139d
SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA
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OverviewOverview
This paper reports on the solution structure of a parallel-stranded, G-quadruplex formed by the Tetrahymena telomeric sequence d(T-T-G-G-G-G-T), whose NMR parameters in potassium cation containing solution were, previously published from our laboratory. The structure was determined by, combining a quantitative analysis of the NMR data with molecular dynamics, calculations including relaxation matrix refinement. The combined, NMR-computational approach yielded a set of seven distance-refined, structures with pairwise RMSDs ranging from 0.66 to 1.30 A for the central, G-G-G-G tetranucleotide segment. Four of the seven structures were refined, further using complete relaxation-matrix calculations to yield solution, structures with pairwise RMSDs ranging from 0.64 to 1.04 A for the same, tetranucleotide segment. The R-factors also decreased on proceeding from, the distance-refined to relaxation matrix-refined structures. The four, strands of the G-quadruplex are aligned in parallel and are related by a, 4-fold symmetry axis coincident with the helix axis. Individual guanines, from each strand form planar G.G.G.G tetrad arrangements with each tetrad, stabilized by eight hydrogen bonds involving the Watson-Crick and, Hoogsteen edges of the guanine bases. All guanines adopt anti glycosidic, torsion angles and S type sugar puckers in this right-handed, parallel-stranded G-quadruplex structure. The four G.G.G.G tetrad planes, stack on each other with minimal overlap of adjacent guanine base planes, within individual strands. The thymine residues are under-defined in the, solution structure of the d(T-T-G-G-G-G-T) G-quadruplex and sample amongst, multiple conformations in solution.
About this StructureAbout this Structure
139D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Solution structure of a parallel-stranded G-quadruplex DNA., Wang Y, Patel DJ, J Mol Biol. 1993 Dec 20;234(4):1171-83. PMID:8263919
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