1nev
From Proteopedia
(New page: 200px<br /><applet load="1nev" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nev" /> '''A-tract decamer'''<br /> ==Overview== DNA s...) |
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| - | [[Image:1nev.gif|left|200px]]<br /><applet load="1nev" size=" | + | [[Image:1nev.gif|left|200px]]<br /><applet load="1nev" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''A-tract decamer'''<br /> | '''A-tract decamer'''<br /> | ||
==Overview== | ==Overview== | ||
| - | DNA sequences containing short adenine tracts are intrinsically curved and | + | DNA sequences containing short adenine tracts are intrinsically curved and play a role in transcriptional regulation. Despite many high-resolution NMR and x-ray studies, the origins of curvature remain disputed. Long-range restraints provided by 85 residual dipolar couplings were measured for a DNA decamer containing an adenine (A)(4)-tract and used to refine the structure. The overall bend in the molecule is a result of in-phase negative roll in the A-tract and positive roll at its 5' junction, as well as positive and negative tilt inside the A-tract and near its junctions. The bend magnitude and direction obtained from NMR structures is 9.0 degrees into the minor groove in a coordinate frame located at the third AT base pair. We evaluated long-range and wedge models for DNA curvature and concluded that our data for A-tract curvature are best explained by a "delocalized bend" model. The global bend magnitude and direction of the NMR structure are in excellent agreement with the junction model parameters used to rationalize gel electrophoretic data and with preliminary results of a cyclization kinetics assay from our laboratory. |
==About this Structure== | ==About this Structure== | ||
| - | 1NEV 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:// | + | 1NEV 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=1NEV OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Barbic, A.]] | [[Category: Barbic, A.]] | ||
| - | [[Category: Crothers, D | + | [[Category: Crothers, D M.]] |
| - | [[Category: Zimmer, D | + | [[Category: Zimmer, D P.]] |
[[Category: a-tract]] | [[Category: a-tract]] | ||
[[Category: dna bending]] | [[Category: dna bending]] | ||
[[Category: dna decamer]] | [[Category: dna decamer]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:05:21 2008'' |
Revision as of 12:05, 21 February 2008
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A-tract decamer
Overview
DNA sequences containing short adenine tracts are intrinsically curved and play a role in transcriptional regulation. Despite many high-resolution NMR and x-ray studies, the origins of curvature remain disputed. Long-range restraints provided by 85 residual dipolar couplings were measured for a DNA decamer containing an adenine (A)(4)-tract and used to refine the structure. The overall bend in the molecule is a result of in-phase negative roll in the A-tract and positive roll at its 5' junction, as well as positive and negative tilt inside the A-tract and near its junctions. The bend magnitude and direction obtained from NMR structures is 9.0 degrees into the minor groove in a coordinate frame located at the third AT base pair. We evaluated long-range and wedge models for DNA curvature and concluded that our data for A-tract curvature are best explained by a "delocalized bend" model. The global bend magnitude and direction of the NMR structure are in excellent agreement with the junction model parameters used to rationalize gel electrophoretic data and with preliminary results of a cyclization kinetics assay from our laboratory.
About this Structure
1NEV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural origins of adenine-tract bending., Barbic A, Zimmer DP, Crothers DM, Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2369-73. Epub 2003 Feb 13. PMID:12586860
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