1dk9: Difference between revisions
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==SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)== | ==SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)== | ||
<StructureSection load='1dk9' size='340' side='right'caption='[[1dk9 | <StructureSection load='1dk9' size='340' side='right'caption='[[1dk9]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1dk9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DK9 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[1dk9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DK9 FirstGlance]. <br> | ||
</td></tr><tr id=' | </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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dk9 OCA], [https://pdbe.org/1dk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dk9 RCSB], [https://www.ebi.ac.uk/pdbsum/1dk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dk9 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: Bergstrom | [[Category: Bergstrom DE]] | ||
[[Category: Davisson | [[Category: Davisson VJ]] | ||
[[Category: Hoskins | [[Category: Hoskins A]] | ||
[[Category: Klewer | [[Category: Klewer DA]] | ||
[[Category: LiWang | [[Category: LiWang AC]] | ||
Latest revision as of 14:45, 22 November 2023
SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)
Structural highlights
Publication Abstract from PubMedThe three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was observed between final structures derived from A- and B-form starting geometries for both 1 and 2. Structures of 1 and 2 are right-handed duplexes within the B-form conformational regime. Furthermore, the structures of 1 and 2 are highly similar, with differences in the structures localized to the vicinity of residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation and it is displaced towards the major groove. Furthermore, unlike T14 in 2, the base of X14 has reduced pi-pi stacking interactions with C13 and C15 and the nitro group of X14 is pointing out of the major groove. The structures presented here establish the basis of the thermal data of DNA duplexes containing X and should be informative during the design of improved wild card nucleobase analogs. NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control.,Klewer DA, Hoskins A, Zhang P, Davisson VJ, Bergstrom DE, LiWang AC Nucleic Acids Res. 2000 Nov 15;28(22):4514-22. PMID:11071940[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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