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2o7z

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Duplex DNA containing an abasic site with an opposite T (beta anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)

Structural highlights

2o7z is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic site and ultimately, its recognition and repair, remains elusive. In the present study, duplex DNAs with three different bases (G, C or T) opposite an abasic site have been synthesized in the same sequence context (5'-CCA AAG6 XA8C CGG G-3', where X denotes the abasic site) and characterized by 2D NMR spectroscopy. Studies on a duplex DNA with an A opposite the abasic site in the same sequence has recently been reported [Chen,J., Dupradeau,F.-Y., Case,D.A., Turner,C.J. and Stubbe,J. (2007) Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites. Biochemistry, 46, 3096-3107]. Molecular modeling based on NMR-derived distance and dihedral angle restraints and molecular dynamics calculations have been applied to determine structural models and conformational flexibility of each duplex. The results indicate that all four duplexes adopt an overall B-form conformation with each unpaired base stacked between adjacent bases intrahelically. The conformation around the abasic site is more perturbed when the base opposite to the lesion is a pyrimidine (C or T) than a purine (G or A). In both the former cases, the neighboring base pairs (G6-C21 and A8-T19) are closer to each other than those in B-form DNA. Molecular dynamics simulations reveal that transient H-bond interactions between the unpaired pyrimidine (C20 or T20) and the base 3' to the abasic site play an important role in perturbing the local conformation. These results provide structural insight into the dynamics of abasic sites that are intrinsically modulated by the bases opposite the abasic site.

DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics.,Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J Nucleic Acids Res. 2008 Jan;36(1):253-62. Epub 2007 Nov 19. PMID:18025040^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J. DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Res. 2008 Jan;36(1):253-62. Epub 2007 Nov 19. PMID:18025040 doi:10.1093/nar/gkm622

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2o7z"

@@ Line 1: / Line 1: @@
 ==Duplex DNA containing an abasic site with an opposite T (beta anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)==
-<StructureSection load='2o7z' size='340' side='right' caption='[[2o7z]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''>
+<StructureSection load='2o7z' size='340' side='right'caption='[[2o7z]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2o7z]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O7Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2o7z]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O7Z FirstGlance]. <br>
-</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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o7z RCSB], [http://www.ebi.ac.uk/pdbsum/2o7z PDBsum]</span></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=2o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7z OCA], [https://pdbe.org/2o7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o7z RCSB], [https://www.ebi.ac.uk/pdbsum/2o7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7z ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 14: / Line 16: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2o7z" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Case, D A]]
+[[Category: Large Structures]]
-[[Category: Chen, J]]
+[[Category: Case DA]]
-[[Category: Dupradeau, F Y]]
+[[Category: Chen J]]
-[[Category: Stubbe, J]]
+[[Category: Dupradeau FY]]
-[[Category: Turner, C J]]
+[[Category: Stubbe J]]
-[[Category: Abasic]]
+[[Category: Turner CJ]]
-[[Category: Amber]]
-[[Category: Ape1]]
-[[Category: Dna]]
-[[Category: Dna damage]]
-[[Category: Molecular dynamic]]

2o7z

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Duplex DNA containing an abasic site with an opposite T (beta anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)

Structural highlights

Publication Abstract from PubMed

References

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