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| [[Image:2hsl.gif|left|200px]]<br /><applet load="2hsl" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="2hsl" />
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| '''NMR structure of 13mer duplex DNA containing an abasic site, averaged structure (alpha anomer)'''<br />
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| ==Overview== | | ==NMR structure of 13mer duplex DNA containing an abasic site, averaged structure (alpha anomer)== |
| 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.
| | <StructureSection load='2hsl' size='340' side='right'caption='[[2hsl]]' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[2hsl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSL FirstGlance]. <br> |
| 2HSL 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://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSL OCA].
| | </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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr> |
| ==Reference== | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hsl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsl OCA], [https://pdbe.org/2hsl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsl RCSB], [https://www.ebi.ac.uk/pdbsum/2hsl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsl ProSAT]</span></td></tr> |
| 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17323932 17323932]
| | </table> |
| [[Category: Protein complex]] | | __TOC__ |
| [[Category: Case, D A.]] | | </StructureSection> |
| [[Category: Chen, J.]] | | [[Category: Large Structures]] |
| [[Category: Dupradeau, F Y.]] | | [[Category: Synthetic construct]] |
| [[Category: Stubbe, J.]] | | [[Category: Case DA]] |
| [[Category: Turner, C J.]] | | [[Category: Chen J]] |
| [[Category: abasic site]] | | [[Category: Dupradeau FY]] |
| [[Category: ape1]] | | [[Category: Stubbe J]] |
| [[Category: base excision repair]] | | [[Category: Turner CJ]] |
| [[Category: dna lesion]] | |
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:45:14 2008''
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