ArticleNucleic acids research2005
The contribution of phosphate-phosphate repulsions to the free energy of DNA bending.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 40 citations in OpenAlex.
- Nonradiative Deactivation of the Fluorescent AgThe journal of physical chemistry letters · 2024Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Mechanical properties of DNA-like polymers.Nucleic acids research · 2013Article
- Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- DNA curvature and flexibility in vitro and in vivo.Quarterly reviews of biophysics · 2010Review
- DNA on a tube: electrostatic contribution to stiffness.The journal of physical chemistry. B · 2008Article
- Electrostatic free energy landscapes for DNA helix bending.Biophysical journal · 2008Article
- Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts.Biophysical journal · 2008Article
- Interplay of ion binding and attraction in DNA condensed by multivalent cations.Nucleic acids research · 2008Article
- Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method.Biochemistry · 2007Article
- DNA bending by bHLH charge variants.Nucleic acids research · 2006Article
- Curved DNA molecules migrate anomalously slowly in free solution.Nucleic acids research · 2005Article
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Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate-phosphate repulsions. In the present work, the electrostatic contribution of phosphate-phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate-phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate-phosphate repulsions account for approximately 30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.
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