139D

SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA

Summary for 139D

• Entry DOI: 10.2210/pdb139d/pdb
• Descriptor: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3') (1 entity in total)
• Functional Keywords: dna, g-quadruplex, anti glycosidic torsion angles
• Total number of polymer chains: 4
• Total formula weight: 8737.78

Authors

Patel, D.J.,Wang, Y. (deposition date: 1993-09-28, release date: 1994-01-31, Last modification date: 2024-05-22)

Primary citation

Wang, Y.,Patel, D.J.
Solution structure of a parallel-stranded G-quadruplex DNA.
J.Mol.Biol., 234:1171-1183, 1993

PubMed Abstract: 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.

PubMed: 8263919
DOI: 10.1006/jmbi.1993.1668

Experimental method

SOLUTION NMR