Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra

DNA can adopt structures in solution apart from the well-known Watson-Click double helix, ranging from disordered single strands to high-order structures such as triplexes or quadruplexes. Moreover, different topologies can be adopted depending on the polarity of the DNA strands. The elucidation of...

Descripción completa

Detalles Bibliográficos
Autores: Jaumot, Joaquim, Eritja Casadellà, Ramón, Navea, Susana, Gargallo, Raimundo
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2009
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/109763
Acceso en línea:http://hdl.handle.net/10261/109763
Access Level:acceso abierto
Palabra clave:DNA structure
Principal Component Analysis
Partial Least Squares Discriminant Analysis
Clustering
Circular dichroism spectroscopy
id ES_20ca3d3af12afebec41fdab048a8b372
oai_identifier_str oai:digital.csic.es:10261/109763
network_acronym_str ES
network_name_str España
repository_id_str
spelling Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectraJaumot, JoaquimEritja Casadellà, RamónNavea, SusanaGargallo, RaimundoDNA structurePrincipal Component AnalysisPartial Least Squares Discriminant AnalysisClusteringCircular dichroism spectroscopyDNA can adopt structures in solution apart from the well-known Watson-Click double helix, ranging from disordered single strands to high-order structures such as triplexes or quadruplexes. Moreover, different topologies can be adopted depending on the polarity of the DNA strands. The elucidation of the structure and topology adopted by a DNA sequence is usually carried out by means of spectroscopic techniques, such as circular dichroism. In this work, the ability of several chemometric methods to efficiently classify DNA structures from circular dichroism data is tested. With this objective in mind, a data set including 50 experimental spectra corresponding to different DNA structures (random coil, duplex, hairpin, reversed and normal triplex, parallel and antiparallel G-quadruplex, and i-motif) has been analyzed by means of unsupervised Hierarchical Clustering Analysis, Principal Component Analysis and Partial Least Squares Discriminant Analysis. The results have shown than those methods allow efficiently the classification of DNA structures from circular dichroism spectra. Moreover, these classification methods also provided the most characteristic wavelengths used in the classification procedures.Peer reviewedConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]201520152009info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/109763reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglésdx.doi.org/10.1016/j.aca.2008.12.052Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1097632026-05-22T06:33:51Z
dc.title.none.fl_str_mv Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
title Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
spellingShingle Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
Jaumot, Joaquim
DNA structure
Principal Component Analysis
Partial Least Squares Discriminant Analysis
Clustering
Circular dichroism spectroscopy
title_short Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
title_full Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
title_fullStr Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
title_full_unstemmed Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
title_sort Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra
dc.creator.none.fl_str_mv Jaumot, Joaquim
Eritja Casadellà, Ramón
Navea, Susana
Gargallo, Raimundo
author Jaumot, Joaquim
author_facet Jaumot, Joaquim
Eritja Casadellà, Ramón
Navea, Susana
Gargallo, Raimundo
author_role author
author2 Eritja Casadellà, Ramón
Navea, Susana
Gargallo, Raimundo
author2_role author
author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv DNA structure
Principal Component Analysis
Partial Least Squares Discriminant Analysis
Clustering
Circular dichroism spectroscopy
topic DNA structure
Principal Component Analysis
Partial Least Squares Discriminant Analysis
Clustering
Circular dichroism spectroscopy
description DNA can adopt structures in solution apart from the well-known Watson-Click double helix, ranging from disordered single strands to high-order structures such as triplexes or quadruplexes. Moreover, different topologies can be adopted depending on the polarity of the DNA strands. The elucidation of the structure and topology adopted by a DNA sequence is usually carried out by means of spectroscopic techniques, such as circular dichroism. In this work, the ability of several chemometric methods to efficiently classify DNA structures from circular dichroism data is tested. With this objective in mind, a data set including 50 experimental spectra corresponding to different DNA structures (random coil, duplex, hairpin, reversed and normal triplex, parallel and antiparallel G-quadruplex, and i-motif) has been analyzed by means of unsupervised Hierarchical Clustering Analysis, Principal Component Analysis and Partial Least Squares Discriminant Analysis. The results have shown than those methods allow efficiently the classification of DNA structures from circular dichroism spectra. Moreover, these classification methods also provided the most characteristic wavelengths used in the classification procedures.
publishDate 2009
dc.date.none.fl_str_mv 2009
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/109763
url http://hdl.handle.net/10261/109763
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv dx.doi.org/10.1016/j.aca.2008.12.052
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869404479250497536
score 15,811543

Similares en LA Referencia