1ikk
From Proteopedia
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'''Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts''' | '''Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts''' | ||
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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=1IKK OCA]. | |
==Reference== | ==Reference== | ||
Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts., Mack DR, Chiu TK, Dickerson RE, J Mol Biol. 2001 Oct 5;312(5):1037-49. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11580248 11580248] | Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts., Mack DR, Chiu TK, Dickerson RE, J Mol Biol. 2001 Oct 5;312(5):1037-49. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11580248 11580248] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Chiu, T K.]] | [[Category: Chiu, T K.]] | ||
[[Category: Dickerson, R E.]] | [[Category: Dickerson, R E.]] | ||
[[Category: Mack, D R.]] | [[Category: Mack, D R.]] | ||
| - | [[Category: | + | [[Category: A-tract containing a t-a step]] |
| - | [[Category: | + | [[Category: B-dna double helix]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:06:11 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 17:06, 2 May 2008
Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts
Overview
Introduction of a T-A or pyrimidine-purine step into a straight and rigid A-tract can cause a positive roll deformation that kinks the DNA helix at that step. In CCTTTAAAGG, the central T-A step has an 8.6 degrees bend toward the major groove. We report the structural analysis of CCTTTAAAGG and a comparison with 25 other representative crystal structures from the NDB containing at least four consecutive A or T bases. On average, more local bending occurs at the disruptive T-A step (8.21 degrees ) than at an A-T step (5.71 degrees ). In addition, A-tracts containing an A-T step are more bent than are pure A-tracts, and hence A-A and A-T steps are not equivalent. All T-A steps examined exhibit positive roll, bending towards the major groove, while A-T steps display negative roll and bend slightly towards the minor groove. This illustrates how inherent negative and positive roll are, respectively, at A-T and T-A steps within A-tracts. T-A steps are more deformable, showing larger and more variable deformations of minor groove width, rise, cup, twist, and buckle. Standard deviations of twist, rise, and cup for T-A steps are 6.66 degrees, 0.55 A, and 15.90 degrees, versus 2.28 degrees, 0.21 A, and 2.99 degrees for A-T steps. Packing constraints determine which local values of these helical parameters an individual T-A step will adopt. For instance, with CCTTTAAAGG and three isomorphous structures, CGATTAATCG, CGATATATCG, and CGATCGATCG, crystal packing forces lead to a series of correlated changes: widened minor groove, large slide, low twist, and large rise. The difference in helical parameters between A-T steps lying within A-tracts, versus A-T steps within alternating AT sequences, demonstrates the importance of neighboring steps on the conformation of a given dinucleotide step.
About this Structure
Full crystallographic information is available from OCA.
Reference
Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts., Mack DR, Chiu TK, Dickerson RE, J Mol Biol. 2001 Oct 5;312(5):1037-49. PMID:11580248 Page seeded by OCA on Fri May 2 20:06:11 2008
