Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations

Autores
Soria, Federico Ariel; Siani, Paulo; Di Valentin, Cristiana
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We used molecular dynamics simulations to investigate the adsorption behavior of single-stranded deoxy-ribonucleic acid (ssDNA) segments on the anatase (101) surface. Four different ssDNA oligonucleotides, eachconsisting of six/twelve adenine (A6 and A12), six guanine (G6), six cytosine (C6) or six/twelve thymine (T6 andT12) nucleobases, were considered. We observed that the initial interaction between the ssDNA and the surfaceoccurs primarily through hydrogen bonding between the nucleobases and the surface, followed by strongchemical bonding between the terminal phosphate group and the anatase surface. The interactions between thenucleobases and the surface varied between the different ssDNA segments. Adenine showed the highest affinityfor the surface, whereas thymine showed the lowest affinity. In addition, the purine bases interact more stronglywhen the surface is negatively charged (as it would be at physiological pH) than in neutral surface (slightly acidicconditions), in agreement with experimental data from fluorescence experiments and ATR-FTIR spectroscopy.Moreover, our study provides mechanistic insights into the dynamic behavior of ssDNA on the anatase surfaceand comparative analyses on how different conditions (pH, fragment length, composition, etc.) affect DNA/TiO2interactions. Therefore, we expect that experimental scientists will benefit from our work in the design of optimalnanoconjugates for their specific final goals and applications.
Fil: Soria, Federico Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Siani, Paulo. Università Di Milano Bicocca; Italia
Fil: Di Valentin, Cristiana. Università Di Milano Bicocca; Italia
Materia
ssDNA
TiO2
Molecular Dynamics
Adsorption
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/264260
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulationsSoria, Federico ArielSiani, PauloDi Valentin, CristianassDNATiO2Molecular DynamicsAdsorptionhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1We used molecular dynamics simulations to investigate the adsorption behavior of single-stranded deoxy-ribonucleic acid (ssDNA) segments on the anatase (101) surface. Four different ssDNA oligonucleotides, eachconsisting of six/twelve adenine (A6 and A12), six guanine (G6), six cytosine (C6) or six/twelve thymine (T6 andT12) nucleobases, were considered. We observed that the initial interaction between the ssDNA and the surfaceoccurs primarily through hydrogen bonding between the nucleobases and the surface, followed by strongchemical bonding between the terminal phosphate group and the anatase surface. The interactions between thenucleobases and the surface varied between the different ssDNA segments. Adenine showed the highest affinityfor the surface, whereas thymine showed the lowest affinity. In addition, the purine bases interact more stronglywhen the surface is negatively charged (as it would be at physiological pH) than in neutral surface (slightly acidicconditions), in agreement with experimental data from fluorescence experiments and ATR-FTIR spectroscopy.Moreover, our study provides mechanistic insights into the dynamic behavior of ssDNA on the anatase surfaceand comparative analyses on how different conditions (pH, fragment length, composition, etc.) affect DNA/TiO2interactions. Therefore, we expect that experimental scientists will benefit from our work in the design of optimalnanoconjugates for their specific final goals and applications.Fil: Soria, Federico Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Siani, Paulo. Università Di Milano Bicocca; ItaliaFil: Di Valentin, Cristiana. Università Di Milano Bicocca; ItaliaElsevier2024-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/264260Soria, Federico Ariel; Siani, Paulo; Di Valentin, Cristiana ; Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations; Elsevier; Surfaces and Interfaces; 52; 9-2024; 104889-1049032468-0230CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S2468023024010459info:eu-repo/semantics/altIdentifier/doi/10.1016/j.surfin.2024.104889info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:12:50Zoai:ri.conicet.gov.ar:11336/264260instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-10 13:12:50.833CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
title Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
spellingShingle Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
Soria, Federico Ariel
ssDNA
TiO2
Molecular Dynamics
Adsorption
title_short Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
title_full Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
title_fullStr Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
title_full_unstemmed Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
title_sort Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
dc.creator.none.fl_str_mv Soria, Federico Ariel
Siani, Paulo
Di Valentin, Cristiana
author Soria, Federico Ariel
author_facet Soria, Federico Ariel
Siani, Paulo
Di Valentin, Cristiana
author_role author
author2 Siani, Paulo
Di Valentin, Cristiana
author2_role author
author
dc.subject.none.fl_str_mv ssDNA
TiO2
Molecular Dynamics
Adsorption
topic ssDNA
TiO2
Molecular Dynamics
Adsorption
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We used molecular dynamics simulations to investigate the adsorption behavior of single-stranded deoxy-ribonucleic acid (ssDNA) segments on the anatase (101) surface. Four different ssDNA oligonucleotides, eachconsisting of six/twelve adenine (A6 and A12), six guanine (G6), six cytosine (C6) or six/twelve thymine (T6 andT12) nucleobases, were considered. We observed that the initial interaction between the ssDNA and the surfaceoccurs primarily through hydrogen bonding between the nucleobases and the surface, followed by strongchemical bonding between the terminal phosphate group and the anatase surface. The interactions between thenucleobases and the surface varied between the different ssDNA segments. Adenine showed the highest affinityfor the surface, whereas thymine showed the lowest affinity. In addition, the purine bases interact more stronglywhen the surface is negatively charged (as it would be at physiological pH) than in neutral surface (slightly acidicconditions), in agreement with experimental data from fluorescence experiments and ATR-FTIR spectroscopy.Moreover, our study provides mechanistic insights into the dynamic behavior of ssDNA on the anatase surfaceand comparative analyses on how different conditions (pH, fragment length, composition, etc.) affect DNA/TiO2interactions. Therefore, we expect that experimental scientists will benefit from our work in the design of optimalnanoconjugates for their specific final goals and applications.
Fil: Soria, Federico Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Siani, Paulo. Università Di Milano Bicocca; Italia
Fil: Di Valentin, Cristiana. Università Di Milano Bicocca; Italia
description We used molecular dynamics simulations to investigate the adsorption behavior of single-stranded deoxy-ribonucleic acid (ssDNA) segments on the anatase (101) surface. Four different ssDNA oligonucleotides, eachconsisting of six/twelve adenine (A6 and A12), six guanine (G6), six cytosine (C6) or six/twelve thymine (T6 andT12) nucleobases, were considered. We observed that the initial interaction between the ssDNA and the surfaceoccurs primarily through hydrogen bonding between the nucleobases and the surface, followed by strongchemical bonding between the terminal phosphate group and the anatase surface. The interactions between thenucleobases and the surface varied between the different ssDNA segments. Adenine showed the highest affinityfor the surface, whereas thymine showed the lowest affinity. In addition, the purine bases interact more stronglywhen the surface is negatively charged (as it would be at physiological pH) than in neutral surface (slightly acidicconditions), in agreement with experimental data from fluorescence experiments and ATR-FTIR spectroscopy.Moreover, our study provides mechanistic insights into the dynamic behavior of ssDNA on the anatase surfaceand comparative analyses on how different conditions (pH, fragment length, composition, etc.) affect DNA/TiO2interactions. Therefore, we expect that experimental scientists will benefit from our work in the design of optimalnanoconjugates for their specific final goals and applications.
publishDate 2024
dc.date.none.fl_str_mv 2024-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/264260
Soria, Federico Ariel; Siani, Paulo; Di Valentin, Cristiana ; Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations; Elsevier; Surfaces and Interfaces; 52; 9-2024; 104889-104903
2468-0230
CONICET Digital
CONICET
url http://hdl.handle.net/11336/264260
identifier_str_mv Soria, Federico Ariel; Siani, Paulo; Di Valentin, Cristiana ; Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations; Elsevier; Surfaces and Interfaces; 52; 9-2024; 104889-104903
2468-0230
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S2468023024010459
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.surfin.2024.104889
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.993085

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