2hsk

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[[Image:2hsk.png|left|200px]]
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==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==
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<StructureSection load='2hsk' size='340' side='right' caption='[[2hsk]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HSK FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hou|2hou]], [[2hpx|2hpx]], [[2hss|2hss]], [[2hsl|2hsl]], [[2hsr|2hsr]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk PDBsum]</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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A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
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{{STRUCTURE_2hsk| PDB=2hsk | SCENE= }}
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Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.,Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:17323932<ref>PMID:17323932</ref>
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===NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_17323932}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:017323932</ref><references group="xtra"/>
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[[Category: Case, D A.]]
[[Category: Case, D A.]]
[[Category: Chen, J.]]
[[Category: Chen, J.]]

Revision as of 15:27, 12 October 2014

NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)

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