1nev

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[[Image:1nev.gif|left|200px]]
 
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==A-tract decamer==
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The line below this paragraph, containing "STRUCTURE_1nev", creates the "Structure Box" on the page.
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<StructureSection load='1nev' size='340' side='right'caption='[[1nev]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_1nev| PDB=1nev | SCENE= }}
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</table>
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<div style="background-color:#fffaf0;">
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'''A-tract decamer'''
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== Publication Abstract from PubMed ==
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==Overview==
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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.
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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Full crystallographic information is available from [http://oca.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://www.ncbi.nlm.nih.gov/pubmed/12586860 12586860]
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</div>
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[[Category: Barbic, A.]]
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<div class="pdbe-citations 1nev" style="background-color:#fffaf0;"></div>
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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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<references/>
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[[Category: A-tract]]
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__TOC__
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[[Category: Dna bending]]
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</StructureSection>
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[[Category: Dna decamer]]
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[[Category: Large Structures]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:26:54 2008''
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[[Category: Barbic A]]
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[[Category: Crothers DM]]
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[[Category: Zimmer DP]]

Current revision

A-tract decamer

PDB ID 1nev

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