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New page: left|200px<br /> <applet load="1ttd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ttd" /> '''SOLUTION-STATE STRUCTURE OF A DNA DODECAMER... |
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== | ==SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER== | ||
The solution structures of a duplex DNA dodecamer containing a cis-syn | <StructureSection load='1ttd' size='340' side='right'caption='[[1ttd]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ttd]] is a 2 chain structure. The July 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Thymine Dimers'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_7 10.2210/rcsb_pdb/mom_2007_7]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TTD FirstGlance]. <br> | |||
</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=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=1ttd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ttd OCA], [https://pdbe.org/1ttd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ttd RCSB], [https://www.ebi.ac.uk/pdbsum/1ttd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ttd ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data. The implications of the structural data for the mechanism by which cis-syn dimers are recognized by repair enzymes and bypassed by DNA polymerases are also discussed. | |||
Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA.,McAteer K, Jing Y, Kao J, Taylor JS, Kennedy MA J Mol Biol. 1998 Oct 9;282(5):1013-32. PMID:9753551<ref>PMID:9753551</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1ttd" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: RCSB PDB Molecule of the Month]] | |||
[[Category: Thymine Dimers]] | [[Category: Thymine Dimers]] | ||
[[Category: Jing | [[Category: Jing Y]] | ||
[[Category: Kao | [[Category: Kao J]] | ||
[[Category: Kennedy | [[Category: Kennedy MA]] | ||
[[Category: Mcateer | [[Category: Mcateer K]] | ||
[[Category: Taylor | [[Category: Taylor J-S]] | ||
Latest revision as of 09:04, 5 July 2023
SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMERSOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER
Structural highlights
Publication Abstract from PubMedThe solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data. The implications of the structural data for the mechanism by which cis-syn dimers are recognized by repair enzymes and bypassed by DNA polymerases are also discussed. Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA.,McAteer K, Jing Y, Kao J, Taylor JS, Kennedy MA J Mol Biol. 1998 Oct 9;282(5):1013-32. PMID:9753551[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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