1x2x
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(New page: 200px<br /><applet load="1x2x" size="450" color="white" frame="true" align="right" spinBox="true" caption="1x2x" /> '''NMR solution structures of a DNA dodecamer c...)
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Revision as of 23:13, 24 November 2007
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NMR solution structures of a DNA dodecamer containing a tandem GT mismatches using NOE and residual dipolar couplings
Overview
We have carried out a solution study of two non-labelled, self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by, NMR, the second sequence composed of two G-T mismatches. Structures were, determined using distances extracted from NOE effects alone or using both, NOE and RDC constraints, measured in three different liquid crystalline, media. We ensured that our data on the influence of the mesogen on the DNA, structures, and the way in which the RDCs were incorporated as constraints, in the protocol refinement, were consistent. We also tested the influence, of different sets of RDCs and the best means of optimizing the calculation, of D(a) and R. Resolution and accuracy of the ten best energy final, structures were compared. The addition of a small set of RDC constraints, significantly improves the final determined structures. We took advantage, of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the, duplexes do not have a large curvature. For the G-T base pair, we, observed, in this particular sequence (tandem of G-T mismatches), a new, pattern of base pairing, which involved the formation of a bifurcated, hydrogen bond.
About this Structure
1X2X is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G-T mismatches., Alvarez-Salgado F, Desvaux H, Boulard Y, Magn Reson Chem. 2006 Dec;44(12):1081-9. PMID:16972306
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