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| [[Image:285d.gif|left|200px]]<br /><applet load="285d" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="285d, resolution 2.500Å" />
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| '''X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE'''<br />
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| ==Overview== | | ==X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE== |
| 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.
| | <StructureSection load='285d' size='340' side='right'caption='[[285d]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[285d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=285D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=285D FirstGlance]. <br> |
| 285D 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=285D OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> |
| ==Reference== | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=285d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=285d OCA], [https://pdbe.org/285d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=285d RCSB], [https://www.ebi.ac.uk/pdbsum/285d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=285d ProSAT]</span></td></tr> |
| 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9126841 9126841] | | </table> |
| [[Category: Protein complex]]
| | __TOC__ |
| [[Category: Luisi, B.F.]] | | </StructureSection> |
| [[Category: Shakked, Z.]]
| | [[Category: Large Structures]] |
| [[Category: Shatzky-Schwartz, M.]]
| | [[Category: Luisi BF]] |
| [[Category: b-dna]] | | [[Category: Shakked Z]] |
| [[Category: double helix]] | | [[Category: Shatzky-Schwartz M]] |
| [[Category: modified]] | |
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:50:40 2008''
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