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167d
From Proteopedia
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THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS
Overview
The single-crystal X-ray analysis of trigonal C-C-A-T-T-A-A-T-G-G, and its, comparison with orthorhombic C-G-A-T-T-A-A-T-C-G, have shown that the, A-T-T-A-A-T sequence has limited polymorphism under the influence of, packing forces from neighboring molecules in the crystal. The T-A step is, intrinsically variable. It is not inconsistent with a large propeller, twist, a narrow minor groove, and a single spine of hydration, as has, sometimes been claimed on theoretical grounds. The T-A step does show a, persistent positive roll, in a direction that compresses the major groove, and this may be a significant factor in macroscopic DNA curvature induced, by phased A-tracts. A-tracts, as understood in this paper, include A-A and, A-T steps, but not the T-A step, which is disruptive. Three conclusions, regarding A-tract-induced curvature can be drawn from this and other X-ray, crystal structure analyses, and from key gel retardation experiments: (1), The A-tract bending model is disqualified on two grounds: (i) tilt-wedge, bending within A-tracts is incompatible with the observed direction of, curvature; (ii) roll-wedge bending within A-tracts is contradicted by, every crystal structure analysis, and is inconsistent with gel retardation, results for (G-C-A-A-A-A-T-T-T-T)n and for (A-A-A-A-A-T-T-T-T-T)n. (2) The, junction bend model is contradicted by crystallography because: (i) the, inclination of base-pairs does not change between A-tract and non-A-tract, regions of helix; and (ii) the observed bends at GC/AT junctions are, roll-wedge bends, not tilt-wedge as the junction bend model demands. (3), The non-A-tract bending model is consistent with both gel retardation data, and with X-ray crystallography, and must be regarded as the only, consistent model for A-tract bending.
About this Structure
167D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps., Goodsell DS, Kaczor-Grzeskowiak M, Dickerson RE, J Mol Biol. 1994 May 27;239(1):79-96. PMID:8196049
Page seeded by OCA on Sat Nov 24 22:02:41 2007
