2hsr: Difference between revisions
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==13mer duplex DNA containing an abasic site with beta anomer== | ==13mer duplex DNA containing an abasic site with beta anomer== | ||
<StructureSection load='2hsr' size='340' side='right' caption='[[2hsr]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | <StructureSection load='2hsr' size='340' side='right' caption='[[2hsr]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | ||
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hsk|2hsk]], [[2hsl|2hsl]], [[2hou|2hou]], [[2hpk|2hpk]], [[2hss|2hss]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hsk|2hsk]], [[2hsl|2hsl]], [[2hou|2hou]], [[2hpk|2hpk]], [[2hss|2hss]]</td></tr> | ||
<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=2hsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsr OCA], [http://pdbe.org/2hsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsr RCSB], [http://www.ebi.ac.uk/pdbsum/2hsr PDBsum]</span></td></tr> | <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=2hsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsr OCA], [http://pdbe.org/2hsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsr RCSB], [http://www.ebi.ac.uk/pdbsum/2hsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 09:09, 27 June 2018
13mer duplex DNA containing an abasic site with beta anomer13mer duplex DNA containing an abasic site with beta anomer
Structural highlights
Publication Abstract from PubMedA 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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