1nev

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(New page: 200px<br /><applet load="1nev" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nev" /> '''A-tract decamer'''<br /> ==Overview== DNA s...)
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[[Image:1nev.gif|left|200px]]<br /><applet load="1nev" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nev" />
 
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'''A-tract decamer'''<br />
 
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==Overview==
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==A-tract decamer==
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DNA sequences containing short adenine tracts are intrinsically curved and, play a role in transcriptional regulation. Despite many high-resolution, NMR and x-ray studies, the origins of curvature remain disputed., Long-range restraints provided by 85 residual dipolar couplings were, measured for a DNA decamer containing an adenine (A)(4)-tract and used to, refine the structure. The overall bend in the molecule is a result of, in-phase negative roll in the A-tract and positive roll at its 5', junction, as well as positive and negative tilt inside the A-tract and, near its junctions. The bend magnitude and direction obtained from NMR, structures is 9.0 degrees into the minor groove in a coordinate frame, located at the third AT base pair. We evaluated long-range and wedge, models for DNA curvature and concluded that our data for A-tract curvature, are best explained by a "delocalized bend" model. The global bend, magnitude and direction of the NMR structure are in excellent agreement, with the junction model parameters used to rationalize gel electrophoretic, data and with preliminary results of a cyclization kinetics assay from our, laboratory.
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<StructureSection load='1nev' size='340' side='right'caption='[[1nev]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nev]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NEV FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nev OCA], [https://pdbe.org/1nev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nev RCSB], [https://www.ebi.ac.uk/pdbsum/1nev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nev ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA sequences containing short adenine tracts are intrinsically curved and play a role in transcriptional regulation. Despite many high-resolution NMR and x-ray studies, the origins of curvature remain disputed. Long-range restraints provided by 85 residual dipolar couplings were measured for a DNA decamer containing an adenine (A)(4)-tract and used to refine the structure. The overall bend in the molecule is a result of in-phase negative roll in the A-tract and positive roll at its 5' junction, as well as positive and negative tilt inside the A-tract and near its junctions. The bend magnitude and direction obtained from NMR structures is 9.0 degrees into the minor groove in a coordinate frame located at the third AT base pair. We evaluated long-range and wedge models for DNA curvature and concluded that our data for A-tract curvature are best explained by a "delocalized bend" model. The global bend magnitude and direction of the NMR structure are in excellent agreement with the junction model parameters used to rationalize gel electrophoretic data and with preliminary results of a cyclization kinetics assay from our laboratory.
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==About this Structure==
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Structural origins of adenine-tract bending.,Barbic A, Zimmer DP, Crothers DM Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2369-73. Epub 2003 Feb 13. PMID:12586860<ref>PMID:12586860</ref>
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1NEV 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NEV OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural origins of adenine-tract bending., Barbic A, Zimmer DP, Crothers DM, Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2369-73. Epub 2003 Feb 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12586860 12586860]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1nev" style="background-color:#fffaf0;"></div>
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[[Category: Barbic, A.]]
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== References ==
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[[Category: Crothers, D.M.]]
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<references/>
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[[Category: Zimmer, D.P.]]
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__TOC__
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[[Category: a-tract]]
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</StructureSection>
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[[Category: dna bending]]
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[[Category: Large Structures]]
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[[Category: dna decamer]]
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[[Category: Barbic A]]
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[[Category: Crothers DM]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:01:32 2007''
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[[Category: Zimmer DP]]

Current revision

A-tract decamer

PDB ID 1nev

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