1fv8
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(New page: 200px<br /><applet load="1fv8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fv8" /> '''NMR STUDY OF AN HETEROCHIRAL HAIRPIN'''<br /...)
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Revision as of 22:16, 24 November 2007
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NMR STUDY OF AN HETEROCHIRAL HAIRPIN
Overview
We carried out a structural study of the DNA heterochiral strand d, (AGCTTATCAT(L)CGATAAGCT), -AT(L)C-, where T(L) (L thymine ) replaces T, (natural D-thymine). -AT(L)C- is a structural analog of -ATC- that belongs, to a strong topoisomerase II DNA cleavage site and which has been shown to, resolve into a hairpin structure with a stem formed by eight Waston-Crick, base-pairs and a single residue loop closed by an A.C sheared base-pair., Although - AT(L)C-, like its parent -ATC-, folds into a hairpin structure, at low and high DNA concentrations it displays a lower stability (Tm of 56, degrees C versus 58.5 degrees C). Several NMR features in -AT(L)C- account, for the disruption of the A.C pairing in the loop and a weakening of the, C.G base-pair stability at the stem-loop junction. For instance, the, exchange of the loop imino protons with solvent is accelerated compared, with the natural oligonucleotide -ATC-. The higher flexibility of the, heterochiral loop is confirmed by the results of NMR restrained molecular, dynamics. In the calculated final structures of -AT(L)C-, the T10(L), residue moves the A9 and C11 residues away, thus preventing the loop, closure through a C.A sheared base-pair and the achievement of a good, base-base or sugar-base stacking. Actually, most of the stabilizing, interactions present in -ATC- are lost in the heterochiral - AT(L)C-, explaining its weaker stability.
About this Structure
1FV8 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop., El Amri C, Mauffret O, Santamariar F, Tevanian G, Rayner S, Fermandjian S, J Biomol Struct Dyn. 2001 Dec;19(3):459-70. PMID:11790144
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