Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches

The number of innovative applications for DNA nowadays is growingquickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deepunderstanding of the charge-transfer process along the strand, as well as its redoxproperties. These features are computationally simulated and ana...

Full description

Bibliographic Details
Authors: Lucía Tamudo, Jesús, Díaz-Tendero Victoria, Sergio, Nogueira Pérez, Juan José
Format: article
Publication Date:2024
Country:España
Institution:Universidad Autónoma de Madrid
Repository:Biblos-e Archivo. Repositorio Institucional de la UAM
Language:English
OAI Identifier:oai:repositorio.uam.es:10486/713291
Online Access:http://hdl.handle.net/10486/713291
https://dx.doi.org/10.1021/acs.jcim.4c00528
Access Level:Open access
Keyword:DNA
Electrons
Molecular Dynamics Simulation
Nucleic Acid Conformation
Oxidation Reduction
Química
id ES_9667dbe3c4e56206a1f4b2cd2ccccaed
oai_identifier_str oai:repositorio.uam.es:10486/713291
network_acronym_str ES
network_name_str España
repository_id_str
spelling Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approachesLucía Tamudo, JesúsDíaz-Tendero Victoria, SergioNogueira Pérez, Juan JoséDNAElectronsMolecular Dynamics SimulationNucleic Acid ConformationOxidation ReductionQuímicaThe number of innovative applications for DNA nowadays is growingquickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deepunderstanding of the charge-transfer process along the strand, as well as its redoxproperties. These features are computationally simulated and analyzed in detailthroughout this work by combining molecular dynamics, multilayer schemes, and theMarcus theory. One-electron oxidation potential and hole delocalization have beenanalyzed for six DNA double strands that cover all possible binary combinations ofnucleotides. The results have revealed that the one-electron oxidation potentialdecreases with respect to the single-stranded DNA, giving evidence that the greaterrigidity of a double helix induces an increase in the capacity of storing the positivecharge generated upon oxidation. In addition, the hole is mainly stored in nucleobaseswith large reducer character, i.e., purines, especially when those are arranged in astacked configuration in the same strand. From the computational point of view, thesampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number ofrepresentative conformations generated by clustering analysis provides accurate results when compared with those obtained fromsampling, reducing considerably the computational costThis work was partially supported by the MICINN−Spanish Ministry of Science and Innovation Projects PID2022-138470NB-I00 and PID2020-117806GA-I00 funded by MCIN/AEI/10.13039/ 501100011033, and the “María de Maeztu” (CEX2018000805-M) Program for Centers of Excellence in R&D. J.J.N. acknowledge the Comunidad de Madrid for funding through the Attraction of Talent Program (grant reference 2022-5A/BMD-24244). J.L.T. acknowledges the FPU19/ 02292 grant from the Spanish Ministry of University. AdditionallyAmerican Chemical SocietyDepartamento de QuímicaFacultad de Ciencias20242024-06-10research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/713291https://dx.doi.org/10.1021/acs.jcim.4c00528reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/7132912026-06-23T12:46:27Z
dc.title.none.fl_str_mv Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
title Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
spellingShingle Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
Lucía Tamudo, Jesús
DNA
Electrons
Molecular Dynamics Simulation
Nucleic Acid Conformation
Oxidation Reduction
Química
title_short Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
title_full Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
title_fullStr Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
title_full_unstemmed Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
title_sort Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
dc.creator.none.fl_str_mv Lucía Tamudo, Jesús
Díaz-Tendero Victoria, Sergio
Nogueira Pérez, Juan José
author Lucía Tamudo, Jesús
author_facet Lucía Tamudo, Jesús
Díaz-Tendero Victoria, Sergio
Nogueira Pérez, Juan José
author_role author
author2 Díaz-Tendero Victoria, Sergio
Nogueira Pérez, Juan José
author2_role author
author
dc.contributor.none.fl_str_mv Departamento de Química
Facultad de Ciencias
dc.subject.none.fl_str_mv DNA
Electrons
Molecular Dynamics Simulation
Nucleic Acid Conformation
Oxidation Reduction
Química
topic DNA
Electrons
Molecular Dynamics Simulation
Nucleic Acid Conformation
Oxidation Reduction
Química
description The number of innovative applications for DNA nowadays is growingquickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deepunderstanding of the charge-transfer process along the strand, as well as its redoxproperties. These features are computationally simulated and analyzed in detailthroughout this work by combining molecular dynamics, multilayer schemes, and theMarcus theory. One-electron oxidation potential and hole delocalization have beenanalyzed for six DNA double strands that cover all possible binary combinations ofnucleotides. The results have revealed that the one-electron oxidation potentialdecreases with respect to the single-stranded DNA, giving evidence that the greaterrigidity of a double helix induces an increase in the capacity of storing the positivecharge generated upon oxidation. In addition, the hole is mainly stored in nucleobaseswith large reducer character, i.e., purines, especially when those are arranged in astacked configuration in the same strand. From the computational point of view, thesampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number ofrepresentative conformations generated by clustering analysis provides accurate results when compared with those obtained fromsampling, reducing considerably the computational cost
publishDate 2024
dc.date.none.fl_str_mv 2024
2024-06-10
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/10486/713291
https://dx.doi.org/10.1021/acs.jcim.4c00528
url http://hdl.handle.net/10486/713291
https://dx.doi.org/10.1021/acs.jcim.4c00528
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
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
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
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
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
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869413947388461056
score 15,300719

Similar Items