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| | == Structural highlights == | | == Structural highlights == |
| | <table><tr><td colspan='2'>[[3ot0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OT0 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3ot0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OT0 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=EXC:3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-8-HYDROXY-7,7,9,9-TETRAMETHYL-7,8,9,11-TETRAHYDROPYRIMIDO[4,5 5,6][1,4]OXAZINO[2,3-F]ISOINDOL-2(3H)-ONE+RADICAL'>EXC</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7004Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dpl|1dpl]], [[1kgk|1kgk]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EXC:3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-8-HYDROXY-7,7,9,9-TETRAMETHYL-7,8,9,11-TETRAHYDROPYRIMIDO[4,5 5,6][1,4]OXAZINO[2,3-F]ISOINDOL-2(3H)-ONE+RADICAL'>EXC</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</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=3ot0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ot0 OCA], [https://pdbe.org/3ot0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ot0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ot0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ot0 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=3ot0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ot0 OCA], [https://pdbe.org/3ot0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ot0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ot0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ot0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| Line 22: |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Edwards, T E]] | + | [[Category: Edwards TE]] |
| - | [[Category: 2'-o-methyl u]]
| + | |
| - | [[Category: C-spin]]
| + | |
| - | [[Category: Deoxycytosine analog]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Epr spectroscopy]]
| + | |
| - | [[Category: Fluorescence spectroscopy]]
| + | |
| - | [[Category: Modified nucleic acid]]
| + | |
| - | [[Category: Nitroxide]]
| + | |
| - | [[Category: Peldor]]
| + | |
| - | [[Category: Phenoxazine]]
| + | |
| - | [[Category: Spectroscopic probe]]
| + | |
| - | [[Category: Spin-label]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Previously, we developed the deoxycytosine analog C (C-spin) as a bi-functional spectroscopic probe for the study of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. To understand the effect of C on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 A resolution crystal structure of C within a decamer duplex A-form DNA confirmed that C forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA C adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base c displayed a approximately 20 degrees bend at the oxazine linkage. Density function theory calculations revealed that the bent and planar conformations are close in energy and exhibit the same frequency for bending. These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-pi electron ring system. Within DNA, the amplitude of the bending motion is restricted, presumably due to base-stacking interactions. This structural analysis shows that the C forms a planar, structurally non-perturbing base pair with G indicating it can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies.
Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.,Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferre-D'Amare AR, Schiemann O, Sigurdsson ST Nucleic Acids Res. 2011 May 1;39(10):4419-26. Epub 2011 Jan 19. PMID:21252294[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferre-D'Amare AR, Schiemann O, Sigurdsson ST. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Nucleic Acids Res. 2011 May 1;39(10):4419-26. Epub 2011 Jan 19. PMID:21252294 doi:10.1093/nar/gkr015
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