pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs

We study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C+ base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability o...

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Autores: Serrano Chacón, Israel, Mir, Bartomeu, Cupellini, Lorenzo, Colizzi, Francesco, Orozco López, Modesto, Escaja Sánchez, Núria, González, Carlos
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/193584
Acceso en línea:https://hdl.handle.net/2445/193584
Access Level:acceso abierto
Palabra clave:Oligonucleòtids
Àcids nucleics
ADN
Oligonucleotides
Nucleic acids
DNA
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spelling pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-MotifsSerrano Chacón, IsraelMir, BartomeuCupellini, LorenzoColizzi, FrancescoOrozco López, ModestoEscaja Sánchez, NúriaGonzález, CarlosOligonucleòtidsÀcids nucleicsADNOligonucleotidesNucleic acidsDNAWe study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C+ base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability of this structure are mainly due to the favorable effect of the minor groove tetrads on their adjacent positively charged C:C+ base pairs. At pH 5, we observe a more elongated i-motif structure consisting of four C:C+ base pairs capped by two G:T:G:T tetrads. Molecular dynamics calculations show that the conformational transition between the two structures is driven by the protonation state of key cytosines. In spite of large conformational differences, the transition between the acidic and neutral structures can occur without unfolding of the i-motif. These results represent the first case of a conformational switch between two different i-motif structures and illustrate the dramatic pH-dependent plasticity of this fascinating DNA motif.ACS Publications2023202320232023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion10 p.application/pdfhttps://hdl.handle.net/2445/193584Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1021/jacs.2c13043Journal of the American Chemical Society, 2023, vol. 145, num. 6, p. 3696–3705https://doi.org/10.1021/jacs.2c13043cc by (c) Serrano Chacón, Israel et al., 2023http://creativecommons.org/licenses/by/3.0/es/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1935842026-05-29T05:05:01Z
dc.title.none.fl_str_mv pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
title pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
spellingShingle pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
Serrano Chacón, Israel
Oligonucleòtids
Àcids nucleics
ADN
Oligonucleotides
Nucleic acids
DNA
title_short pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
title_full pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
title_fullStr pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
title_full_unstemmed pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
title_sort pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs
dc.creator.none.fl_str_mv Serrano Chacón, Israel
Mir, Bartomeu
Cupellini, Lorenzo
Colizzi, Francesco
Orozco López, Modesto
Escaja Sánchez, Núria
González, Carlos
author Serrano Chacón, Israel
author_facet Serrano Chacón, Israel
Mir, Bartomeu
Cupellini, Lorenzo
Colizzi, Francesco
Orozco López, Modesto
Escaja Sánchez, Núria
González, Carlos
author_role author
author2 Mir, Bartomeu
Cupellini, Lorenzo
Colizzi, Francesco
Orozco López, Modesto
Escaja Sánchez, Núria
González, Carlos
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Oligonucleòtids
Àcids nucleics
ADN
Oligonucleotides
Nucleic acids
DNA
topic Oligonucleòtids
Àcids nucleics
ADN
Oligonucleotides
Nucleic acids
DNA
description We study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C+ base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability of this structure are mainly due to the favorable effect of the minor groove tetrads on their adjacent positively charged C:C+ base pairs. At pH 5, we observe a more elongated i-motif structure consisting of four C:C+ base pairs capped by two G:T:G:T tetrads. Molecular dynamics calculations show that the conformational transition between the two structures is driven by the protonation state of key cytosines. In spite of large conformational differences, the transition between the acidic and neutral structures can occur without unfolding of the i-motif. These results represent the first case of a conformational switch between two different i-motif structures and illustrate the dramatic pH-dependent plasticity of this fascinating DNA motif.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/193584
url https://hdl.handle.net/2445/193584
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1021/jacs.2c13043
Journal of the American Chemical Society, 2023, vol. 145, num. 6, p. 3696–3705
https://doi.org/10.1021/jacs.2c13043
dc.rights.none.fl_str_mv cc by (c) Serrano Chacón, Israel et al., 2023
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc by (c) Serrano Chacón, Israel et al., 2023
http://creativecommons.org/licenses/by/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 10 p.
application/pdf
dc.publisher.none.fl_str_mv ACS Publications
publisher.none.fl_str_mv ACS Publications
dc.source.none.fl_str_mv Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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