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[[ | ==NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)== | ||
<StructureSection load='1kxs' size='340' side='right' caption='[[1kxs]], [[NMR_Ensembles_of_Models | 2 NMR models]]' scene=''> | |||
< | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KXS FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEU:3-(2-HYDROXYETHYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>HEU</scene></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=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://pdbe.org/1kxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB], [http://www.ebi.ac.uk/pdbsum/1kxs PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
'' | |||
== | |||
Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)*d(CGTTTTAGACTTGC) containing a 3-(2-hydroxyethyl)-2'-deoxyuridine*deoxyadenine (HE*A) base pair is reported. The three-dimensional solution structure, determined starting from 512 models via restrained molecular mechanics using inter-proton distances and torsion angles, converged to two final families of structures. For both families the HE and the opposite A residues are intrahelical and in the anti conformation. The hydroxyethyl chain lies close to the helix axis and for one family the hydroxyl group is above the HE*A plane and in the other case it is below. These two models were used to start molecular dynamic calculations with explicit solvent to explore the hydrogen bonding possibilities of the HE*A base pair. The dynamics calculations converge finally to one model structure in which two hydrogen bonds are formed. The first is formed all the time and is between HEO4 and the amino group of A, and the second, an intermittent one, is between the hydroxyl group and the N1 of A. When this second hydrogen bond is not formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All the best structures show an increase in the C1'-C1' distance relative to a Watson-Crick base pair. | Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)*d(CGTTTTAGACTTGC) containing a 3-(2-hydroxyethyl)-2'-deoxyuridine*deoxyadenine (HE*A) base pair is reported. The three-dimensional solution structure, determined starting from 512 models via restrained molecular mechanics using inter-proton distances and torsion angles, converged to two final families of structures. For both families the HE and the opposite A residues are intrahelical and in the anti conformation. The hydroxyethyl chain lies close to the helix axis and for one family the hydroxyl group is above the HE*A plane and in the other case it is below. These two models were used to start molecular dynamic calculations with explicit solvent to explore the hydrogen bonding possibilities of the HE*A base pair. The dynamics calculations converge finally to one model structure in which two hydrogen bonds are formed. The first is formed all the time and is between HEO4 and the amino group of A, and the second, an intermittent one, is between the hydroxyl group and the N1 of A. When this second hydrogen bond is not formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All the best structures show an increase in the C1'-C1' distance relative to a Watson-Crick base pair. | ||
The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies.,Boulard Y, Fazakerley GV, Sowers LC Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:11884635<ref>PMID:11884635</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: Boulard, Y | <div class="pdbe-citations 1kxs" style="background-color:#fffaf0;"></div> | ||
[[Category: Fazakerley, G V | == References == | ||
[[Category: Sowers, L C | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Boulard, Y]] | |||
[[Category: Fazakerley, G V]] | |||
[[Category: Sowers, L C]] | |||
[[Category: Deoxyribonucleic acid]] | [[Category: Deoxyribonucleic acid]] | ||
[[Category: Dna]] | |||
[[Category: Modified base]] | [[Category: Modified base]] | ||
[[Category: Mutagenesis]] | [[Category: Mutagenesis]] | ||