ArticleBiophysical journal1999
Brownian dynamics simulation of DNA condensation.
Article in Biophysical journal, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Abundant positively-charged proteins underlie JCVI-Syn3A's expanded nucleoid and ribosome distribution.PLoS computational biology · 2026Article
- Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.The journal of physical chemistry. B · 2023Article
- Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling.Biophysical journal · 2020Article
- Inferential modeling of 3D chromatin structure.Nucleic acids research · 2015Article
- Azimuthal frustration and bundling in columnar DNA aggregates.Biophysical journal · 2003Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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