1IKK

Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts

Summary for 1IKK

• Entry DOI: 10.2210/pdb1ikk/pdb
• Descriptor: 5'-D(*CP*CP*TP*TP*TP*AP*AP*AP*GP*G)-3', MAGNESIUM ION (3 entities in total)
• Functional Keywords: b-dna double helix, a-tract containing a t-a step, dna
• Total number of polymer chains: 2
• Total formula weight: 6185.25

Authors

Mack, D.R.,Chiu, T.K.,Dickerson, R.E. (deposition date: 2001-05-03, release date: 2001-10-05, Last modification date: 2024-04-03)

Primary citation

Mack, D.R.,Chiu, T.K.,Dickerson, R.E.
Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts.
J.Mol.Biol., 312:1037-1049, 2001

PubMed Abstract: 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.

PubMed: 11580248
DOI: 10.1006/jmbi.2001.4994

Experimental method

X-RAY DIFFRACTION (1.6 Å)