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| | ==DNA duplex containing a ribonolactone lesion== | | ==DNA duplex containing a ribonolactone lesion== |
| - | <StructureSection load='5hqf' size='340' side='right'caption='[[5hqf]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='5hqf' size='340' side='right'caption='[[5hqf]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5hqf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HQF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5hqf]] 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=5HQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HQF FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63T:[(2R,3S)-3-HYDROXY-5-OXOTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE+(NON-PREFERRED+NAME)'>63T</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5hqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hqf OCA], [http://pdbe.org/5hqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hqf RCSB], [http://www.ebi.ac.uk/pdbsum/5hqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hqf ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=63T:[(2R,3S)-3-HYDROXY-5-OXOTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE+(NON-PREFERRED+NAME)'>63T</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</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=5hqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hqf OCA], [https://pdbe.org/5hqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hqf RCSB], [https://www.ebi.ac.uk/pdbsum/5hqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hqf ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Constant, J F]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Jourdan, M]] | + | [[Category: Constant JF]] |
| - | [[Category: Zalesak, J]] | + | [[Category: Jourdan M]] |
| - | [[Category: Cluster 8-oxo-guanine ribonolactone]] | + | [[Category: Zalesak J]] |
| - | [[Category: Dna]]
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| - | [[Category: Dna lesion]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Ionizing radiation, free radicals, and reactive oxygen species produce hundreds of different DNA lesions. Clustered lesions are typical for ionizing radiation. They compromise the efficiency of the base excision repair (BER) pathway, and as a consequence, they are much more toxic and mutagenic than isolated lesions. Despite their biological relevance, e.g., in cancer radiotherapy and accidental exposure, they are not very well studied from a structural point of view, and while insights provided by structural studies contribute to the understanding of the repair process, only three nuclear magnetic resonance (NMR) studies of DNA containing clusters of lesions were reported. Herein, we report the first NMR solution structure of two DNAs containing a bistranded cluster with the 2'-deoxyribonolactone and 8-oxoguanine lesions. Both DNA duplexes feature a 2'-deoxyribonolactone site in the middle of the sequence of one strand and differ by the relative position of the 8-oxoguanine, staggered 3' or 5' side on the complementary strand at a three-nucleotide distance. Depending on its relative position, the repair of the 8-oxoguanine lesion by the base excision repair protein Fpg is either almost complete or inhibited. We found that the structures of the two DNAs containing a bistranded cluster of two lesions are similar and do not deviate very much from the standard B-form. As no obvious structural deformations were observed between the two duplexes, we concluded that the differences in Fpg activity are not due to differences in their global conformation.
Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions.,Zalesak J, Constant JF, Jourdan M Biochemistry. 2016 Jul 19;55(28):3899-906. doi: 10.1021/acs.biochem.6b00396. Epub, 2016 Jul 8. PMID:27322640[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zalesak J, Constant JF, Jourdan M. Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions. Biochemistry. 2016 Jul 19;55(28):3899-906. doi: 10.1021/acs.biochem.6b00396. Epub, 2016 Jul 8. PMID:27322640 doi:http://dx.doi.org/10.1021/acs.biochem.6b00396
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