Stacking correlation length in single-stranded DNA

Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base pairing, making their measurement challenging. We conduct unz...

Descripción completa

Detalles Bibliográficos
Autores: Viader-Godoy, Xavier, Mañosas Castejón, María, Ritort Farran, Fèlix
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
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:2445/222159
Acceso en línea:https://hdl.handle.net/2445/222159
Access Level:acceso abierto
Palabra clave:ADN
Àcids nucleics
Estructura molecular
DNA
Nucleic acids
Molecular structure
id ES_be2cdb3f4042c14daceff7f78aca57cc
oai_identifier_str oai:recercat.cat:2445/222159
network_acronym_str ES
network_name_str España
repository_id_str
spelling Stacking correlation length in single-stranded DNAViader-Godoy, XavierMañosas Castejón, MaríaRitort Farran, FèlixADNÀcids nucleicsEstructura molecularDNANucleic acidsMolecular structureBase stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base pairing, making their measurement challenging. We conduct unzipping experiments with optical tweezers of short poly-purine (dA and alternating dG and dA) sequences of 20–40 bases. We introduce a helix-coil model of the stacking–unstacking transition that includes finite length effects and reproduces the force-extension curves. Fitting the model to the experimental data, we derive the stacking energy per base, finding the salt-independent value kcal/mol for poly-dA and kcal/mol for poly-dGdA. Stacking in these polymeric sequences is predominantly cooperative with a correlation length of ∼4 bases at zero force . The correlation length reaches a maximum of ∼10 and 5 bases at the stacking–unstacking transition force of ∼10 and 20 pN for poly-dA and poly-dGdA, respectively. The salt dependencies of the cooperativity parameter in ssDNA and the energy of DNA hybridization are in agreement, suggesting that double-helix stability is primarily due to stacking. Analysis of poly-rA and poly-rC RNA sequences shows a larger stacking stability but a lower stacking correlation length of ∼2 bases.Oxford University Press2025202520242025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion12 p.application/pdfhttps://hdl.handle.net/2445/222159Articles publicats en revistes (Física de la Matèria Condensada)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/https://doi.org/10.1093/nar/gkae934Nucleic Acids Research, 2024, vol. 52, num.21, p. 13243-13254https://doi.org/https://doi.org/10.1093/nar/gkae934cc-by-nc (c) X Viader-Godoy et al., 2024http://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/2221592026-05-29T05:05:01Z
dc.title.none.fl_str_mv Stacking correlation length in single-stranded DNA
title Stacking correlation length in single-stranded DNA
spellingShingle Stacking correlation length in single-stranded DNA
Viader-Godoy, Xavier
ADN
Àcids nucleics
Estructura molecular
DNA
Nucleic acids
Molecular structure
title_short Stacking correlation length in single-stranded DNA
title_full Stacking correlation length in single-stranded DNA
title_fullStr Stacking correlation length in single-stranded DNA
title_full_unstemmed Stacking correlation length in single-stranded DNA
title_sort Stacking correlation length in single-stranded DNA
dc.creator.none.fl_str_mv Viader-Godoy, Xavier
Mañosas Castejón, María
Ritort Farran, Fèlix
author Viader-Godoy, Xavier
author_facet Viader-Godoy, Xavier
Mañosas Castejón, María
Ritort Farran, Fèlix
author_role author
author2 Mañosas Castejón, María
Ritort Farran, Fèlix
author2_role author
author
dc.subject.none.fl_str_mv ADN
Àcids nucleics
Estructura molecular
DNA
Nucleic acids
Molecular structure
topic ADN
Àcids nucleics
Estructura molecular
DNA
Nucleic acids
Molecular structure
description Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base pairing, making their measurement challenging. We conduct unzipping experiments with optical tweezers of short poly-purine (dA and alternating dG and dA) sequences of 20–40 bases. We introduce a helix-coil model of the stacking–unstacking transition that includes finite length effects and reproduces the force-extension curves. Fitting the model to the experimental data, we derive the stacking energy per base, finding the salt-independent value kcal/mol for poly-dA and kcal/mol for poly-dGdA. Stacking in these polymeric sequences is predominantly cooperative with a correlation length of ∼4 bases at zero force . The correlation length reaches a maximum of ∼10 and 5 bases at the stacking–unstacking transition force of ∼10 and 20 pN for poly-dA and poly-dGdA, respectively. The salt dependencies of the cooperativity parameter in ssDNA and the energy of DNA hybridization are in agreement, suggesting that double-helix stability is primarily due to stacking. Analysis of poly-rA and poly-rC RNA sequences shows a larger stacking stability but a lower stacking correlation length of ∼2 bases.
publishDate 2024
dc.date.none.fl_str_mv 2024
2025
2025
2025
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/2445/222159
url https://hdl.handle.net/2445/222159
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/https://doi.org/10.1093/nar/gkae934
Nucleic Acids Research, 2024, vol. 52, num.21, p. 13243-13254
https://doi.org/https://doi.org/10.1093/nar/gkae934
dc.rights.none.fl_str_mv cc-by-nc (c) X Viader-Godoy et al., 2024
http://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by-nc (c) X Viader-Godoy et al., 2024
http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 12 p.
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv Articles publicats en revistes (Física de la Matèria Condensada)
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
_version_ 1869418263626121217
score 15.811543

Similares en LA Referencia