1a8w: Difference between revisions

Revision as of 12:42, 21 February 2008

A K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C REPEATS, NMR, 8 STRUCTURES

OverviewOverview

We have identified a unique structural transition (in slow exchange on the NMR time scale) in the tertiary fold of the d(G-G-G-C-T4-G-G-G-C) quadruplex on proceeding from Na+ to K+ as counterion in aqueous solution. Both monovalent cation-dependent conformations exhibit certain common structural features, which include head-to-tail dimerization of two symmetry-related stem-hairpin loops, adjacent strands which are antiparallel to each other and adjacent stacked G(syn).G(anti). G(syn).G(anti) tetrads in the central core of the quadruplexes. The Na and K cation stabilized structures of the d(G-G-G-C-T4-G-G-G-C) quadruplexes differ in the conformations of the T-T-T-T loops, the relative alignment of G.C base-pairs positioned opposite each other through their major groove edges and potentially in the number of monovalent cation binding sites. We have identified potential K cation binding cavities within the symmetry-related T-T-T-G segments, suggesting the potential for two additional monovalent cation binding sites in the K cation-stabilized quadruplex relative to its Na cation-stabilized counterpart. Modeling studies suggest that the major groove edges of guanine residues in Watson-Crick G.C base-pairs could potentially be bridged by coordinated K cations in the d(G-G-G-C-T4-G-G-G-C) quadruplex in KCl solution in contrast to formation of G.C.G.C tetrads for the corresponding quadruplex in NaCl solution. Our results defining the molecular basis of a Na to K cation-dependent conformational switch in the loop spanning segment of the d(G-G-G-C-T4-G-G-G-C) quadruplex may have relevance to recent observations that specific K cation coordinated loop conformations within quadruplexes exhibit inhibitory activity against HIV integrase.

About this StructureAbout this Structure

1A8W is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats., Bouaziz S, Kettani A, Patel DJ, J Mol Biol. 1998 Sep 25;282(3):637-52. PMID:9737927

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 '''A K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C REPEATS, NMR, 8 STRUCTURES'''<br />
 ==Overview==
-We have identified a unique structural transition (in slow exchange on the, NMR time scale) in the tertiary fold of the d(G-G-G-C-T4-G-G-G-C), quadruplex on proceeding from Na+ to K+ as counterion in aqueous solution., Both monovalent cation-dependent conformations exhibit certain common, structural features, which include head-to-tail dimerization of two, symmetry-related stem-hairpin loops, adjacent strands which are, antiparallel to each other and adjacent stacked G(syn).G(anti)., G(syn).G(anti) tetrads in the central core of the quadruplexes. The Na and, K cation stabilized structures of the d(G-G-G-C-T4-G-G-G-C) quadruplexes, differ in the conformations of the T-T-T-T loops, the relative alignment, of G.C base-pairs positioned opposite each other through their major, groove edges and potentially in the number of monovalent cation binding, sites. We have identified potential K cation binding cavities within the, symmetry-related T-T-T-G segments, suggesting the potential for two, additional monovalent cation binding sites in the K cation-stabilized, quadruplex relative to its Na cation-stabilized counterpart. Modeling, studies suggest that the major groove edges of guanine residues in, Watson-Crick G.C base-pairs could potentially be bridged by coordinated K, cations in the d(G-G-G-C-T4-G-G-G-C) quadruplex in KCl solution in, contrast to formation of G.C.G.C tetrads for the corresponding quadruplex, in NaCl solution. Our results defining the molecular basis of a Na to K, cation-dependent conformational switch in the loop spanning segment of the, d(G-G-G-C-T4-G-G-G-C) quadruplex may have relevance to recent observations, that specific K cation coordinated loop conformations within quadruplexes, exhibit inhibitory activity against HIV integrase.
+We have identified a unique structural transition (in slow exchange on the NMR time scale) in the tertiary fold of the d(G-G-G-C-T4-G-G-G-C) quadruplex on proceeding from Na+ to K+ as counterion in aqueous solution. Both monovalent cation-dependent conformations exhibit certain common structural features, which include head-to-tail dimerization of two symmetry-related stem-hairpin loops, adjacent strands which are antiparallel to each other and adjacent stacked G(syn).G(anti). G(syn).G(anti) tetrads in the central core of the quadruplexes. The Na and K cation stabilized structures of the d(G-G-G-C-T4-G-G-G-C) quadruplexes differ in the conformations of the T-T-T-T loops, the relative alignment of G.C base-pairs positioned opposite each other through their major groove edges and potentially in the number of monovalent cation binding sites. We have identified potential K cation binding cavities within the symmetry-related T-T-T-G segments, suggesting the potential for two additional monovalent cation binding sites in the K cation-stabilized quadruplex relative to its Na cation-stabilized counterpart. Modeling studies suggest that the major groove edges of guanine residues in Watson-Crick G.C base-pairs could potentially be bridged by coordinated K cations in the d(G-G-G-C-T4-G-G-G-C) quadruplex in KCl solution in contrast to formation of G.C.G.C tetrads for the corresponding quadruplex in NaCl solution. Our results defining the molecular basis of a Na to K cation-dependent conformational switch in the loop spanning segment of the d(G-G-G-C-T4-G-G-G-C) quadruplex may have relevance to recent observations that specific K cation coordinated loop conformations within quadruplexes exhibit inhibitory activity against HIV integrase.
 ==About this Structure==
-A8W 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1A8W OCA].
+A8W 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=1A8W OCA].
 ==Reference==
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 [[Category: Bouaziz, S.]]
 [[Category: Kettani, A.]]
-[[Category: Patel, D.J.]]
+[[Category: Patel, D J.]]
 [[Category: cation dependent conformational transitions]]
 [[Category: deoxyribonucleic acid]]
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 [[Category: monovalent]]
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