Two Adhesive Sites Can Enhance the Knotting Probability of DNA

Self-entanglement, or knotting, is entropically favored in long polymers. Relatively short polymers such as proteins can knot as well, but in this case the entanglement is mainly driven by fine-tuned, sequence-specific interactions. The relation between the sequence of a long polymer and its topolog...

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Detalles Bibliográficos
Autores principales: Najafi, Saeed, Potestio, Raffaello
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489926/
https://www.ncbi.nlm.nih.gov/pubmed/26136125
http://dx.doi.org/10.1371/journal.pone.0132132
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author Najafi, Saeed
Potestio, Raffaello
author_facet Najafi, Saeed
Potestio, Raffaello
author_sort Najafi, Saeed
collection PubMed
description Self-entanglement, or knotting, is entropically favored in long polymers. Relatively short polymers such as proteins can knot as well, but in this case the entanglement is mainly driven by fine-tuned, sequence-specific interactions. The relation between the sequence of a long polymer and its topological state is here investigated by means of a coarse-grained model of DNA. We demonstrate that the introduction of two adhesive regions along the sequence of a self-avoiding chain substantially increases the probability of forming a knot.
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spelling pubmed-44899262015-07-15 Two Adhesive Sites Can Enhance the Knotting Probability of DNA Najafi, Saeed Potestio, Raffaello PLoS One Research Article Self-entanglement, or knotting, is entropically favored in long polymers. Relatively short polymers such as proteins can knot as well, but in this case the entanglement is mainly driven by fine-tuned, sequence-specific interactions. The relation between the sequence of a long polymer and its topological state is here investigated by means of a coarse-grained model of DNA. We demonstrate that the introduction of two adhesive regions along the sequence of a self-avoiding chain substantially increases the probability of forming a knot. Public Library of Science 2015-07-02 /pmc/articles/PMC4489926/ /pubmed/26136125 http://dx.doi.org/10.1371/journal.pone.0132132 Text en © 2015 Najafi, Potestio http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Najafi, Saeed
Potestio, Raffaello
Two Adhesive Sites Can Enhance the Knotting Probability of DNA
title Two Adhesive Sites Can Enhance the Knotting Probability of DNA
title_full Two Adhesive Sites Can Enhance the Knotting Probability of DNA
title_fullStr Two Adhesive Sites Can Enhance the Knotting Probability of DNA
title_full_unstemmed Two Adhesive Sites Can Enhance the Knotting Probability of DNA
title_short Two Adhesive Sites Can Enhance the Knotting Probability of DNA
title_sort two adhesive sites can enhance the knotting probability of dna
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489926/
https://www.ncbi.nlm.nih.gov/pubmed/26136125
http://dx.doi.org/10.1371/journal.pone.0132132
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