132d
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(New page: 200px<br /><applet load="132d" size="450" color="white" frame="true" align="right" spinBox="true" caption="132d" /> '''SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX G...)
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Revision as of 19:44, 24 November 2007
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SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE
Overview
The solution structure of the self-complementary DNA duplex, [d(GCCGTTAACGGC)]2, which contains the HpaI restriction site GTTAAC, has, been elucidated by two-dimensional NMR, distance geometry (DG), and NOE, back-calculation methods. Initial distance constraints were determined by, polynomial fitting the two-spin initial NOE rates; backbone constraints, from NOE and J-coupling observations (Kim et al., 1992) were included., RMSDs between initial-distance-refined structures derived from, random-embedded DG, A-DNA, and B-DNA starting structures were all in the, range 0.5-1.0 A, indicating good convergence properties of the algorithm, regardless of the starting structure. A semiautomatic back-calculation, refinement procedure was developed and used to generate more refined, structures for which the BKCALC-simulated NOE volumes matched the, experimental data. The six final structures refined from various starting, structures exhibit very good agreement with the experimental data (R, values = 0.18) and converge well to within 0.8-A RMSD differences for the, central 8 base pairs. The torsion and pseudorotation phase angles were, found to be well determined by the data, and the local helical parameters, for each base step converged quite well. The final structures show that, the central T6-A7 step is somewhat underwound (twist angle ca. 29, degrees), with a large negative cup and a normal (wide) minor groove, width, while the T5-T6 and A7-A8 steps have a partially narrowed minor, groove.
About this Structure
132D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site., Kim SG, Reid BR, Biochemistry. 1992 Dec 8;31(48):12103-16. PMID:1457407
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