgg) triplet repeat, gcgc tetrads, dna
• Total number of polymer chains: 2
• Total formula weight: 6842.44

Authors

Kettani, A.,Kumar, R.A.,Patel, D.J. (deposition date: 1998-02-25, release date: 1998-06-17, Last modification date: 2024-05-22)

Primary citation

Kettani, A.,Kumar, R.A.,Patel, D.J.
Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat.
J.Mol.Biol., 254:638-656, 1995

PubMed Abstract: 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.

PubMed: 7500339
DOI: 10.1006/jmbi.1995.0644

Experimental method

SOLUTION NMR