Cargando…

The contribution of phosphate–phosphate repulsions to the free energy of DNA bending

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 phosp...

Descripción completa

Detalles Bibliográficos
Autores principales: Range, Kevin, Mayaan, Evelyn, Maher, L. J., York, Darrin M.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC552960/
https://www.ncbi.nlm.nih.gov/pubmed/15741179
http://dx.doi.org/10.1093/nar/gki272
_version_ 1782122487629217792
author Range, Kevin
Mayaan, Evelyn
Maher, L. J.
York, Darrin M.
author_facet Range, Kevin
Mayaan, Evelyn
Maher, L. J.
York, Darrin M.
author_sort Range, Kevin
collection PubMed
description 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 ∼30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.
format Text
id pubmed-552960
institution National Center for Biotechnology Information
language English
publishDate 2005
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-5529602005-03-10 The contribution of phosphate–phosphate repulsions to the free energy of DNA bending Range, Kevin Mayaan, Evelyn Maher, L. J. York, Darrin M. Nucleic Acids Res Article 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 ∼30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle. Oxford University Press 2005 2005-03-01 /pmc/articles/PMC552960/ /pubmed/15741179 http://dx.doi.org/10.1093/nar/gki272 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Range, Kevin
Mayaan, Evelyn
Maher, L. J.
York, Darrin M.
The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
title The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
title_full The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
title_fullStr The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
title_full_unstemmed The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
title_short The contribution of phosphate–phosphate repulsions to the free energy of DNA bending
title_sort contribution of phosphate–phosphate repulsions to the free energy of dna bending
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC552960/
https://www.ncbi.nlm.nih.gov/pubmed/15741179
http://dx.doi.org/10.1093/nar/gki272
work_keys_str_mv AT rangekevin thecontributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT mayaanevelyn thecontributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT maherlj thecontributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT yorkdarrinm thecontributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT rangekevin contributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT mayaanevelyn contributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT maherlj contributionofphosphatephosphaterepulsionstothefreeenergyofdnabending
AT yorkdarrinm contributionofphosphatephosphaterepulsionstothefreeenergyofdnabending