Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples

Autores
Mautner, Martín E.; Perez Santangelo, Agustin; Corti Bielsa, Rodrigo M.; Sala, Andrea; Ginart, Santiago; Corach, Daniel
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA).
Fil: Mautner, Martín E.. Biodynamics SRL; Argentina
Fil: Perez Santangelo, Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Torcuato Di Tella; Argentina
Fil: Corti Bielsa, Rodrigo M.. Biodynamics SRL; Argentina
Fil: Sala, Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina
Fil: Ginart, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina
Fil: Corach, Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina
Materia
long ssDNA polynucleotides
degraded DNA
forensic
STR
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/48810
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/48810
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samplesMautner, Martín E.Perez Santangelo, AgustinCorti Bielsa, Rodrigo M.Sala, AndreaGinart, SantiagoCorach, Daniellong ssDNA polynucleotidesdegraded DNAforensicSTRhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA).Fil: Mautner, Martín E.. Biodynamics SRL; ArgentinaFil: Perez Santangelo, Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Torcuato Di Tella; ArgentinaFil: Corti Bielsa, Rodrigo M.. Biodynamics SRL; ArgentinaFil: Sala, Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Ginart, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Corach, Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaPublic Library of Science2017-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/48810Mautner, Martín E.; Perez Santangelo, Agustin; Corti Bielsa, Rodrigo M.; Sala, Andrea; Ginart, Santiago; et al.; Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples; Public Library of Science; Plos One; 12; 11; 11-2017; 1-201932-6203CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0187190info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187190info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:35:12Zoai:ri.conicet.gov.ar:11336/48810instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:35:12.491CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
title Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
spellingShingle Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
Mautner, Martín E.
long ssDNA polynucleotides
degraded DNA
forensic
STR
title_short Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
title_full Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
title_fullStr Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
title_full_unstemmed Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
title_sort Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
dc.creator.none.fl_str_mv Mautner, Martín E.
Perez Santangelo, Agustin
Corti Bielsa, Rodrigo M.
Sala, Andrea
Ginart, Santiago
Corach, Daniel
author Mautner, Martín E.
author_facet Mautner, Martín E.
Perez Santangelo, Agustin
Corti Bielsa, Rodrigo M.
Sala, Andrea
Ginart, Santiago
Corach, Daniel
author_role author
author2 Perez Santangelo, Agustin
Corti Bielsa, Rodrigo M.
Sala, Andrea
Ginart, Santiago
Corach, Daniel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv long ssDNA polynucleotides
degraded DNA
forensic
STR
topic long ssDNA polynucleotides
degraded DNA
forensic
STR
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA).
Fil: Mautner, Martín E.. Biodynamics SRL; Argentina
Fil: Perez Santangelo, Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Torcuato Di Tella; Argentina
Fil: Corti Bielsa, Rodrigo M.. Biodynamics SRL; Argentina
Fil: Sala, Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina
Fil: Ginart, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina
Fil: Corach, Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina
description Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA).
publishDate 2017
dc.date.none.fl_str_mv 2017-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/48810
Mautner, Martín E.; Perez Santangelo, Agustin; Corti Bielsa, Rodrigo M.; Sala, Andrea; Ginart, Santiago; et al.; Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples; Public Library of Science; Plos One; 12; 11; 11-2017; 1-20
1932-6203
CONICET Digital
CONICET
url http://hdl.handle.net/11336/48810
identifier_str_mv Mautner, Martín E.; Perez Santangelo, Agustin; Corti Bielsa, Rodrigo M.; Sala, Andrea; Ginart, Santiago; et al.; Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples; Public Library of Science; Plos One; 12; 11; 11-2017; 1-20
1932-6203
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0187190
info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187190
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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