167d
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:167d.gif|left|200px]] | [[Image:167d.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_167d", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_167d| PDB=167d | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS''' | '''THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=167D OCA]. | |
==Reference== | ==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://www.ncbi.nlm.nih.gov/pubmed/8196049 8196049] | 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://www.ncbi.nlm.nih.gov/pubmed/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: Kaczor-Grzeskowiak, M.]] | ||
| - | [[Category: | + | [[Category: B-dna]] |
| - | [[Category: | + | [[Category: Double helix]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:32:15 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 06:32, 2 May 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
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
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 Fri May 2 09:32:15 2008
