Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

Nature Protocols
Marie-Theres Gansauge, Matthias Meyer

Abstract

This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of short or degraded DNA from other sources, and it can also be used for sequencing oligonucleotides. Single-stranded library preparation is performed by ligating a biotinylated adapter oligonucleotide to the 3' ends of heat-denatured DNA. The resulting strands are then immobilized on streptavidin-coated beads and copied with a polymerase. A second adapter is attached by blunt-end ligation, and library preparation is completed by PCR amplification. We estimate that intact DNA strands are recovered in the library with ∼50% efficiency. Libraries can be generated from up to 12 DNA or oligonucleotide samples in parallel within 2 d.

References

Nov 25, 1995·Nucleic Acids Research·M M DeAngelisT L Hawkins
Jul 23, 2002·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·Shan-Rong ShiClive R Taylor
May 7, 2005·Proceedings. Biological Sciences·Eske Willerslev, Alan Cooper
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Dec 6, 2005·Analytical Biochemistry·Tian W Li, Kevin M Weeks
Mar 30, 2007·BioTechniques·Nadin Rohland, Michael Hofreiter
Aug 24, 2007·Proceedings of the National Academy of Sciences of the United States of America·Adrian W BriggsSvante Pääbo
Nov 7, 2008·Nature·David R BentleyAnthony J Smith
Nov 21, 2008·Nature·Webb MillerStephan C Schuster
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 18, 2009·Science·Adrian W BriggsSvante Pääbo
Dec 24, 2009·Nucleic Acids Research·Adrian W BriggsSvante Pääbo
Jan 5, 2010·Current Biology : CB·Johannes KrauseSvante Pääbo
Feb 12, 2010·Nature·Morten RasmussenEske Willerslev
May 8, 2010·Science·Richard E GreenSvante Pääbo
May 8, 2010·Science·Hernán A BurbanoSvante Pääbo
Jun 3, 2010·Cold Spring Harbor Protocols·Matthias Meyer, Martin Kircher
Nov 26, 2010·PloS One·Tomislav MaricicSvante Pääbo
Jul 22, 2011·Nature·Jonathan M RothbergJames Bustillo
Oct 25, 2011·Nucleic Acids Research·Martin KircherMatthias Meyer
Feb 23, 2012·Scientific Reports·María C Ávila-ArcosM Thomas P Gilbert
Sep 1, 2012·Science·Matthias MeyerSvante Pääbo

Citations

Sep 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jesse DabneyMatthias Meyer
Dec 10, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·M ParksDavid M Lambert
Dec 10, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Clio Der SarkissianLudovic Orlando
Dec 10, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kelly M HarkinsAnne C Stone
Aug 8, 2014·Nucleic Acids Research·Gabriel RenaudJanet Kelso
Jan 15, 2016·Gastroenterology·Ana I RoblesNickolas Papadopoulos
Aug 8, 2015·Journal of Forensic Sciences·Leon Huynen, David M Lambert
Oct 28, 2015·Proceedings of the National Academy of Sciences of the United States of America·Justin C TackneyDennis H O'Rourke
Aug 20, 2015·Proceedings of the National Academy of Sciences of the United States of America·Tatiana G SenkevichBernard Moss
Aug 31, 2016·Topics in Current Chemistry·Stefania VaiDavid Caramelli
Sep 10, 2014·Analytical Chemistry·Leyla EsfandiariJacob J Schmidt
Jun 18, 2015·Scientific Reports·Peter B DamgaardMorten E Allentoft
Nov 22, 2014·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Michael HofreiterMatthew J Collins
Jun 23, 2015·Nature·Qiaomei FuSvante Pääbo
Dec 4, 2014·Journal of Human Evolution·Guido BrandtWolfgang Haak
Jun 10, 2015·Nature Reviews. Genetics·Ludovic OrlandoEske Willerslev
May 6, 2015·Investigative Genetics·Michael KnappMichael Hofreiter
Apr 20, 2016·Nature Communications·Johann ElbazChristopher A Voigt
Dec 24, 2013·Bio Systems·José M Chaves-González, Miguel A Vega-Rodríguez
May 14, 2014·Trends in Ecology & Evolution·Kristine BohmannMark de Bruyn
Jan 21, 2015·Journal of Human Evolution·Stephanie MarciniakHendrik N Poinar
Dec 24, 2014·Journal of Human Evolution·Andrew S BurrellChristina M Bergey
Mar 24, 2015·Trends in Biochemical Sciences·Chun Kit KwokPhilip C Bevilacqua
Feb 27, 2014·American Journal of Human Genetics·Meredith L CarpenterCarlos D Bustamante
Nov 25, 2014·Applied Microbiology and Biotechnology·Jitendra KeshriMaggy N B Momba
Feb 3, 2015·Nature Reviews. Microbiology·Jennifer R Brum, Matthew B Sullivan
Jun 9, 2016·Proceedings of the National Academy of Sciences of the United States of America·Montgomery Slatkin, Fernando Racimo
Jul 20, 2016·Royal Society Open Science·Clemens L WeißHernán A Burbano
Jun 14, 2014·BioTechniques·E Andrew BennettThierry Grange
Sep 13, 2016·Trends in Microbiology·Cheryl P AndamMichael G Campana
Sep 15, 2016·Molecular Biology and Evolution·Kristian HanghøjLudovic Orlando
Sep 27, 2016·ELife·Beatrice DemarchiMatthew J Collins
Dec 21, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Bastien LlamasLudovic Orlando
Dec 23, 2016·Molecular Biology and Evolution·Karolina WecekAxel Barlow
Feb 15, 2017·BioTechniques·Rafal M GutakerHernán A Burbano
Nov 5, 2016·Annual Review of Animal Biosciences·David E MacHughLudovic Orlando
Jan 26, 2017·Nucleic Acids Research·Marie-Theres GansaugeMatthias Meyer
Feb 16, 2017·Molecular Ecology Resources·John S Sproul, David R Maddison
Jun 28, 2017·Nature Communications·Michael V WestburyMichael Hofreiter
Apr 15, 2017·Genome Research·Isabelle Glocke, Matthias Meyer
Mar 8, 2018·Nucleic Acids Research·Morgane BooneNico Callewaert
Sep 5, 2017·Alimentary Pharmacology & Therapeutics·S R CardingL Hoyles
Dec 22, 2017·BMC Research Notes·Nikolas BaslerAxel Barlow
Dec 7, 2013·Nature·Matthias MeyerSvante Pääbo
Dec 20, 2013·Nature·Kay PrüferSvante Pääbo
Jun 22, 2018·PLoS Neglected Tropical Diseases·Verena J SchuenemannJohannes Krause
Jun 8, 2018·Molecular Ecology Resources·Federica AlbertiAxel Barlow
Jun 23, 2018·Bioinformatics·Kay Prüfer
Aug 9, 2017·Molecular and Cellular Biology·Chuanhe YuZhiguo Zhang
Oct 13, 2018·Genome Génome / Conseil National De Recherches Canada·Bastian EgeterGuillermo Velo-Antón
Sep 16, 2018·Nature Reviews. Urology·Rhana Hassan Zakri, Jonathon Olsburgh
Feb 13, 2019·International Journal of Cancer. Journal International Du Cancer·Jian WuJinke Wang
Mar 9, 2018·Scientific Reports·Petra KorlevićMatthias Meyer
May 2, 2017·Annual Review of Genomics and Human Genetics·Christina WarinnerJohannes Krause
Feb 15, 2019·Journal of the American Society of Nephrology : JASN·Karsten B SieberShreeram Akilesh
Mar 9, 2019·Molecular Ecology Resources·Tom van der ValkKaterina Guschanski
Feb 7, 2019·Molecular Ecology·Maria Del Carmen Gomez CabreraAlan Cooper
May 1, 2019·Proceedings of the National Academy of Sciences of the United States of America·Barry ShawRobert Layfield
Sep 12, 2017·Nature Reviews. Genetics·Stephanie Marciniak, George H Perry
Sep 7, 2017·Proceedings of the National Academy of Sciences of the United States of America·Thibaut DevièseTom Higham
Aug 28, 2019·Proceedings of the National Academy of Sciences of the United States of America·Alexandre Pellan ChengIwijn De Vlaminck
Sep 14, 2019·Science Advances·E Andrew BennettEva-Maria Geigl
Oct 7, 2017·Science·Kay PrüferSvante Pääbo
Jun 5, 2020·American Journal of Physical Anthropology·Alexandra CoutinhoMattias Jakobsson
Jul 1, 2020·PloS One·Johanna L A PaijmansDaniel W G Foerster
Sep 3, 2020·Open Biology·Alexis ZukowskiSrinivas Ramachandran
Mar 16, 2017·Proceedings of the National Academy of Sciences of the United States of America·Duane FroeseBeth Shapiro
Apr 30, 2017·Science·Viviane SlonMatthias Meyer
Jul 22, 2018·Nature Communications·Matthew J RossiB Franklin Pugh
Jul 7, 2018·Clinical Microbiology Reviews·Naveen KumarBarry T Rouse
Mar 16, 2019·Science·Iñigo OlaldeDavid Reich
May 3, 2019·Nature·Fahu ChenJean-Jacques Hublin
Mar 24, 2020·Journal of Thrombosis and Haemostasis : JTH·Stefano BarcoHeidi Rossmann
Jan 13, 2017·Proceedings. Biological Sciences·Christian KehlmaierUwe Fritz
Jul 12, 2017·Science Advances·Viviane SlonSvante Pääbo
Oct 24, 2018·BMC Evolutionary Biology·Johanna L A PaijmansMichael Hofreiter
Jun 30, 2019·Science Advances·Stéphane PeyrégneKay Prüfer
Apr 9, 2020·Nature Reviews. Genetics·Laurent A F FrantzLudovic Orlando
Mar 11, 2015·Proceedings of the National Academy of Sciences of the United States of America·Hannes SchroederM Thomas P Gilbert
Dec 3, 2015·Proceedings of the National Academy of Sciences of the United States of America·Susanna SawyerSvante Pääbo
Mar 14, 2017·Nature Communications·Cameron MyhrvoldPeng Yin
Mar 17, 2018·Science·Marieke van de LoosdrechtJohannes Krause
Apr 1, 2018·American Journal of Physical Anthropology·Maria A Nieves-ColónAnne C Stone
Aug 29, 2018·Nature Ecology & Evolution·Axel BarlowMichael Hofreiter
Jun 27, 2020·BMC Genomics·Clemens L WeißHernán A Burbano
Jul 11, 2020·Scientific Reports·A F HarudaI Arzhantseva
Jul 30, 2020·Scientific Reports·David W G StantonLove Dalén
Apr 10, 2019·Proceedings. Biological Sciences·G González-FortesG Barbujani
Feb 25, 2017·Nature Reviews. Cancer·Jonathan C M WanNitzan Rosenfeld
Jun 22, 2018·Nature Communications·Philip BurnhamIwijn De Vlaminck
Mar 5, 2020·Nature Reviews. Genetics·Fernando RacimoCarles Lalueza-Fox
Mar 22, 2018·Nature·Mateja HajdinjakJanet Kelso
Nov 20, 2020·Current Protocols in Plant Biology·Sergio M LatorreRafal M Gutaker
Nov 20, 2020·BMC Medical Genomics·Daniela NachmansonOlivier Harismendy
Oct 13, 2016·Genetics·Pablo LibradoLudovic Orlando
Dec 20, 2020·Forensic Science International : Synergy·Anna SenovskaPetr Kos
Jan 28, 2021·Genes·Ulrike H TaronMichael Hofreiter
Jan 24, 2021·Scientific Reports·Elisabeth HempelFrank E Zachos
Feb 5, 2021·American Journal of Physical Anthropology·Alexandra CoutinhoMattias Jakobsson
Dec 4, 2020·BMC Genomics·Nicolas DussexDavid Díez-Del-Molino
Dec 4, 2020·Science Advances·Seita Miyazawa
Feb 11, 2021·Scientific Reports·Christian KehlmaierUwe Fritz
Feb 17, 2021·Current Biology : CB·Axel BarlowMichael Hofreiter
Feb 19, 2021·Nature·Tom van der ValkLove Dalén

Related Concepts

DNA, Single-Stranded
cDNA Library
Nested Polymerase Chain Reaction
Sequence Determinations, DNA
Oligonucleotide Primers
Biotinylation
High-Throughput Nucleotide Sequencing
DNA
Ligation
Oligonucleotides

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