Alpha/gamma Transitions in the B-DNA backbone

Varnai, Peter, Djuranovic, Dragana, Lavery, Richard and Hartmann, Brigitte (2002) Alpha/gamma Transitions in the B-DNA backbone. Nucleic Acids Research, 30 (24). pp. 5398-5406. ISSN 0305-1048

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Abstract

In the crystal structures of protein complexes with B DNA, a and ¿ DNA backbone torsion angles often exhibit non canonical values. It is not known if these alternative backbone conformations are easily accessible in solution and can contribute to the specific recognition of DNA by proteins. We have analysed the coupled transition of the a and ¿ torsion angles within the central GpC step of a B DNA dodecamer by computer simulations. Five stable or metastable non canonical a/¿ sub states are found. The most favourable pathway from the canonical a/¿ structure to any unusual form involves a counter rotation of a and ¿, via the trans conformation. However, the corresponding free energy indicates that spontaneous flipping of the torsions is improbable in free B DNA. This is supported by an analysis of the available high resolution crystallographic structures showing that unusual a/¿ states are only encountered in B DNA complexed to proteins. An analysis of the structural consequences of a/¿ transitions shows that the non canonical backbone geometry influences essentially the roll and twist values and reduces the equilibrium dispersion of structural parameters. Our results support the hypothesis that unusual a/¿ backbones arise during protein¿DNA complexation, assisting the fine structural adjustments between the two partners and playing a role in the overall complexation free energy.

Item Type: Article
Additional Information: PV+ BH designed research, DD performed crystal database analysis, PV performed computer simulations and analyzed data, PV, RL+ BH wrote the paper. First combined survey of conformational transitions in the B-DNA backbone from crystal structures and computer simulations identifying five conformational sub-states, cited 28 times.
Schools and Departments: School of Life Sciences > Chemistry
Depositing User: Peter Varnai
Date Deposited: 06 Feb 2012 18:51
Last Modified: 07 Mar 2017 03:42
URI: http://sro.sussex.ac.uk/id/eprint/18679

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