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2o7y

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Revision as of 07:50, 2 March 2022

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

Structural highlights

2o7y is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
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/2o7y"

@@ Line 3: / Line 3: @@
 <StructureSection load='2o7y' size='340' side='right'caption='[[2o7y]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2o7y]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2O7Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2o7y]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O7Y FirstGlance]. <br>
 </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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7y OCA], [http://pdbe.org/2o7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o7y RCSB], [http://www.ebi.ac.uk/pdbsum/2o7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7y ProSAT]</span></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=2o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7y OCA], [https://pdbe.org/2o7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o7y RCSB], [https://www.ebi.ac.uk/pdbsum/2o7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7y ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">

2o7y

From Proteopedia

Revision as of 07:50, 2 March 2022

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

Structural highlights

Publication Abstract from PubMed

References

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