The intrinsic mechanics of B-DNA in solution characterized by NMR

Nucleic Acids Research
Akli Ben ImeddoureneBrigitte Hartmann

Abstract

Experimental characterization of the structural couplings in free B-DNA in solution has been elusive, because of subtle effects that are challenging to tackle. Here, the exploitation of the NMR measurements collected on four dodecamers containing a substantial set of dinucleotide sequences provides new, consistent correlations revealing the DNA intrinsic mechanics. The difference between two successive residual dipolar couplings (ΔRDCs) involving C6/8-H6/8, C3'-H3' and C4'-H4' vectors are correlated to the (31)P chemical shifts (δP), which reflect the populations of the BI and BII backbone states. The δPs are also correlated to the internucleotide distances (Dinter) involving H6/8, H2' and H2″ protons. Calculations of NMR quantities on high resolution X-ray structures and controlled models of DNA enable to interpret these couplings: the studied ΔRDCs depend mostly on roll, while Dinter are mainly sensitive to twist or slide. Overall, these relations demonstrate how δP measurements inform on key inter base parameters, in addition to probe the BI↔BII backbone equilibrium, and shed new light into coordinated motions of phosphate groups and bases in free B-DNA in solution. Inspection of the 5' and 3' ends of the dodecamers also sup...Continue Reading

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Citations

Dec 22, 2016·International Journal of Molecular Sciences·Qiulong ZhangGe Zhang
Jun 7, 2016·Scientific Reports·Akiko HatakeyamaMalcolm Buckle
Aug 19, 2017·Journal of Biomolecular Structure & Dynamics·Justin P PetersL James Maher
Apr 9, 2019·Nucleic Acids Research·Alexandra BalaceanuModesto Orozco
Oct 2, 2017·Journal of Molecular Modeling·Debasish Mukherjee, Dhananjay Bhattacharyya
Sep 24, 2019·Nucleic Acids Research·Timothy D CraggsAchillefs N Kapanidis
Nov 6, 2020·Scientific Reports·A Ben ImeddoureneO Mauffret
Mar 4, 2020·ACS Central Science·Camilla CalabreseEmilio J Cocinero
Apr 21, 2020·Journal of Structural Biology·Romain RetureauBrigitte Hartmann
Nov 28, 2017·The Journal of Physical Chemistry. B·Loussiné ZargarianOlivier Mauffret

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