View source for 1dk6


==NMR structure analysis of the DNA nine base pair duplex D(CATGAGTAC) D(GTAC(NP3)CATG)==
<StructureSection load='1dk6' size='340' side='right'caption='[[1dk6]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dk6]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DK6 FirstGlance]. <br>
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NP3:1-[2-DEOXY-RIBOFURANOSYL]-1H-[3-NITRO-PYRROL]-5-PHOSPHATE'>NP3</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=1dk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dk6 OCA], [https://pdbe.org/1dk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dk6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dk6 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
The 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<ref>PMID:11071940</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1dk6" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Bergstrom DE]]
[[Category: Davisson VJ]]
[[Category: Hoskins A]]
[[Category: Klewer DA]]
[[Category: LiWang AC]]