Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding

Proceedings of the National Academy of Sciences of the United States of America
T M OkonogiBruce H Robinson

Abstract

An important component of protein-DNA recognition is the charge neutralization of DNA backbone phosphates and subsequent protein-induced DNA bending. Replacement of phosphates by neutral methylphosphonates has previously been shown to be a model for protein-induced bending. In addition to bending, the neutralization process may change the inherent flexibility of the DNA--a feature never before tested. We have developed a method to measure the differential flexibility of duplex DNA when methylphosphonate substitutions are made and find that the local flexibility is increased up to 40%. These results imply that backbone-neutralization-dependent DNA flexibility augments DNA-binding motifs in protein-DNA recognition processes.

References

Mar 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·A D Mirzabekov, A Rich
Feb 1, 1992·Biopolymers·R A Friedman, B Honig
Jan 1, 1990·Biopolymers·L Song, J M Schurr
Apr 1, 1989·Journal of Biomolecular Structure & Dynamics·G S ManningA Rich
Dec 16, 1994·Science·J K Strauss, L J Maher
Jul 12, 1996·Journal of Molecular Biology·K R Hagerman, P J Hagerman
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·G Patikoglou, S K Burley
Aug 19, 1997·Biochemistry·J K Strauss-Soukup, L J Maher
Feb 12, 1998·The Journal of Biological Chemistry·J K Strauss-Soukup, L J Maher
Feb 10, 1998·Biochemistry·J K Strauss-Soukup, L J Maher
Jan 1, 1997·Biopolymers·V A Bloomfield
Jul 1, 1998·Annual Review of Biophysics and Biomolecular Structure·J Widom
Aug 6, 1998·Biophysical Chemistry·J K Strauss-SoukupL J Maher
Mar 3, 1999·Journal of Biomolecular Structure & Dynamics·R Gurlie, K Zakrzewska
Dec 10, 1999·Biophysical Journal·T M OkonogiB H Robinson
Apr 25, 2000·Biophysical Journal·T M OkonogiB H Robinson
Oct 13, 2006·Biophysical Chemistry·A Sivolob, S N Khrapunov

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Citations

Dec 4, 2003·Journal of the American Society for Mass Spectrometry·Allison S Danell, Joel H Parks
May 19, 2010·Quarterly Reviews of Biophysics·Justin P Peters, L James Maher
May 23, 2012·Journal of the American Chemical Society·Heera Krishna, Marvin H Caruthers
Feb 14, 2006·Nature Structural & Molecular Biology·Robert L Eoff, Kevin D Raney
Aug 4, 2004·Nucleic Acids Research·Janine B Mills, Paul J Hagerman
Mar 4, 2008·Nucleic Acids Research·Songon AnKarin Musier-Forsyth
Sep 23, 2008·Nucleic Acids Research·Pavol CekanSnorri Th Sigurdsson
Nov 13, 2013·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Janice WilsonDiane M Stearns
Dec 24, 2002·Biophysical Journal·T M OkonogiB H Robinson
Apr 30, 2003·Biopolymers·Gerald S Manning
Oct 26, 2018·Physical Chemistry Chemical Physics : PCCP·Liangzhen ZhengYuguang Mu
Dec 13, 2018·Nucleic Acids Research·Korbinian Liebl, Martin Zacharias
Feb 17, 2007·The Journal of Biological Chemistry·Vincent J Cannistraro, John-Stephen Taylor
Nov 15, 2019·Methods : a Companion to Methods in Enzymology·Pata-Eting Kougnassoukou TcharaJean-Philippe Lambert
Apr 21, 2020·Journal of Structural Biology·Romain RetureauBrigitte Hartmann
Jun 12, 2012·Journal of Chemical Theory and Computation·Justin SpiritiArjan van der Vaart
Nov 1, 2018·Chemical Reviews·Alexandre Esadze, James T Stivers
May 6, 2015·The Journal of Physical Chemistry. B·Soumen Saha, G Narahari Sastry
Jan 10, 2018·Journal of the American Chemical Society·Jeffrey R ViereggMatthew V Tirrell
Oct 8, 2004·Journal of the American Chemical Society·Junji IwaharaG Marius Clore

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