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

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 he...

Full description

Saved in:
Bibliographic Details
Published in:PloS one 2017-11, Vol.12 (11), p.e0187190-e0187190
Main Authors: Mautner, Martín E, Pérez Santángelo, Agustín, Corti Bielsa, Rodrigo M, Sala, Andrea, Ginart, Santiago, Corach, Daniel
Format: Article
Language:English
Subjects:
Annealing
Assaying
Base sequence
Biochemistry
Biology and Life Sciences
Capillary electrophoresis
Degradation
Deoxyribonucleic acid
DNA
DNA fingerprints
DNA Primers
DNA, Single-Stranded - genetics
Earth sciences
Electrophoresis
Genetic markers
Genetic testing
Genetics
Genotyping
Laboratories
Loci
Markers
Medicine and Health Sciences
Methods
Microsatellite Repeats
Multiplexing
Nucleic acids
Nucleotide sequence
Pharmacy
Physical sciences
Polymerase chain reaction
Polymerase Chain Reaction - methods
Polymers
Polynucleotides
Polynucleotides - genetics
Primers
Research and Analysis Methods
Short tandem repeats
Social Sciences
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763
cites cdi_FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763
container_end_page e0187190
container_issue 11
container_start_page e0187190
container_title PloS one
container_volume 12
creator Mautner, Martín E
Pérez Santángelo, Agustín
Corti Bielsa, Rodrigo M
Sala, Andrea
Ginart, Santiago
Corach, Daniel
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).
doi_str_mv 10.1371/journal.pone.0187190
format article
fullrecord <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1959661476</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A513148875</galeid><doaj_id>oai_doaj_org_article_f9726b39c30448a6aa547b2fa64d15a2</doaj_id><sourcerecordid>A513148875</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763</originalsourceid><addsrcrecordid>eNqNkl1v0zAUhiMEYmPwDxBEQkJw0RJ_xzdI1fiqNJi0FW4txx-pKzfu4gTRf4-zZlODdoEiJZb9vO_JOX6z7CUo5gAx8GET-raRfr4LjZkXoGSAF4-yU8ARnFFYoMdH65PsWYyboiCopPRpdgJ5wXmJ2Gn2_Wd0TZ37kF4xfvqxyHfB75teeRM6p03Mu5DL7c47u8-vV1cxocrlrsm1qVupjc4HURwQE59nT6z00bwYv2fZ6svn1fm32cXl1-X54mKmKIfdDKkSG1ZCAkqrLcYUEmt1gSsDDCoqiBikRJcMQ8ArwIhhihCb-ispNIyis-z1wXbnQxTjIKIAnHBKAb4llgdCB7kRu9ZtZbsXQTpxuxHaWsi2c6lLYXmqViGuUIFxKamUBLMKWkmxBkTC5PVxrNZXW6OVabpW-onp9KRxa1GH34JQyjFEyeDdaNCGm97ETmxdVMZ72ZjQD_9NKcSYgaHWm3_Qh7sbqVqmBlxjQ6qrBlOxIAABXJaMJGr-AJUebbZOpdRYl_YngvcTQWI686erZR-jWF5f_T97-WvKvj1i10b6bh2D7zsXmjgF8QFUbYixNfZ-yKAQQ-jvpiGG0Isx9En26viC7kV3KUd_ATyY-ao</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1959661476</pqid></control><display><type>article</type><title>Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples</title><source>Publicly Available Content Database</source><source>PubMed Central</source><creator>Mautner, Martín E ; Pérez Santángelo, Agustín ; Corti Bielsa, Rodrigo M ; Sala, Andrea ; Ginart, Santiago ; Corach, Daniel</creator><contributor>Kalendar, Ruslan</contributor><creatorcontrib>Mautner, Martín E ; Pérez Santángelo, Agustín ; Corti Bielsa, Rodrigo M ; Sala, Andrea ; Ginart, Santiago ; Corach, Daniel ; Kalendar, Ruslan</creatorcontrib><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).</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0187190</identifier><identifier>PMID: 29099837</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Annealing ; Assaying ; Base sequence ; Biochemistry ; Biology and Life Sciences ; Capillary electrophoresis ; Degradation ; Deoxyribonucleic acid ; DNA ; DNA fingerprints ; DNA Primers ; DNA, Single-Stranded - genetics ; Earth sciences ; Electrophoresis ; Genetic markers ; Genetic testing ; Genetics ; Genotyping ; Laboratories ; Loci ; Markers ; Medicine and Health Sciences ; Methods ; Microsatellite Repeats ; Multiplexing ; Nucleic acids ; Nucleotide sequence ; Pharmacy ; Physical sciences ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Polymers ; Polynucleotides ; Polynucleotides - genetics ; Primers ; Research and Analysis Methods ; Short tandem repeats ; Social Sciences</subject><ispartof>PloS one, 2017-11, Vol.12 (11), p.e0187190-e0187190</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Mautner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2017 Mautner et al 2017 Mautner et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763</citedby><cites>FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763</cites><orcidid>0000-0001-9098-1225</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1959661476/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1959661476?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29099837$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kalendar, Ruslan</contributor><creatorcontrib>Mautner, Martín E</creatorcontrib><creatorcontrib>Pérez Santángelo, Agustín</creatorcontrib><creatorcontrib>Corti Bielsa, Rodrigo M</creatorcontrib><creatorcontrib>Sala, Andrea</creatorcontrib><creatorcontrib>Ginart, Santiago</creatorcontrib><creatorcontrib>Corach, Daniel</creatorcontrib><title>Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples</title><title>PloS one</title><addtitle>PLoS One</addtitle><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).</description><subject>Annealing</subject><subject>Assaying</subject><subject>Base sequence</subject><subject>Biochemistry</subject><subject>Biology and Life Sciences</subject><subject>Capillary electrophoresis</subject><subject>Degradation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA fingerprints</subject><subject>DNA Primers</subject><subject>DNA, Single-Stranded - genetics</subject><subject>Earth sciences</subject><subject>Electrophoresis</subject><subject>Genetic markers</subject><subject>Genetic testing</subject><subject>Genetics</subject><subject>Genotyping</subject><subject>Laboratories</subject><subject>Loci</subject><subject>Markers</subject><subject>Medicine and Health Sciences</subject><subject>Methods</subject><subject>Microsatellite Repeats</subject><subject>Multiplexing</subject><subject>Nucleic acids</subject><subject>Nucleotide sequence</subject><subject>Pharmacy</subject><subject>Physical sciences</subject><subject>Polymerase chain reaction</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymers</subject><subject>Polynucleotides</subject><subject>Polynucleotides - genetics</subject><subject>Primers</subject><subject>Research and Analysis Methods</subject><subject>Short tandem repeats</subject><subject>Social Sciences</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl1v0zAUhiMEYmPwDxBEQkJw0RJ_xzdI1fiqNJi0FW4txx-pKzfu4gTRf4-zZlODdoEiJZb9vO_JOX6z7CUo5gAx8GET-raRfr4LjZkXoGSAF4-yU8ARnFFYoMdH65PsWYyboiCopPRpdgJ5wXmJ2Gn2_Wd0TZ37kF4xfvqxyHfB75teeRM6p03Mu5DL7c47u8-vV1cxocrlrsm1qVupjc4HURwQE59nT6z00bwYv2fZ6svn1fm32cXl1-X54mKmKIfdDKkSG1ZCAkqrLcYUEmt1gSsDDCoqiBikRJcMQ8ArwIhhihCb-ispNIyis-z1wXbnQxTjIKIAnHBKAb4llgdCB7kRu9ZtZbsXQTpxuxHaWsi2c6lLYXmqViGuUIFxKamUBLMKWkmxBkTC5PVxrNZXW6OVabpW-onp9KRxa1GH34JQyjFEyeDdaNCGm97ETmxdVMZ72ZjQD_9NKcSYgaHWm3_Qh7sbqVqmBlxjQ6qrBlOxIAABXJaMJGr-AJUebbZOpdRYl_YngvcTQWI686erZR-jWF5f_T97-WvKvj1i10b6bh2D7zsXmjgF8QFUbYixNfZ-yKAQQ-jvpiGG0Isx9En26viC7kV3KUd_ATyY-ao</recordid><startdate>20171103</startdate><enddate>20171103</enddate><creator>Mautner, Martín E</creator><creator>Pérez Santángelo, Agustín</creator><creator>Corti Bielsa, Rodrigo M</creator><creator>Sala, Andrea</creator><creator>Ginart, Santiago</creator><creator>Corach, Daniel</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-9098-1225</orcidid></search><sort><creationdate>20171103</creationdate><title>Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples</title><author>Mautner, Martín E ; Pérez Santángelo, Agustín ; Corti Bielsa, Rodrigo M ; Sala, Andrea ; Ginart, Santiago ; Corach, Daniel</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Annealing</topic><topic>Assaying</topic><topic>Base sequence</topic><topic>Biochemistry</topic><topic>Biology and Life Sciences</topic><topic>Capillary electrophoresis</topic><topic>Degradation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA fingerprints</topic><topic>DNA Primers</topic><topic>DNA, Single-Stranded - genetics</topic><topic>Earth sciences</topic><topic>Electrophoresis</topic><topic>Genetic markers</topic><topic>Genetic testing</topic><topic>Genetics</topic><topic>Genotyping</topic><topic>Laboratories</topic><topic>Loci</topic><topic>Markers</topic><topic>Medicine and Health Sciences</topic><topic>Methods</topic><topic>Microsatellite Repeats</topic><topic>Multiplexing</topic><topic>Nucleic acids</topic><topic>Nucleotide sequence</topic><topic>Pharmacy</topic><topic>Physical sciences</topic><topic>Polymerase chain reaction</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymers</topic><topic>Polynucleotides</topic><topic>Polynucleotides - genetics</topic><topic>Primers</topic><topic>Research and Analysis Methods</topic><topic>Short tandem repeats</topic><topic>Social Sciences</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mautner, Martín E</creatorcontrib><creatorcontrib>Pérez Santángelo, Agustín</creatorcontrib><creatorcontrib>Corti Bielsa, Rodrigo M</creatorcontrib><creatorcontrib>Sala, Andrea</creatorcontrib><creatorcontrib>Ginart, Santiago</creatorcontrib><creatorcontrib>Corach, Daniel</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Opposing Viewpoints Resource Center</collection><collection>Science (Gale in Context)</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>ProQuest Nursing and Allied Health Journals</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological &amp; Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health &amp; Medical Complete (ProQuest Database)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science &amp; Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>Advanced Technologies &amp; Aerospace Database‎ (1962 - current)</collection><collection>Agricultural &amp; Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing &amp; Allied Health Database (Alumni Edition)</collection><collection>Meteorological &amp; Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agriculture Science Database</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>ProQuest Biological Science Journals</collection><collection>Engineering Database</collection><collection>Nursing &amp; Allied Health Premium</collection><collection>ProQuest advanced technologies &amp; aerospace journals</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials science collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mautner, Martín E</au><au>Pérez Santángelo, Agustín</au><au>Corti Bielsa, Rodrigo M</au><au>Sala, Andrea</au><au>Ginart, Santiago</au><au>Corach, Daniel</au><au>Kalendar, Ruslan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-11-03</date><risdate>2017</risdate><volume>12</volume><issue>11</issue><spage>e0187190</spage><epage>e0187190</epage><pages>e0187190-e0187190</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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).</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29099837</pmid><doi>10.1371/journal.pone.0187190</doi><tpages>e0187190</tpages><orcidid>https://orcid.org/0000-0001-9098-1225</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1932-6203
ispartof PloS one, 2017-11, Vol.12 (11), p.e0187190-e0187190
issn 1932-6203
1932-6203
language eng
recordid cdi_plos_journals_1959661476
source Publicly Available Content Database; PubMed Central
subjects Annealing
Assaying
Base sequence
Biochemistry
Biology and Life Sciences
Capillary electrophoresis
Degradation
Deoxyribonucleic acid
DNA
DNA fingerprints
DNA Primers
DNA, Single-Stranded - genetics
Earth sciences
Electrophoresis
Genetic markers
Genetic testing
Genetics
Genotyping
Laboratories
Loci
Markers
Medicine and Health Sciences
Methods
Microsatellite Repeats
Multiplexing
Nucleic acids
Nucleotide sequence
Pharmacy
Physical sciences
Polymerase chain reaction
Polymerase Chain Reaction - methods
Polymers
Polynucleotides
Polynucleotides - genetics
Primers
Research and Analysis Methods
Short tandem repeats
Social Sciences
title Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T13%3A05%3A39IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Using%20long%20ssDNA%20polynucleotides%20to%20amplify%20STRs%20loci%20in%20degraded%20DNA%20samples&rft.jtitle=PloS%20one&rft.au=Mautner,%20Mart%C3%ADn%20E&rft.date=2017-11-03&rft.volume=12&rft.issue=11&rft.spage=e0187190&rft.epage=e0187190&rft.pages=e0187190-e0187190&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0187190&rft_dat=%3Cgale_plos_%3EA513148875%3C/gale_plos_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c692t-3c84e782518fdf44625ffd04be1e30b237265d874219b175e7c55f190862e763%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1959661476&rft_id=info:pmid/29099837&rft_galeid=A513148875&rfr_iscdi=true