1rvh
From Proteopedia
(New page: 200px<br /><applet load="1rvh" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rvh" /> '''SOLUTION STRUCTURE OF THE DNA DODECAMER GCAA...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1rvh.jpg|left|200px]]<br /><applet load="1rvh" size=" | + | [[Image:1rvh.jpg|left|200px]]<br /><applet load="1rvh" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rvh" /> | caption="1rvh" /> | ||
'''SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC'''<br /> | '''SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC'''<br /> | ||
==Overview== | ==Overview== | ||
| - | DNA A-tracts have been defined as four or more consecutive A.T base pairs | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1RVH 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:// | + | 1RVH 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=1RVH OCA]. |
==Reference== | ==Reference== | ||
| Line 19: | Line 19: | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:54:59 2008'' |
Revision as of 12:54, 21 February 2008
|
SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC
Overview
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.
About this Structure
1RVH is a Protein complex structure of sequences from [1]. Full crystallographic 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 Thu Feb 21 14:54:59 2008
