The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.

Base Sequence DNA / chemistry DNA, B-Form / chemistry Molecular Dynamics Simulation

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
02 12 2019
Historique:
accepted: 06 10 2019
revised: 25 09 2019
received: 18 05 2019
pubmed: 19 10 2019
medline: 12 5 2020
entrez: 19 10 2019
Statut: ppublish

Résumé

We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distribution of its stochastic dynamics. Our analysis includes a study of first and second moments of the equilibrium distribution, which can be accurately captured by a harmonic model, but with nonlocal sequence-dependence. We characterize the sequence-dependent choreography of backbone and base movements modulating the non-Gaussian or anharmonic effects manifested in the higher moments of the dynamics of the duplex when sampling the equilibrium distribution. Contrary to prior assumptions, such anharmonic deformations are not rare in DNA and can play a significant role in determining DNA conformation within complexes. Polymorphisms in helical geometries are particularly prevalent for certain tetranucleotide sequence contexts and are always coupled to a complex network of coordinated changes in the backbone. The analysis of our simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine-Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.

Identifiants

DOI: 10.1093/nar/gkz905 PMID: 31624840 PMC: PMC6868377
pubmed: 31624840
pii: 5590661
doi: 10.1093/nar/gkz905
pmc: PMC6868377
doi:

Substances chimiques

DNA, B-Form 0
DNA 9007-49-2

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

11090-11102

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

Références

J Mol Biol. 1982 Oct 25;161(2):343-52
pubmed: 7154084
Nucleic Acids Res. 2010 Jan;38(1):299-313
pubmed: 19850719
J Biol Chem. 1982 Dec 25;257(24):14686-707
pubmed: 7174662
Nucleic Acids Res. 2009 Sep;37(17):5917-29
pubmed: 19625494
Nucleic Acids Res. 2014 Oct;42(18):11304-20
pubmed: 25223784
Nucleic Acids Res. 2016 May 19;44(9):4052-66
pubmed: 27084952
Biophys J. 2005 Dec;89(6):3721-40
pubmed: 16169978
Nucleic Acids Res. 1993 Feb 11;21(3):561-8
pubmed: 8441668
BMC Bioinformatics. 2006 Oct 03;7:429
pubmed: 17018151
Curr Opin Struct Biol. 2016 Apr;37:29-45
pubmed: 26708341
Nat Chem Biol. 2009 Nov;5(11):789-96
pubmed: 19841628
J Am Chem Soc. 2007 Nov 28;129(47):14739-45
pubmed: 17985896
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
J Am Chem Soc. 2006 Jul 19;128(28):9170-7
pubmed: 16834390
Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9
pubmed: 5040245
Curr Protoc Nucleic Acid Chem. 2001 Nov;Chapter 7:Unit 7.5
pubmed: 18428873
Nucleic Acids Res. 2014 Nov 10;42(20):e153
pubmed: 25228467
Nucleic Acids Res. 2012 Apr;40(8):3714-22
pubmed: 22180536
Structure. 2006 Oct;14(10):1527-34
pubmed: 17027501
Biophys J. 2007 Jun 1;92(11):3817-29
pubmed: 17351000
J Am Chem Soc. 2006 May 31;128(21):6885-92
pubmed: 16719468
Nucleic Acids Res. 2012 Nov;40(21):10668-78
pubmed: 23012264
Annu Rev Biochem. 2010;79:233-69
pubmed: 20334529
Phys Rev Lett. 2003 Apr 4;90(13):138101
pubmed: 12689326
J Chem Theory Comput. 2013 Sep 10;9(9):3878-88
pubmed: 26592383
J Mol Biol. 2008 Oct 17;382(4):956-70
pubmed: 18680751
Nat Methods. 2016 Jan;13(1):55-8
pubmed: 26569599
Nucleic Acids Res. 2016 Jun 20;44(11):5450-6
pubmed: 27098037
J Chem Theory Comput. 2013 Jul 9;9(7):3084-95
pubmed: 26583988
Nucleic Acids Res. 2002 Dec 15;30(24):5398-406
pubmed: 12490708
J Biomol Struct Dyn. 2005 Aug;23(1):13-27
pubmed: 15918673
J Chem Phys. 2013 Feb 7;138(5):055102
pubmed: 23406150
Bioinformatics. 2013 Jul 01;29(13):i71-9
pubmed: 23813011
Nucleic Acids Res. 2017 Apr 20;45(7):4217-4230
pubmed: 28088759
J Phys Chem Lett. 2017 Jan 5;8(1):21-28
pubmed: 27935717
J Phys Chem B. 2009 Mar 5;113(9):2596-603
pubmed: 18717548
Nucleic Acids Res. 2019 May 21;47(9):4418-4430
pubmed: 30957854
PLoS Comput Biol. 2015 Dec 10;11(12):e1004631
pubmed: 26657165
J Chem Theory Comput. 2017 Apr 11;13(4):1539-1555
pubmed: 28029797
Acc Chem Res. 2012 Feb 21;45(2):196-205
pubmed: 21830782
J Biomol Struct Dyn. 2003 Jun;20(6):771-88
pubmed: 12744707
Nucleic Acids Res. 2018 Jul 2;46(W1):W5-W10
pubmed: 29905876
Philos Trans R Soc Lond B Biol Sci. 2004 Aug 29;359(1448):1237-47; discussion 1247-8
pubmed: 15306379
J Chem Theory Comput. 2013;9(1):707-721
pubmed: 23976886
Nucleic Acids Res. 2014 Oct 29;42(19):12272-83
pubmed: 25260586
Biochemistry. 2007 Feb 6;46(5):1152-66
pubmed: 17260945
J Biomol Struct Dyn. 2000 Jun;17(6):1001-9
pubmed: 10949167
J Mol Biol. 1983 May 25;166(3):419-41
pubmed: 6854650
Biophys J. 2004 Dec;87(6):3799-813
pubmed: 15326025
J Chem Inf Model. 2017 Feb 27;57(2):275-287
pubmed: 28059516
Nucleic Acids Res. 2008 Jun;36(11):3690-706
pubmed: 18477633
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W47-55
pubmed: 23685436
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021903
pubmed: 23005781
Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
pubmed: 9736707
J Am Chem Soc. 2006 Jan 25;128(3):678-9
pubmed: 16417331
Nucleic Acids Res. 2016 Jan 4;44(D1):D272-8
pubmed: 26612862

Auteurs

Pablo D Dans (PD)

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.
Department of Biological Sciences, University of the Republic (UdelaR), CENUR Gral. Rivera 1350, 50000 Salto, Uruguay.

Alexandra Balaceanu (A)

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Marco Pasi (M)

LBPA, École normale supérieure Paris-Saclay, 61 Av. du Pdt Wilson, Cachan 94235, France.
Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France.

Alessandro S Patelli (AS)

Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.

Daiva Petkevičiūtė (D)

Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Studentų g. 50, 51368 Kaunas, Lithuania.

Jürgen Walther (J)

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Adam Hospital (A)

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Genís Bayarri (G)

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Richard Lavery (R)

Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France.

John H Maddocks (JH)

Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.

Modesto Orozco (M)

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.
Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › The static and dynamic structural...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › The static and dynamic structural...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Forme B de l'ADN › The static and dynamic structural...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Simulation numérique › Simulation de dynamique moléculaire › The static and dynamic structural...