2ge2

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[[Image:2ge2.gif|left|200px]]
 
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==Solution structure of the Duplex DNA Containing the 3-(Deoxyguanosin-N2-yl)-2-Acetoaminofluorene==
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The line below this paragraph, containing "STRUCTURE_2ge2", creates the "Structure Box" on the page.
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<StructureSection load='2ge2' size='340' side='right'caption='[[2ge2]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2ge2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GE2 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AFF:2-ACETYLAMINOFLUORENE-3-YL'>AFF</scene></td></tr>
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{{STRUCTURE_2ge2| PDB=2ge2 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ge2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ge2 OCA], [https://pdbe.org/2ge2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ge2 RCSB], [https://www.ebi.ac.uk/pdbsum/2ge2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ge2 ProSAT]</span></td></tr>
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</table>
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'''Solution structure of the Duplex DNA Containing the 3-(Deoxyguanosin-N2-yl)-2-Acetoaminofluorene'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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The carcinogenic environmental pollutant 2-nitrofluorene produces several DNA adducts including the minor 3-(deoxyguanosin-N(2)-yl)-2-acetylaminofluorene (dG(N(2))-AAF) lesion, which persists for long times in rat tissue DNA after discontinuation of carcinogen administration. Here, we present the solution structure of a dG(N(2))-AAF duplex as determined by NMR spectroscopy and restrained molecular dynamics. The data establish a regular right-handed conformation with Watson-Crick base pair alignments throughout the duplex. The AAF moiety resides in the minor grove of the helix with its long axis directed toward the 5'-end of the modified strand. Restrained molecular dynamics shows that the duplex structure adjusts to the AAF lesion, reducing its exposure to water molecules. Analysis of UV melting profiles shows that the presence of dG(N(2))-AAF increases the thermal and thermodynamic stability of duplex DNA, an effect that is driven by a favorable entropy. The structure and stability of the dG(N(2))-AAF duplex have important implications in understanding the recognition of bulky lesions by the DNA repair system.
The carcinogenic environmental pollutant 2-nitrofluorene produces several DNA adducts including the minor 3-(deoxyguanosin-N(2)-yl)-2-acetylaminofluorene (dG(N(2))-AAF) lesion, which persists for long times in rat tissue DNA after discontinuation of carcinogen administration. Here, we present the solution structure of a dG(N(2))-AAF duplex as determined by NMR spectroscopy and restrained molecular dynamics. The data establish a regular right-handed conformation with Watson-Crick base pair alignments throughout the duplex. The AAF moiety resides in the minor grove of the helix with its long axis directed toward the 5'-end of the modified strand. Restrained molecular dynamics shows that the duplex structure adjusts to the AAF lesion, reducing its exposure to water molecules. Analysis of UV melting profiles shows that the presence of dG(N(2))-AAF increases the thermal and thermodynamic stability of duplex DNA, an effect that is driven by a favorable entropy. The structure and stability of the dG(N(2))-AAF duplex have important implications in understanding the recognition of bulky lesions by the DNA repair system.
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==About this Structure==
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Structure and stability of duplex DNA containing the 3-(deoxyguanosin-N2-yl)-2-acetylaminofluorene (dG(N2)-AAF) lesion: a bulky adduct that persists in cellular DNA.,Zaliznyak T, Bonala R, Johnson F, de Los Santos C Chem Res Toxicol. 2006 Jun;19(6):745-52. PMID:16780352<ref>PMID:16780352</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GE2 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure and stability of duplex DNA containing the 3-(deoxyguanosin-N2-yl)-2-acetylaminofluorene (dG(N2)-AAF) lesion: a bulky adduct that persists in cellular DNA., Zaliznyak T, Bonala R, Johnson F, de Los Santos C, Chem Res Toxicol. 2006 Jun;19(6):745-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16780352 16780352]
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</div>
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[[Category: Santos, C de los.]]
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<div class="pdbe-citations 2ge2" style="background-color:#fffaf0;"></div>
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[[Category: Zaliznyak, T.]]
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== References ==
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[[Category: Dna]]
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<references/>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:00:01 2008''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Zaliznyak T]]
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[[Category: De los Santos C]]

Current revision

Solution structure of the Duplex DNA Containing the 3-(Deoxyguanosin-N2-yl)-2-Acetoaminofluorene

PDB ID 2ge2

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