View source for 1rvh


==SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC==
<StructureSection load='1rvh' size='340' side='right'caption='[[1rvh]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rvh]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVH FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1rvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvh OCA], [https://pdbe.org/1rvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvh RCSB], [https://www.ebi.ac.uk/pdbsum/1rvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvh ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
DNA A-tracts have been defined as four or more consecutive A.T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed &gt;20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals that the former forms a left-handed superhelix with a diameter of approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of &gt;250 A and diameter of approximately 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.

DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum.,Stefl R, Wu H, Ravindranathan S, Sklenar V, Feigon J Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1177-82. Epub 2004 Jan 22. PMID:14739342<ref>PMID:14739342</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Feigon J]]
[[Category: Ravindranathan S]]
[[Category: Sklenar V]]
[[Category: Stefl R]]
[[Category: Wu H]]