1rvh
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(New page: 200px<br /><applet load="1rvh" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rvh" /> '''SOLUTION STRUCTURE OF THE DNA DODECAMER GCAA...)
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Revision as of 21:13, 24 November 2007
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SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC
Overview
DNA A-tracts have been defined as four or more consecutive A.T base pairs, without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on, polyacrylamide gels, first observed >20 years ago. An unsolved conundrum, is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures, of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG), [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including, refinement with residual dipolar couplings. Analysis of the structures, shows that the ApT step has a large negative roll, resulting in a local, bend toward the minor groove, whereas the TpA step has a positive roll and, locally bends toward the major groove. For A4T4, this bend is nearly in, phase with bends at the two A-tract junctions, resulting in an overall, bend toward the minor groove of the A-tract, whereas for T4A4, the bends, oppose each other, resulting in a relatively straight helix. NMR-based, structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals, that the former forms a left-handed superhelix with a diameter of, approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter, of approximately 50 A. Results of gel electrophoretic mobility studies are, consistent with the higher-order structure of the DNA and furthermore, depend on the nature of the monovalent cation present in the running, buffer.
About this Structure
1RVH is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum., Stefl R, Wu H, Ravindranathan S, Sklenar V, Feigon J, Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1177-82. Epub 2004 Jan 22. PMID:14739342
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