Brownian dynamics simulation of DNA condensation.

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State: Public
Version: Final published version
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Sous embargo indéterminé.
State: Public
Version: Supplementary document
Serval ID
serval:BIB_8761F0EA0012
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Brownian dynamics simulation of DNA condensation.
Journal
Biophysical Journal
Author(s)
Sottas P.E., Larquet E., Stasiak A., Dubochet J.
ISSN
0006-3495
Publication state
Published
Issued date
10/1999
Peer-reviewed
Oui
Volume
77
Number
4
Pages
1858-1870
Language
english
Notes
Publication types: Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.
Keywords
Biopolymers, Computer Simulation, DNA/chemistry, DNA/metabolism, DNA, Superhelical/chemistry, DNA, Superhelical/metabolism, Diffusion, Magnesium Chloride/pharmacology, Methanol/pharmacology, Models, Chemical, Models, Molecular, Nucleic Acid Conformation/drug effects, Poisson Distribution, Salts/pharmacology, Solvents, Static Electricity, Thermodynamics
Pubmed
Open Access
Yes
Create date
24/01/2008 11:25
Last modification date
20/08/2019 15:46
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