1ssv
From Proteopedia
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Compensating bends in a 16 base-pair DNA oligomer containing a T3A3 segment
Overview
In-phase ligated DNA containing T(n)A(n) segments fail to exhibit the, retarded polyacrylamide gel electrophoresis (PAGE) migration observed for, in-phase ligated A(n)T(n) segments, a behavior thought to be correlated, with macroscopic DNA curvature. The lack of macroscopic curvature in, ligated T(n)A(n) segments is thought to be due to cancellation of bending, in regions flanking the TpA steps. To address this issue, solution-state, NMR, including residual dipolar coupling (RDC) restraints, was used to, determine a high-resolution structure of [d(CGAGGTTTAAACCTCG)2], a DNA, oligomer containing a T3A3 tract. The overall magnitude and direction of, bending, including the regions flanking the central TpA step, was measured, using a radius of curvature, Rc, analysis. The Rc for the overall molecule, indicated a small magnitude of global bending (Rc = 138 +/- 23 nm) towards, the major groove, whereas the Rc for the two halves (72 +/- 33 nm and 69, +/- 14 nm) indicated greater localized bending into the minor groove. The, direction of bending in the regions flanking the TpA step is in partial, opposition (109 degrees), contributing to cancellation of bending. The, cancellation of bending did not correlate with a pattern of roll values at, the TpA step, or at the 5' and 3' junctions, of the T3A3 segment, suggesting a simple junction/roll model is insufficient to predict, cancellation of DNA bending in all T(n)A(n) junction sequence contexts., Importantly, Rc analysis of structures refined without RDC restraints, lacked the precision and accuracy needed to reliably measure bending.
About this Structure
1SSV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature., McAteer K, Aceves-Gaona A, Michalczyk R, Buchko GW, Isern NG, Silks LA, Miller JH, Kennedy MA, Biopolymers. 2004 Dec 15;75(6):497-511. PMID:15526287
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