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

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...

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Autores principales: Imeddourene, Akli Ben, Xu, Xiaoqian, Zargarian, Loussiné, Oguey, Christophe, Foloppe, Nicolas, Mauffret, Olivier, Hartmann, Brigitte
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838374/
https://www.ncbi.nlm.nih.gov/pubmed/26883628
http://dx.doi.org/10.1093/nar/gkw084
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author Imeddourene, Akli Ben
Xu, Xiaoqian
Zargarian, Loussiné
Oguey, Christophe
Foloppe, Nicolas
Mauffret, Olivier
Hartmann, Brigitte
author_facet Imeddourene, Akli Ben
Xu, Xiaoqian
Zargarian, Loussiné
Oguey, Christophe
Foloppe, Nicolas
Mauffret, Olivier
Hartmann, Brigitte
author_sort Imeddourene, Akli Ben
collection PubMed
description 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 (D(inter)) 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 D(inter) 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 supplies new information on the fraying events, otherwise neglected.
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spelling pubmed-48383742016-04-21 The intrinsic mechanics of B-DNA in solution characterized by NMR Imeddourene, Akli Ben Xu, Xiaoqian Zargarian, Loussiné Oguey, Christophe Foloppe, Nicolas Mauffret, Olivier Hartmann, Brigitte Nucleic Acids Res Structural Biology 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 (D(inter)) 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 D(inter) 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 supplies new information on the fraying events, otherwise neglected. Oxford University Press 2016-04-20 2016-02-15 /pmc/articles/PMC4838374/ /pubmed/26883628 http://dx.doi.org/10.1093/nar/gkw084 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Structural Biology
Imeddourene, Akli Ben
Xu, Xiaoqian
Zargarian, Loussiné
Oguey, Christophe
Foloppe, Nicolas
Mauffret, Olivier
Hartmann, Brigitte
The intrinsic mechanics of B-DNA in solution characterized by NMR
title The intrinsic mechanics of B-DNA in solution characterized by NMR
title_full The intrinsic mechanics of B-DNA in solution characterized by NMR
title_fullStr The intrinsic mechanics of B-DNA in solution characterized by NMR
title_full_unstemmed The intrinsic mechanics of B-DNA in solution characterized by NMR
title_short The intrinsic mechanics of B-DNA in solution characterized by NMR
title_sort intrinsic mechanics of b-dna in solution characterized by nmr
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838374/
https://www.ncbi.nlm.nih.gov/pubmed/26883628
http://dx.doi.org/10.1093/nar/gkw084
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