DNA structures from phosphate chemical shifts.

Nucleic Acids Research
Joséphine Abi-GhanemBrigitte Hartmann

Abstract

For B-DNA, the strong linear correlation observed by nuclear magnetic resonance (NMR) between the (31)P chemical shifts (deltaP) and three recurrent internucleotide distances demonstrates the tight coupling between phosphate motions and helicoidal parameters. It allows to translate deltaP into distance restraints directly exploitable in structural refinement. It even provides a new method for refining DNA oligomers with restraints exclusively inferred from deltaP. Combined with molecular dynamics in explicit solvent, these restraints lead to a structural and dynamical view of the DNA as detailed as that obtained with conventional and more extensive restraints. Tests with the Jun-Fos oligomer show that this deltaP-based strategy can provide a simple and straightforward method to capture DNA properties in solution, from routine NMR experiments on unlabeled samples.

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Citations

Jan 1, 2013·Nucleic Acids Research·Josephine Abi-GhanemM Teresa Pisabarro
Jun 27, 2013·BMC Bioinformatics·Petr ČechDaniel Svozil
Jul 31, 2012·PloS One·Marc GuéroultBrigitte Hartmann
Jul 26, 2013·The Journal of Chemical Physics·Reynier SuardíazMichele Vendruscolo
Nov 16, 2010·Journal of the American Chemical Society·Jana PřecechtělováVladimír Sklenář
Dec 6, 2019·Stem Cell Research & Therapy·Karl-Henrik GrinnemoCecilia Österholm
Jun 13, 2020·Analytical Chemistry·Fatema BhinderwalaRobert Powers
Mar 12, 2013·Journal of Chemical Theory and Computation·Jana PřecechtělováVladimír Sklenář
Dec 10, 2016·The Journal of Physical Chemistry Letters·Alexandra BalaceanuModesto Orozco
Sep 17, 2021·Journal of Chemical Information and Modeling·Ivan A StrelnikovElena A Zubova
Dec 31, 2010·Biophysical Journal·Sergei L GrokhovskyYury D Nechipurenko
Nov 4, 2021·Journal of Computational Chemistry·Jiří FukalVladimír Sychrovský

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Methods Mentioned

BETA
conventional
NMR
X-ray

Software Mentioned

MD
AMBER
ref
CHESHIRE
SHAKE
Parmbsc0
Parm98
δP

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