1NEV

A-tract decamer

Summary for 1NEV

• Entry DOI: 10.2210/pdb1nev/pdb
• Descriptor: 5'-D(*GP*GP*CP*AP*AP*AP*AP*CP*GP*G)-3', 5'-D(*CP*CP*GP*TP*TP*TP*TP*GP*CP*C)-3' (2 entities in total)
• Functional Keywords: a-tract, dna bending, dna decamer, dna
• Total number of polymer chains: 2
• Total formula weight: 6090.01

Authors

Barbic, A.,Zimmer, D.P.,Crothers, D.M. (deposition date: 2002-12-11, release date: 2003-03-11, Last modification date: 2024-05-22)

Primary citation

Barbic, A.,Zimmer, D.P.,Crothers, D.M.
Structural origins of adenine-tract bending
Proc.Natl.Acad.Sci.USA, 100:2369-2373, 2003

PubMed Abstract: 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.

PubMed: 12586860
DOI: 10.1073/pnas.0437877100

Experimental method

SOLUTION NMR