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...
Autores principales: | , , , |
---|---|
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 |