Ancient DNA pp 121-128 | Cite as

Hybridization Capture of Ancient DNA Using RNA Baits

  • André E. R. Soares
Part of the Methods in Molecular Biology book series (MIMB, volume 1963)


The majority of DNA recovered from ancient remains is derived from organisms that colonize the remains post-mortem, such as soil microbes, or from contaminants, such as DNA from living humans. Additionally, some ancient DNA research projects aim to target specific genomic regions, such as mitochondrial genomes or variable single nucleotide polymorphisms (SNPs). To overcome the challenge of targeting specific fragments of DNA from within a complex DNA extract, methods have been developed to enrich ancient DNA extracts for target DNA relative to nontarget DNA. This chapter describes a method for target DNA enrichment that uses hybridization to biotinylated RNA baits to capture and amplify specific ancient DNA fragments from within the pool of extracted fragments.

Key words

Ancient DNA DNA capture RNA bait Hybridization 


  1. 1.
    Green RE, Krause J, Briggs AW et al (2010) A draft sequence of the Neandertal genome. Science 328:710–722CrossRefGoogle Scholar
  2. 2.
    Reich D, Green RE, Kircher M et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060CrossRefGoogle Scholar
  3. 3.
    Skoglund P, Malmström H, Raghavan M et al (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336:466–469CrossRefGoogle Scholar
  4. 4.
    Burbano HA, Hodges E, Green RE et al (2010) Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328:723–725CrossRefGoogle Scholar
  5. 5.
    Heintzman PD, Froese D, Ives JW et al (2016) Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada. Proc Natl Acad Sci U S A 113:8057–8063CrossRefGoogle Scholar
  6. 6.
    Gnirke A, Melnikov A, Maguire J et al (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189CrossRefGoogle Scholar
  7. 7.
    Carpenter ML, Buenrostro JD, Valdiosera C et al (2013) Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 93:852–864CrossRefGoogle Scholar
  8. 8.
    Sano T, Vajda S, Cantor CR (1998) Genetic engineering of streptavidin, a versatile affinity tag. J Chromatogr B Biomed Sci Appl 715:85–91CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • André E. R. Soares
    • 1
  1. 1.Laboratório Nacional de Computação CientíficaPetrópolisBrazil

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