Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA

We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at the base moiety, and at the phosphate group, respectively. The sequence dependence is included by considering a step-dependent pa...

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Detalles Bibliográficos
Autores: Assenza, Salvatore, Pérez Pérez, Rubén
Tipo de recurso: artículo
Fecha de publicación:2022
País:España
Institución:Universidad Autónoma de Madrid
Repositorio:Biblos-e Archivo. Repositorio Institucional de la UAM
Idioma:inglés
OAI Identifier:oai:repositorio.uam.es:10486/703106
Acceso en línea:http://hdl.handle.net/10486/703106
https://dx.doi.org/10.1021/acs.jctc.2c00138
Access Level:acceso abierto
Palabra clave:Física
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spelling Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNAAssenza, SalvatorePérez Pérez, RubénFísicaWe introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at the base moiety, and at the phosphate group, respectively. The sequence dependence is included by considering a step-dependent parametrization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from the literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist−stretch and twist−bend couplings, the persistence length, and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of single-molecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines. Particularly, an implementation of the model in LAMMPS is made available on an online repository to ease its usage within the DNA research communityWeare thankful for the financial support from the Spanish MINECO project MAT2017-83273-R. We acknowledge support from the Ministerio de Ciencia e Innovación (MICINN) through the project PID2020-115864RB-I00 and the “María de Maeztu” Programme for Units of Excellence in R&D (grant No. CEX2018-000805-M). The project that gave rise to these results received the support of a fellowship from “la Caixa” Foundation (ID 100010434) and from the European Union’s Horizon research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847648. The fellowship code is LCF/BQ/PI20/11760019American Chemical SocietyDepartamento de Física Teórica de la Materia CondensadaFacultad de Ciencias20222022-04-08research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/703106https://dx.doi.org/10.1021/acs.jctc.2c00138reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/7031062026-06-23T12:46:27Z
dc.title.none.fl_str_mv Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
title Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
spellingShingle Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
Assenza, Salvatore
Física
title_short Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
title_full Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
title_fullStr Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
title_full_unstemmed Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
title_sort Accurate sequence-dependent Coarse-Grained Model for conformational and elastic properties of double-stranded DNA
dc.creator.none.fl_str_mv Assenza, Salvatore
Pérez Pérez, Rubén
author Assenza, Salvatore
author_facet Assenza, Salvatore
Pérez Pérez, Rubén
author_role author
author2 Pérez Pérez, Rubén
author2_role author
dc.contributor.none.fl_str_mv Departamento de Física Teórica de la Materia Condensada
Facultad de Ciencias
dc.subject.none.fl_str_mv Física
topic Física
description We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at the base moiety, and at the phosphate group, respectively. The sequence dependence is included by considering a step-dependent parametrization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from the literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist−stretch and twist−bend couplings, the persistence length, and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of single-molecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines. Particularly, an implementation of the model in LAMMPS is made available on an online repository to ease its usage within the DNA research community
publishDate 2022
dc.date.none.fl_str_mv 2022
2022-04-08
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10486/703106
https://dx.doi.org/10.1021/acs.jctc.2c00138
url http://hdl.handle.net/10486/703106
https://dx.doi.org/10.1021/acs.jctc.2c00138
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv reponame:Biblos-e Archivo. Repositorio Institucional de la UAM
instname:Universidad Autónoma de Madrid
instname_str Universidad Autónoma de Madrid
reponame_str Biblos-e Archivo. Repositorio Institucional de la UAM
collection Biblos-e Archivo. Repositorio Institucional de la UAM
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