Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline

DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bisintercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweeze...

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Authors: Camuñas Soler, Joan, Mañosas Castejón, María, Frutos, Silvia, Albericio Palomera, Fernando, Ritort Farran, Fèlix, Tulla-Puche, Judit
Format: article
Status:Published version
Publication Date:2015
Country:España
Institution:Universidad de Barcelona
Repository:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/101021
Online Access:https://hdl.handle.net/2445/101021
Access Level:Open access
Keyword:Lligands (Bioquímica)
Aminoàcids
ADN
Ligands (Biochemistry)
Amino acids
DNA
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spelling Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of ThiocoralineCamuñas Soler, JoanMañosas Castejón, MaríaFrutos, SilviaAlbericio Palomera, FernandoRitort Farran, FèlixTulla-Puche, JuditLligands (Bioquímica)AminoàcidsADNLigands (Biochemistry)Amino acidsDNADNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bisintercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel singlemolecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines.Oxford University Press2015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/101021Articles publicats en revistes (Física de la Matèria Condensada)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésinfo:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkv087Reproducció del document publicat a: http://dx.doi.org/10.1093/nar/gkv087Nucleic Acids Research, 2015, vol. 43, num. 5, p. 2767-2779http://dx.doi.org/10.1093/nar/gkv087info:eu-repo/grantAgreement/EC/FP7/267862cc-by-nc (c) Camuñas i Soler, Joan et al., 2015http://creativecommons.org/licenses/by-nc/3.0/esinfo:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1010212026-05-27T06:46:51Z
dc.title.none.fl_str_mv Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
title Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
spellingShingle Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
Camuñas Soler, Joan
Lligands (Bioquímica)
Aminoàcids
ADN
Ligands (Biochemistry)
Amino acids
DNA
title_short Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
title_full Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
title_fullStr Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
title_full_unstemmed Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
title_sort Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
dc.creator.none.fl_str_mv Camuñas Soler, Joan
Mañosas Castejón, María
Frutos, Silvia
Albericio Palomera, Fernando
Ritort Farran, Fèlix
Tulla-Puche, Judit
author Camuñas Soler, Joan
author_facet Camuñas Soler, Joan
Mañosas Castejón, María
Frutos, Silvia
Albericio Palomera, Fernando
Ritort Farran, Fèlix
Tulla-Puche, Judit
author_role author
author2 Mañosas Castejón, María
Frutos, Silvia
Albericio Palomera, Fernando
Ritort Farran, Fèlix
Tulla-Puche, Judit
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Lligands (Bioquímica)
Aminoàcids
ADN
Ligands (Biochemistry)
Amino acids
DNA
topic Lligands (Bioquímica)
Aminoàcids
ADN
Ligands (Biochemistry)
Amino acids
DNA
description DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bisintercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel singlemolecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines.
publishDate 2015
dc.date.none.fl_str_mv 2015
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/2445/101021
url https://hdl.handle.net/2445/101021
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkv087
Reproducció del document publicat a: http://dx.doi.org/10.1093/nar/gkv087
Nucleic Acids Research, 2015, vol. 43, num. 5, p. 2767-2779
http://dx.doi.org/10.1093/nar/gkv087
info:eu-repo/grantAgreement/EC/FP7/267862
dc.rights.none.fl_str_mv cc-by-nc (c) Camuñas i Soler, Joan et al., 2015
http://creativecommons.org/licenses/by-nc/3.0/es
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by-nc (c) Camuñas i Soler, Joan et al., 2015
http://creativecommons.org/licenses/by-nc/3.0/es
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 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:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,301603

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