1juu: Difference between revisions
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==NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution== | |||
<StructureSection load='1juu' size='340' side='right'caption='[[1juu]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1juu]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JUU 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1juu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1juu OCA], [https://pdbe.org/1juu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1juu RCSB], [https://www.ebi.ac.uk/pdbsum/1juu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1juu ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1'/H2'/H2") of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded duplex at atomic resolution has been obtained using molecular dynamics simulations under NMR constraints. The simulated structures have torsional angles very similar to those found in B-DNA duplexes, but the base stacking and helicoid parameters are significantly different. | |||
NMR structure of a parallel-stranded DNA duplex at atomic resolution.,Parvathy VR, Bhaumik SR, Chary KV, Govil G, Liu K, Howard FB, Miles HT Nucleic Acids Res. 2002 Apr 1;30(7):1500-11. PMID:11917010<ref>PMID:11917010</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== | <div class="pdbe-citations 1juu" style="background-color:#fffaf0;"></div> | ||
[[ | == References == | ||
[[Category: Bhaumik | <references/> | ||
[[Category: Chary | __TOC__ | ||
[[Category: Govil | </StructureSection> | ||
[[Category: Howard | [[Category: Large Structures]] | ||
[[Category: Liu | [[Category: Bhaumik SR]] | ||
[[Category: Miles | [[Category: Chary KVR]] | ||
[[Category: Parvathy | [[Category: Govil G]] | ||
[[Category: Howard FB]] | |||
[[Category: Liu K]] | |||
[[Category: Miles HT]] | |||
[[Category: Parvathy VR]] | |||
