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New page: left|200px<br /><applet load="2hss" size="350" color="white" frame="true" align="right" spinBox="true" caption="2hss" /> '''13mer duplex DNA containg an abasic site wit...
 
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[[Image:2hss.gif|left|200px]]<br /><applet load="2hss" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2hss" />
'''13mer duplex DNA containg an abasic site with beta anomer, averaged structure'''<br />


==Overview==
==13mer duplex DNA containg an abasic site with beta anomer, averaged structure==
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='2hss' size='340' side='right'caption='[[2hss]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2hss]] 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=2HSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSS FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR,  models</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hss OCA], [https://pdbe.org/2hss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hss RCSB], [https://www.ebi.ac.uk/pdbsum/2hss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hss ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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>
2HSS 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=2HSS OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 2hss" style="background-color:#fffaf0;"></div>
[[Category: Case, D.A.]]
== References ==
[[Category: Chen, J.]]
<references/>
[[Category: Dupradeau, F.Y.]]
__TOC__
[[Category: Stubbe, J.]]
</StructureSection>
[[Category: Turner, C.J.]]
[[Category: Large Structures]]
[[Category: abasic site]]
[[Category: Synthetic construct]]
[[Category: ape1]]
[[Category: Case DA]]
[[Category: base excision repair]]
[[Category: Chen J]]
[[Category: dna damage]]
[[Category: Dupradeau FY]]
 
[[Category: Stubbe J]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:06:48 2008''
[[Category: Turner CJ]]

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13mer duplex DNA containg an abasic site with beta anomer, averaged structure

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