167d: Difference between revisions

Revision as of 12:38, 21 February 2008

THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS

OverviewOverview

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 StructureAbout this Structure

167D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

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

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-[[Image:167d.gif|left|200px]]<br /><applet load="167d" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="167d, resolution 2.300&Aring;" />
 '''THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS'''<br />
 ==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.
+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==
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=167D OCA].
+D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=167D 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8196049 8196049]
 [[Category: Protein complex]]
-[[Category: Dickerson, R.E.]]
+[[Category: Dickerson, R E.]]
-[[Category: Goodsell, D.S.]]
+[[Category: Goodsell, D S.]]
 [[Category: Kaczor-Grzeskowiak, M.]]
 [[Category: b-dna]]
 [[Category: double helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:02:41 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:38:38 2008''