Literature DB >> 22039974

Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?

Alexey Savelyev1, Christopher K Materese, Garegin A Papoian.   

Abstract

Double-stranded DNA is among the stiffest biopolymers, whose bending propensity crucially influences many vital biological processes. It is not fully understood which among the two most likely forces, electrostatic self-repulsion or the compressive base pair stacking, plays a dominant role in determining the DNA's unique rigidity. Different theoretical and experimental studies led so far to contradictory results on this issue. In this Communication, we address this important question by means of Molecular Dynamics (MD) simulations using both atomistic and coarse-grained force fields. Using two independent sets of calculations, we found that electrostatic and nonelectrostatic effects play a comparable role in maintaining DNA's stiffness. Our findings substantially differ from predictions of existing theories for DNA rigidity and may indicate that a new conceptual understanding needs to be developed.
© 2011 American Chemical Society

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Year:  2011        PMID: 22039974     DOI: 10.1021/ja207984z

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  16 in total

1.  Sequence-dependent elasticity and electrostatics of single-stranded DNA: signatures of base-stacking.

Authors:  Dustin B McIntosh; Gina Duggan; Quentin Gouil; Omar A Saleh
Journal:  Biophys J       Date:  2014-02-04       Impact factor: 4.033

2.  All-atom polarizable force field for DNA based on the classical Drude oscillator model.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2014-04-18       Impact factor: 3.376

3.  BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.

Authors:  Archana N Rao; David W Grainger
Journal:  Biomater Sci       Date:  2014-04-01       Impact factor: 6.843

4.  Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2015-03-18       Impact factor: 2.991

5.  Challenge of mimicking the influences of the cellular environment on RNA structure by PEG-induced macromolecular crowding.

Authors:  Jillian Tyrrell; Kevin M Weeks; Gary J Pielak
Journal:  Biochemistry       Date:  2015-10-15       Impact factor: 3.162

6.  Chromatin remodelers fine-tune H3K36me-directed deacetylation of neighbor nucleosomes by Rpd3S.

Authors:  Chul-Hwan Lee; Jun Wu; Bing Li
Journal:  Mol Cell       Date:  2013-09-19       Impact factor: 17.970

7.  Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.

Authors:  Franziska Kriegel; Niklas Ermann; Ruaridh Forbes; David Dulin; Nynke H Dekker; Jan Lipfert
Journal:  Nucleic Acids Res       Date:  2017-06-02       Impact factor: 16.971

8.  Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2017-04-19       Impact factor: 6.006

9.  Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2015-08-26       Impact factor: 6.006

10.  Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA.

Authors:  Aleksander V Drozdetski; Igor S Tolokh; Lois Pollack; Nathan Baker; Alexey V Onufriev
Journal:  Phys Rev Lett       Date:  2016-07-06       Impact factor: 9.161

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