|
|
| (4 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC== | | ==NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC== |
| - | <StructureSection load='2hkb' size='340' side='right' caption='[[2hkb]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2hkb' size='340' side='right'caption='[[2hkb]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2hkb]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HKB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HKB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2hkb]] 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=2HKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HKB FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hkc|2hkc]]</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=2hkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hkb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hkb RCSB], [http://www.ebi.ac.uk/pdbsum/2hkb PDBsum]</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=2hkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hkb OCA], [https://pdbe.org/2hkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hkb RCSB], [https://www.ebi.ac.uk/pdbsum/2hkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hkb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 14: |
Line 15: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2hkb" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DeMuro, N E]] | + | [[Category: Large Structures]] |
| - | [[Category: Elmquist, C E]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Rizzo, C J]] | + | [[Category: DeMuro NE]] |
| - | [[Category: Stone, M P]] | + | [[Category: Elmquist CE]] |
| - | [[Category: Stover, J S]] | + | [[Category: Rizzo CJ]] |
| - | [[Category: Wang, F]] | + | [[Category: Stone MP]] |
| - | [[Category: Anneal]] | + | [[Category: Stover JS]] |
| - | [[Category: Cosy]] | + | [[Category: Wang F]] |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Hsqc]]
| + | |
| - | [[Category: Nar1]]
| + | |
| - | [[Category: Noesy]]
| + | |
| - | [[Category: Rmd calculation]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The solution structure of the oligodeoxynucleotide 5'-d(CTCGGCXCCATC)-3'.5'-d(GATGGCGCCGAG)-3' containing the heterocyclic amine 8-[(3-methyl-3H-imidazo[4,5-f]quinolin-2-yl)amino]-2'-deoxyguanosine adduct (IQ) at the third guanine in the NarI restriction sequence, a hot spot for -2 bp frameshifts, is reported. Molecular dynamics calculations restrained by distances derived from 24 (1)H NOEs between IQ and DNA, and torsion angles derived from (3)J couplings, yielded ensembles of structures in which the adducted guanine was displaced into the major groove with its glycosyl torsion angle in the syn conformation. One proton of its exocyclic amine was approximately 2.8 A from an oxygen of the 5' phosphodiester linkage, suggesting formation of a hydrogen bond. The carcinogen-guanine linkage was defined by torsion angles alpha' [N9-C8-N(IQ)-C2(IQ)] of 159 +/- 7 degrees and beta' [C8-N(IQ)-C2(IQ)-N3(IQ)] of -23 +/- 8 degrees . The complementary cytosine was also displaced into the major groove. This allowed IQ to intercalate between the flanking C.G base pairs. The disruption of Watson-Crick hydrogen bonding was corroborated by chemical-shift perturbations for base aromatic protons in the complementary strand opposite to the modified guanine. Chemical-shift perturbations were also observed for (31)P resonances corresponding to phosphodiester linkages flanking the adduct. The results confirmed that IQ adopted a base-displaced intercalated conformation in this sequence context but did not corroborate the formation of a hydrogen bond between the IQ quinoline nitrogen and the complementary dC [Elmquist, C. E.; Stover, J. S.; Wang, Z.; Rizzo, C. J. J. Am. Chem. Soc. 2004, 126, 11189-11201].
Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions.,Wang F, DeMuro NE, Elmquist CE, Stover JS, Rizzo CJ, Stone MP J Am Chem Soc. 2006 Aug 9;128(31):10085-95. PMID:16881637[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wang F, DeMuro NE, Elmquist CE, Stover JS, Rizzo CJ, Stone MP. Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions. J Am Chem Soc. 2006 Aug 9;128(31):10085-95. PMID:16881637 doi:http://dx.doi.org/10.1021/ja062004v
|
