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==THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N7 POSITION OF GUANINE OPPOSITE AN ADENINE IN THE COMPLEMENTARY STRAND OF AN OLIGODEOXYNUCLEOTIDE DUPLEX, NMR, MINIMIZED AVERAGE STRUCTURE==
==THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N7 POSITION OF GUANINE OPPOSITE AN ADENINE IN THE COMPLEMENTARY STRAND OF AN OLIGODEOXYNUCLEOTIDE DUPLEX, NMR, MINIMIZED AVERAGE STRUCTURE==
<StructureSection load='1ag5' size='340' side='right'caption='[[1ag5]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
<StructureSection load='1ag5' size='340' side='right'caption='[[1ag5]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ag5]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AG5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ag5]] 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=1AG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AG5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AFN:8,9-DIHYDRO-9-HYDROXY-AFLATOXIN+B1'>AFN</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AFN:8,9-DIHYDRO-9-HYDROXY-AFLATOXIN+B1'>AFN</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=1ag5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ag5 OCA], [https://pdbe.org/1ag5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ag5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ag5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ag5 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=1ag5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ag5 OCA], [https://pdbe.org/1ag5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ag5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ag5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ag5 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The solution structure of d(CCATCAFBGATCC).d(GGATCAGATGG), containing the 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 adduct, was refined using molecular dynamics restrained by NOE data obtained from 1H NMR. The modified guanosine was positioned opposite cytosine, while the aflatoxin moiety was positioned opposite adenosine in the complementary strand. Sequential 1H NOEs were interrupted between C5 and AFBG6, but intrastrand NOEs were traced through the aflatoxin moiety, via H6a of aflatoxin and H8 of the modified guanine. Opposite the lesion, the NOE between A16 H1' and G17 H8 was weak. A total of 43 NOEs were observed between DNA protons and aflatoxin protons. Molecular dynamics calculations restrained with 259 experimental and empirical distances, and using sp2 hybridization at AFBG6 N7, refined structures with pairwise rms differences &lt; 0.85 A, excluding terminal base pairs. Relaxation matrix calculations yielded a sixth root rms difference between refined structures and NOE intensity data of 7.3 x 10(-2). The aflatoxin moiety intercalated on the 5'-face of the modified guanine. The extra adenine A16 was inserted between base pair AFBG6.C15 and the aflatoxin moiety. A 36 degree bending between the plane of base pair AFBG6.C15 and the plane of the aflatoxin moiety was predicted. The aflatoxin moiety stacked below the top domain of the oligodeoxynucleotide, which consisted of base pairs C1.G21, C2.G20, A3.T19, T4.A18, and C5.G17. The bottom domain consisted of base pairs AFBG6.C15, A7.T14, T8.A13, C9.G12, and C10.G11. The average winding angle between base pair C5.G17, the intercalated aflatoxin moiety, A16, and base pair AFBG6.C15 was reduced to 10 degrees. The preponderance of base pair substitutions in the aflatoxin B1 mutational spectrum, particularly G--&gt;T transversions, suggests that the stability of this modified oligodeoxynucleotide, which models a templated +1 addition mutation, does not reliably predict the frequency of frame shifts.
Refined solution structure of 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 opposite CpA in the complementary strand of an oligodeoxynucleotide duplex as determined by 1H NMR.,Johnston DS, Stone MP Biochemistry. 1995 Oct 31;34(43):14037-50. PMID:7578001<ref>PMID:7578001</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ag5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Johnson, D S]]
[[Category: Synthetic construct]]
[[Category: Stone, M P]]
[[Category: Johnson DS]]
[[Category: Aflatoxin b1]]
[[Category: Stone MP]]
[[Category: Deoxyribonucleic acid]]
[[Category: Dna]]
[[Category: Dna duplex]]
[[Category: Intercalation]]
[[Category: N7-guanine adduct]]

Latest revision as of 08:05, 10 April 2024

THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N7 POSITION OF GUANINE OPPOSITE AN ADENINE IN THE COMPLEMENTARY STRAND OF AN OLIGODEOXYNUCLEOTIDE DUPLEX, NMR, MINIMIZED AVERAGE STRUCTURE

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