286d

From Proteopedia

(Difference between revisions)

Current revision

X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/286d"

Categories: Large Structures | Luisi BF | Shakked Z | Shatzky-Schwartz M

@@ Line 1: / Line 1: @@
-[[Image:286d.gif|left|200px]]<br /><applet load="286d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="286d, resolution 2.500&Aring;" />
-'''X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE'''<br />
-==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='286d' size='340' side='right'caption='[[286d]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[286d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=286D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=286D FirstGlance]. <br>
-D 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=286D 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]] 2.5&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=286d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=286d OCA], [https://pdbe.org/286d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=286d RCSB], [https://www.ebi.ac.uk/pdbsum/286d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=286d ProSAT]</span></td></tr>
-==Reference==
+</table>
-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]
+__TOC__
-[[Category: Protein complex]]
+</StructureSection>
-[[Category: Luisi, B.F.]]
+[[Category: Large Structures]]
-[[Category: Shakked, Z.]]
+[[Category: Luisi BF]]
-[[Category: Shatzky-Schwartz, M.]]
+[[Category: Shakked Z]]
-[[Category: b-dna]]
+[[Category: Shatzky-Schwartz M]]
-[[Category: double helix]]
-[[Category: modified]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:50:43 2008''

286d

From Proteopedia

Current revision

X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE

Structural highlights

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox