286d
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(New page: 200px<br /><applet load="286d" size="350" color="white" frame="true" align="right" spinBox="true" caption="286d, resolution 2.500Å" /> '''X-RAY AND SOLUTION ...)
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Revision as of 15:50, 29 January 2008
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X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE
Overview
DNA containing short periodic stretches of adenine residues (known as, A-tracts), which are aligned with the helical repeat, exhibit a pronounced, macroscopic curvature. This property is thought to arise from the, cumulative effects of a distinctive structure of the A-tract. It has also, been observed by gel electrophoresis that macroscopic curvature is largely, retained when inosine bases are introduced singly into A-tracts but, decreases abruptly for pure I-tracts. The structural basis of this effect, is unknown. Here we describe X-ray and gel electrophoretic analyses of, several oligomers incorporating adenine or inosine bases or both. We find, that macroscopic curvature is correlated with a distinctive base-stacking, geometry characterized by propeller twisting of the base-pairs. Regions of, alternating adenine and inosine bases display large propeller twisting, comparable to that of pure A-tracts, whereas the values observed for pure, I-tracts are significantly smaller. We also observe in the crystal, structures that propeller twist leads to close cross-strand contacts, between amino groups from adenine and cytosine bases, indicating an, attractive NH-N interaction, which is analogous to the NH-O interaction, proposed for A-tracts. This interaction also occurs between adenine bases, across an A-T step and may explain in part the different behavior of A-T, versus T-A steps in the context of A-tract-induced curvature. We also note, that hydration patterns may contribute to propeller-twisted conformation., Based on the present data and other structural and biophysical studies, we, propose that DNA macroscopic curvature is related to the structural, invariance of A-tract and A-tract-like regions conferred by high propeller, twist, cross-strand interactions and characteristic hydration. The, implications of these findings to the mechanism of DNA bending are, discussed.
About this Structure
286D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature., Shatzky-Schwartz M, Arbuckle ND, Eisenstein M, Rabinovich D, Bareket-Samish A, Haran TE, Luisi BF, Shakked Z, J Mol Biol. 1997 Apr 4;267(3):595-623. PMID:9126841
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