Cargando…

Correlated motions in DNA: beyond base-pair step models of DNA flexibility

Traditional mesoscopic models of DNA flexibility use a reductionist-local approach, which assumes that the flexibility of DNA can be expressed as local harmonic movements (at the base-pair step level) in the helical space, ignoring multimodality and correlations in DNA movements, which have in reali...

Descripción completa

Detalles Bibliográficos
Autores principales: López-Güell, Kim, Battistini, Federica, Orozco, Modesto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085700/
https://www.ncbi.nlm.nih.gov/pubmed/36912082
http://dx.doi.org/10.1093/nar/gkad136
_version_ 1785021990960103424
author López-Güell, Kim
Battistini, Federica
Orozco, Modesto
author_facet López-Güell, Kim
Battistini, Federica
Orozco, Modesto
author_sort López-Güell, Kim
collection PubMed
description Traditional mesoscopic models of DNA flexibility use a reductionist-local approach, which assumes that the flexibility of DNA can be expressed as local harmonic movements (at the base-pair step level) in the helical space, ignoring multimodality and correlations in DNA movements, which have in reality a large impact in modulating DNA movements. We present a new multimodal-harmonic correlated model, which takes both contributions into account, providing, with a small computational cost, results of an unprecedented local and global quality. The accuracy of this method and its computational efficiency make it an alternative to explore the dynamics of long segments of DNA, approaching the chromatin range.
format Online
Article
Text
id pubmed-10085700
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-100857002023-04-11 Correlated motions in DNA: beyond base-pair step models of DNA flexibility López-Güell, Kim Battistini, Federica Orozco, Modesto Nucleic Acids Res Computational Biology Traditional mesoscopic models of DNA flexibility use a reductionist-local approach, which assumes that the flexibility of DNA can be expressed as local harmonic movements (at the base-pair step level) in the helical space, ignoring multimodality and correlations in DNA movements, which have in reality a large impact in modulating DNA movements. We present a new multimodal-harmonic correlated model, which takes both contributions into account, providing, with a small computational cost, results of an unprecedented local and global quality. The accuracy of this method and its computational efficiency make it an alternative to explore the dynamics of long segments of DNA, approaching the chromatin range. Oxford University Press 2023-03-13 /pmc/articles/PMC10085700/ /pubmed/36912082 http://dx.doi.org/10.1093/nar/gkad136 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Computational Biology
López-Güell, Kim
Battistini, Federica
Orozco, Modesto
Correlated motions in DNA: beyond base-pair step models of DNA flexibility
title Correlated motions in DNA: beyond base-pair step models of DNA flexibility
title_full Correlated motions in DNA: beyond base-pair step models of DNA flexibility
title_fullStr Correlated motions in DNA: beyond base-pair step models of DNA flexibility
title_full_unstemmed Correlated motions in DNA: beyond base-pair step models of DNA flexibility
title_short Correlated motions in DNA: beyond base-pair step models of DNA flexibility
title_sort correlated motions in dna: beyond base-pair step models of dna flexibility
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085700/
https://www.ncbi.nlm.nih.gov/pubmed/36912082
http://dx.doi.org/10.1093/nar/gkad136
work_keys_str_mv AT lopezguellkim correlatedmotionsindnabeyondbasepairstepmodelsofdnaflexibility
AT battistinifederica correlatedmotionsindnabeyondbasepairstepmodelsofdnaflexibility
AT orozcomodesto correlatedmotionsindnabeyondbasepairstepmodelsofdnaflexibility