Recognizing DNA

Quarterly Reviews of Biophysics
R Lavery

Abstract

It has become clear that there is no simple 'code' for protein-DNA recognition and that selecting an optimal binding sequence along the DNA double helix corresponds to more than simply forming a set of specific hydrogen bonds or steric interactions. However, it has been difficult to characterize the so-called indirect components of recognition. While DNA deformation certainly underlies indirect recognition, it is not easy to determine how local fine structure and deformability depend on base sequence or exactly what percentage of recognition should be attributed to such factors. Molecular modelling can help to develop these ideas into a quantitative model, provided the calculations can be carried out fast enough to enable a comprehensive survey of base-sequence effects. I present here some recent results from our group and their consequences for improving our understanding of protein-DNA binding, and their potential for predicting, and eventually modulating, protein-DNA binding.

Citations

Aug 28, 2007·Nucleic Acids Research·Jennifer L EklundRaymond J Monnat
Nov 19, 2009·Nucleic Acids Research·Brahim HeddiBrigitte Hartmann
Mar 26, 2010·Annual Review of Biochemistry·Remo RohsRichard S Mann
Sep 13, 2012·BMC Bioinformatics·Piotr SetnyMartin Zacharias
Feb 18, 2016·Nucleic Acids Research·Akli Ben ImeddoureneBrigitte Hartmann
Jul 16, 2014·International Journal of Molecular Sciences·Sabrina Harteis, Sabine Schneider
Feb 17, 2010·Journal of Molecular Biology·C Evalena AnderssonKarin Carlson
Sep 11, 2007·Biochimie·Stavroula A CoulocheriAthanasios G Papavassiliou
Nov 3, 2010·Journal of Molecular Recognition : JMR·F SousaJ A Queiroz
May 9, 2016·Trends in Biochemical Sciences·Jason C Bell, Stephen C Kowalczykowski
Dec 15, 2015·PLoS Computational Biology·Akli Ben ImeddoureneBrigitte Hartmann
Nov 1, 2007·Organic & Biomolecular Chemistry·James Garner, Margaret M Harding
Jun 6, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Chantal PrévostRichard Lavery
May 3, 2018·Nucleic Acids Research·Adam J BogdanoveBarry L Stoddard

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