31P NMR investigation of backbone dynamics in DNA binding sites.

The Journal of Physical Chemistry. B
Ye TianMary E Hatcher

Abstract

The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein--DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here, we use 31P dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson dodecamer, a sequence containing the EcoRI binding site, and confirm solid-state 2H NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps, but this effect is localized to only near neighbors and base-pairing partners. Last, we have been able to characterize the percent BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the noncanonical BII conformation, even at low temperatures. Our results demonstrate that 31P dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful meth...Continue Reading

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Citations

Nov 28, 2009·Nucleic Acids Research·Joséphine Abi-GhanemBrigitte Hartmann
Oct 6, 2015·Biomolecules·Junji IwaharaLevani Zandarashvili
Nov 21, 2015·Journal of Chemical Theory and Computation·Marie ZgarbováPetr Jurečka
Jun 15, 2016·Journal of Chemical Theory and Computation·Rodrigo Galindo-MurilloThomas E Cheatham
Dec 10, 2016·The Journal of Physical Chemistry Letters·Alexandra BalaceanuModesto Orozco
Apr 12, 2017·Journal of Chemical Theory and Computation·Justin A Lemkul, Alexander D MacKerell
Feb 18, 2016·Nucleic Acids Research·Akli Ben ImeddoureneBrigitte Hartmann
Apr 17, 2016·Nucleic Acids Research·Pablo D DansModesto Orozco
Dec 15, 2015·PLoS Computational Biology·Akli Ben ImeddoureneBrigitte Hartmann
Apr 9, 2019·Nucleic Acids Research·Alexandra BalaceanuModesto Orozco
Apr 23, 2014·Journal of Computational Chemistry·Alexey Savelyev, Alexander D MacKerell
Oct 19, 2019·Nucleic Acids Research·Pablo D DansModesto Orozco
Nov 6, 2020·Scientific Reports·A Ben ImeddoureneO Mauffret
Mar 25, 2009·Journal of the American Chemical Society·Eric D HorowitzNicholas V Hud
Apr 21, 2020·Journal of Structural Biology·Romain RetureauBrigitte Hartmann
Nov 16, 2010·Journal of the American Chemical Society·Jana PřecechtělováVladimír Sklenář
Aug 27, 2013·Journal of Chemical Theory and Computation·Tomáš DršataFilip Lankaš
Mar 12, 2013·Journal of Chemical Theory and Computation·Jana PřecechtělováVladimír Sklenář
Sep 24, 2013·Journal of Chemical Theory and Computation·Marie ZgarbováPetr Jurečka
Mar 1, 2012·Journal of Chemical Theory and Computation·Katarina HartAlexander D Mackerell
Oct 24, 2009·Journal of Molecular Biology·Brahim HeddiBrigitte Hartmann
Nov 4, 2021·Journal of Computational Chemistry·Jiří FukalVladimír Sychrovský

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