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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

Dehasque, Marianne ; Pečnerová, Patrícia LU orcid ; Kempe Lagerholm, Vendela ; Ersmark, Erik ; Danilov, Gleb K ; Mortensen, Peter ; Vartanyan, Sergey and Dalén, Love LU (2022) In Genes 13(4).
Abstract

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we... (More)

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.

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author
; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Bone and Bones, DNA/genetics, DNA, Ancient, Silicon Dioxide, Uracil
in
Genes
volume
13
issue
4
article number
687
pages
16 pages
publisher
MDPI AG
external identifiers
  • pmid:35456493
  • scopus:85129129475
ISSN
2073-4425
DOI
10.3390/genes13040687
language
English
LU publication?
no
id
9729a667-5843-49e0-a33d-f70fa9da46c8
date added to LUP
2024-10-10 15:55:57
date last changed
2025-07-05 03:37:42
@article{9729a667-5843-49e0-a33d-f70fa9da46c8,
  abstract     = {{<p>Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.</p>}},
  author       = {{Dehasque, Marianne and Pečnerová, Patrícia and Kempe Lagerholm, Vendela and Ersmark, Erik and Danilov, Gleb K and Mortensen, Peter and Vartanyan, Sergey and Dalén, Love}},
  issn         = {{2073-4425}},
  keywords     = {{Bone and Bones; DNA/genetics; DNA, Ancient; Silicon Dioxide; Uracil}},
  language     = {{eng}},
  month        = {{04}},
  number       = {{4}},
  publisher    = {{MDPI AG}},
  series       = {{Genes}},
  title        = {{Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA}},
  url          = {{http://dx.doi.org/10.3390/genes13040687}},
  doi          = {{10.3390/genes13040687}},
  volume       = {{13}},
  year         = {{2022}},
}