Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding...

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Authors: Viader-Godoy, Xavier, Mañosas Castejón, María, Ritort Farran, Fèlix
Format: article
Status:Published version
Publication Date:2021
Country:España
Institution:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repository:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/181149
Online Access:https://hdl.handle.net/2445/181149
Access Level:Open access
Keyword:Àcids nucleics
ADN
Elasticitat
Espectroscòpia
Molècules
Nucleic acids
DNA
Elasticity
Spectrum analysis
Molecules
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spelling Sugar-Pucker Force-Induced Transition in Single-Stranded DNAViader-Godoy, XavierMañosas Castejón, MaríaRitort Farran, FèlixÀcids nucleicsADNElasticitatEspectroscòpiaMolèculesNucleic acidsDNAElasticitySpectrum analysisMoleculesThe accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60-14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNAMDPI2021202120212021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion13 p.application/pdfhttps://hdl.handle.net/2445/181149Articles 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/10.3390/ijms22094745International Journal of Molecular Sciences, 2021, vol. 22, num. 9, p. 4745https://doi.org/10.3390/ijms22094745info:eu-repo/grantAgreement/EC/H2020/687089cc-by (c) Viader-Godoy, Xavier et al., 2021https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1811492026-05-29T05:05:01Z
dc.title.none.fl_str_mv Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
title Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
spellingShingle Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
Viader-Godoy, Xavier
Àcids nucleics
ADN
Elasticitat
Espectroscòpia
Molècules
Nucleic acids
DNA
Elasticity
Spectrum analysis
Molecules
title_short Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
title_full Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
title_fullStr Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
title_full_unstemmed Sugar-Pucker Force-Induced Transition in Single-Stranded DNA
title_sort Sugar-Pucker Force-Induced Transition 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 Àcids nucleics
ADN
Elasticitat
Espectroscòpia
Molècules
Nucleic acids
DNA
Elasticity
Spectrum analysis
Molecules
topic Àcids nucleics
ADN
Elasticitat
Espectroscòpia
Molècules
Nucleic acids
DNA
Elasticity
Spectrum analysis
Molecules
description The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60-14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNA
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
2021
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/2445/181149
url https://hdl.handle.net/2445/181149
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/10.3390/ijms22094745
International Journal of Molecular Sciences, 2021, vol. 22, num. 9, p. 4745
https://doi.org/10.3390/ijms22094745
info:eu-repo/grantAgreement/EC/H2020/687089
dc.rights.none.fl_str_mv cc-by (c) Viader-Godoy, Xavier et al., 2021
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Viader-Godoy, Xavier et al., 2021
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 13 p.
application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
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
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score 15,812429

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