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| | {{STRUCTURE_1rvh| PDB=1rvh | SCENE= }} | | {{STRUCTURE_1rvh| PDB=1rvh | SCENE= }} |
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| - | '''SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC'''
| + | ===SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC=== |
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| - | ==Overview==
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| - | DNA A-tracts have been defined as four or more consecutive A.T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals that the former forms a left-handed superhelix with a diameter of approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of approximately 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_14739342}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 14739342 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_14739342}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVH OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVH OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Wu, H.]] | | [[Category: Wu, H.]] |
| | [[Category: Double helix]] | | [[Category: Double helix]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:57:31 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:45:31 2008'' |
Revision as of 10:45, 28 July 2008
Template:STRUCTURE 1rvh
SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC
Template:ABSTRACT PUBMED 14739342
About this Structure
Full experimental information is available from OCA.
Reference
DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum., Stefl R, Wu H, Ravindranathan S, Sklenar V, Feigon J, Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1177-82. Epub 2004 Jan 22. PMID:14739342
Page seeded by OCA on Mon Jul 28 13:45:31 2008
