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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/48810
Ver los metadatos del registro completo
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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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1844613094557351936 |
score |
13.070432 |