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Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families
We use Monte Carlo simulation to quantify the change in cyclization J-factor within a dramatically simplified model of DNA that involves parameters for uniform stiffnesses, intrinsic twist, and intrinsic bending (including nonplanar bending). Plots of J versus DNA length over multiple periods of hel...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861124/ https://www.ncbi.nlm.nih.gov/pubmed/29559729 http://dx.doi.org/10.1038/s41598-018-22502-7 |
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author | Tong, Yunjin Manning, Robert S. |
author_facet | Tong, Yunjin Manning, Robert S. |
author_sort | Tong, Yunjin |
collection | PubMed |
description | We use Monte Carlo simulation to quantify the change in cyclization J-factor within a dramatically simplified model of DNA that involves parameters for uniform stiffnesses, intrinsic twist, and intrinsic bending (including nonplanar bending). Plots of J versus DNA length over multiple periods of helical repeat are fit to a simple functional form in order to project the behavior of J over a broad range of these model parameters. In some instances, this process allows us to find families of DNA molecules (within our model) with quite different material properties, but very similar plots of J versus length, so similar as to likely to be indistinguishable by experiments. This effect is seen both for the parameter-pair of bend angle and stiffness scaling, as well as for the parameter-trio of helical repeat, bend angle, and bend non-planarity. |
format | Online Article Text |
id | pubmed-5861124 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-58611242018-03-26 Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families Tong, Yunjin Manning, Robert S. Sci Rep Article We use Monte Carlo simulation to quantify the change in cyclization J-factor within a dramatically simplified model of DNA that involves parameters for uniform stiffnesses, intrinsic twist, and intrinsic bending (including nonplanar bending). Plots of J versus DNA length over multiple periods of helical repeat are fit to a simple functional form in order to project the behavior of J over a broad range of these model parameters. In some instances, this process allows us to find families of DNA molecules (within our model) with quite different material properties, but very similar plots of J versus length, so similar as to likely to be indistinguishable by experiments. This effect is seen both for the parameter-pair of bend angle and stiffness scaling, as well as for the parameter-trio of helical repeat, bend angle, and bend non-planarity. Nature Publishing Group UK 2018-03-20 /pmc/articles/PMC5861124/ /pubmed/29559729 http://dx.doi.org/10.1038/s41598-018-22502-7 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Tong, Yunjin Manning, Robert S. Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families |
title | Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families |
title_full | Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families |
title_fullStr | Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families |
title_full_unstemmed | Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families |
title_short | Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families |
title_sort | quantifying the impact of simple dna parameters on the cyclization j-factor for single-basepair-addition families |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861124/ https://www.ncbi.nlm.nih.gov/pubmed/29559729 http://dx.doi.org/10.1038/s41598-018-22502-7 |
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