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| | ==DNA WITH PYRENE PAIRED AT ABASIC SITE== | | ==DNA WITH PYRENE PAIRED AT ABASIC SITE== |
| - | <StructureSection load='1fzs' size='340' side='right'caption='[[1fzs]], [[NMR_Ensembles_of_Models | 8 NMR models]]' scene=''> | + | <StructureSection load='1fzs' size='340' side='right'caption='[[1fzs]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1fzs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1fzs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZS FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fzl|1fzl]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</scene></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=1fzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzs OCA], [http://pdbe.org/1fzs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzs RCSB], [http://www.ebi.ac.uk/pdbsum/1fzs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzs 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=1fzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzs OCA], [https://pdbe.org/1fzs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzs RCSB], [https://www.ebi.ac.uk/pdbsum/1fzs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzs 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: Kool, E T]] | + | [[Category: Kool ET]] |
| - | [[Category: Matray, T J]] | + | [[Category: Matray TJ]] |
| - | [[Category: Santos, C de los]]
| + | [[Category: Smirnov S]] |
| - | [[Category: Smirnov, S]] | + | [[Category: De los Santos C]] |
| - | [[Category: Dna]] | + | |
| - | [[Category: Furan]]
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| - | [[Category: Non-polar dna pair]]
| + | |
| - | [[Category: Pyrene]]
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| Structural highlights
Publication Abstract from PubMed
DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide (P) opposite tetrahydrofuran (F), an stable abasic site analog, and DNA duplexes containing this non-hydrogen-bonded pair possess a high degree of thermodynamic stability. These observations support the hypothesis that steric complementarity and stacking interactions may be sufficient for maintaining stability of DNA structure and specificity of DNA replication, even in the absence of hydrogen bonds across the base pair. Here we report the NMR characterization and structure determination of two DNA molecules containing pyrene residues. The first is a 13mer duplex with a pyrene.tetrahydrofuran pair (P.F pair) at the ninth position and the second mimics a replication intermediate right after incorporation of a pyrene nucleoside opposite an abasic site. Our data indicate that both molecules adopt right-handed helical conformations with Watson- Crick alignments for all canonical base pairs. The pyrene ring stays inside the helix close to its baseless partner in both molecules. The single-stranded region of the replication intermediate folds back over the opposing strand, sheltering the hydrophobic pyrene moiety from water exposure. The results support the idea that the stability and replication of a P.F pair is due to its ability to mimic Watson-Crick structure.
Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites.,Smirnov S, Matray TJ, Kool ET, de los Santos C Nucleic Acids Res. 2002 Dec 15;30(24):5561-9. PMID:12490724[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Smirnov S, Matray TJ, Kool ET, de los Santos C. Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Res. 2002 Dec 15;30(24):5561-9. PMID:12490724
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