1ag3: Difference between revisions
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< | ==DUPLEX OLIGODEOXYNUCLEOTIDE CONTAINING PROPANODEOXYGUANOSINE OPPOSITE A TWO-BASE DELETION, NMR, MINIMIZED AVERAGE STRUCTURE== | ||
<StructureSection load='1ag3' size='340' side='right'caption='[[1ag3]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ag3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AG3 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=P:2-DEOXY-N1,N2-PROPANO+GUANOSINE+MONOPHOSPHATE'>P</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=1ag3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ag3 OCA], [https://pdbe.org/1ag3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ag3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ag3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ag3 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Structural refinement from solution 1H NMR data was performed on the 5'-d[ATCGC(PdG)-CGGCATG]-3'.5'-d[CATGCCGCGAT]-3' duplex, in which the adducted oligodeoxynucleotide containing the exocyclic lesion 1,N2-propano-2'-deoxyguanosine (PdG) was annealed with the complementary strand which contained a CpG deletion. The resulting duplex required PdG and one adjacent cytosine to be unpaired. A total of 352 distances were utilized to restrain molecular dynamics calculations, of which 264 were NOE-derived. These distances were calculated using complete relaxation matrix methods from hybrid matrices, which were comprised of the experimentally determined distances and additional distances derived from either A-form or B-form DNA. A simulated annealing protocol combined with the distance restraints was able to refine a single structure with an average rms deviation of < 1.35 A. The accuracy of the refined structure was assessed using full relaxation matrix calculations, which gave good agreement with measured NOE intensities. PdG was found to be stacked into the helix below base pair C3.G18, whereas C5 was found to be unpaired and extruded toward the major groove and parallel to base pair G6.C17. This created a localized bend in the DNA helix of approximately 20-35 degrees at the junction between PdG and C5. The bending corroborated previous assays performed on this modified sequence [Moe, J. G., Reddy, G. R., Marnett, L. J., & Stone, M. P. (1994) Chem. Res. Toxicol. 7, 319-328]. | |||
Structure of a duplex oligodeoxynucleotide containing propanodeoxyguanosine opposite a two-base deletion in the (CpG)3 frame shift hotspot of Salmonella typhimurium hisD3052 determined by 1H NMR and restrained molecular dynamics.,Weisenseel JP, Moe JG, Reddy GR, Marnett LJ, Stone MP Biochemistry. 1995 Jan 10;34(1):50-64. PMID:7819223<ref>PMID:7819223</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1ag3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Stone MP]] | |||
[[Category: Weisenseel JP]] | |||
== | |||
[[Category: | |||
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Latest revision as of 14:32, 22 November 2023
DUPLEX OLIGODEOXYNUCLEOTIDE CONTAINING PROPANODEOXYGUANOSINE OPPOSITE A TWO-BASE DELETION, NMR, MINIMIZED AVERAGE STRUCTUREDUPLEX OLIGODEOXYNUCLEOTIDE CONTAINING PROPANODEOXYGUANOSINE OPPOSITE A TWO-BASE DELETION, NMR, MINIMIZED AVERAGE STRUCTURE
Structural highlights
Publication Abstract from PubMedStructural refinement from solution 1H NMR data was performed on the 5'-d[ATCGC(PdG)-CGGCATG]-3'.5'-d[CATGCCGCGAT]-3' duplex, in which the adducted oligodeoxynucleotide containing the exocyclic lesion 1,N2-propano-2'-deoxyguanosine (PdG) was annealed with the complementary strand which contained a CpG deletion. The resulting duplex required PdG and one adjacent cytosine to be unpaired. A total of 352 distances were utilized to restrain molecular dynamics calculations, of which 264 were NOE-derived. These distances were calculated using complete relaxation matrix methods from hybrid matrices, which were comprised of the experimentally determined distances and additional distances derived from either A-form or B-form DNA. A simulated annealing protocol combined with the distance restraints was able to refine a single structure with an average rms deviation of < 1.35 A. The accuracy of the refined structure was assessed using full relaxation matrix calculations, which gave good agreement with measured NOE intensities. PdG was found to be stacked into the helix below base pair C3.G18, whereas C5 was found to be unpaired and extruded toward the major groove and parallel to base pair G6.C17. This created a localized bend in the DNA helix of approximately 20-35 degrees at the junction between PdG and C5. The bending corroborated previous assays performed on this modified sequence [Moe, J. G., Reddy, G. R., Marnett, L. J., & Stone, M. P. (1994) Chem. Res. Toxicol. 7, 319-328]. Structure of a duplex oligodeoxynucleotide containing propanodeoxyguanosine opposite a two-base deletion in the (CpG)3 frame shift hotspot of Salmonella typhimurium hisD3052 determined by 1H NMR and restrained molecular dynamics.,Weisenseel JP, Moe JG, Reddy GR, Marnett LJ, Stone MP Biochemistry. 1995 Jan 10;34(1):50-64. PMID:7819223[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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