139d: Difference between revisions
New page: left|200px<br /><applet load="139d" size="450" color="white" frame="true" align="right" spinBox="true" caption="139d" /> '''SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-... |
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[[Image:139d.jpg|left|200px]]<br /><applet load="139d" size=" | [[Image:139d.jpg|left|200px]]<br /><applet load="139d" size="350" color="white" frame="true" align="right" spinBox="true" | ||
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'''SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA'''<br /> | '''SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA'''<br /> | ||
==Overview== | ==Overview== | ||
This paper reports on the solution structure of a parallel-stranded | 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 Structure== | ==About this Structure== | ||
139D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | 139D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=139D OCA]. | ||
==Reference== | ==Reference== | ||
Solution structure of a parallel-stranded G-quadruplex DNA., Wang Y, Patel DJ, J Mol Biol. 1993 Dec 20;234(4):1171-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8263919 8263919] | Solution structure of a parallel-stranded G-quadruplex DNA., Wang Y, Patel DJ, J Mol Biol. 1993 Dec 20;234(4):1171-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8263919 8263919] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Patel, D | [[Category: Patel, D J.]] | ||
[[Category: Wang, Y.]] | [[Category: Wang, Y.]] | ||
[[Category: anti glycosidic torsion angles]] | [[Category: anti glycosidic torsion angles]] | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:38:06 2008'' | ||
Revision as of 12:38, 21 February 2008
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SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA
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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