Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments
Abstract Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10,000 to 400,000 years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks; single- and double-stranded breaks;...
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Online Access: | http://dx.doi.org/10.1534/genetics.106.057349 https://academic.oup.com/genetics/article-pdf/173/2/1175/42067708/genetics1175.pdf |
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croxfordunivpr:10.1534/genetics.106.057349 2024-09-15T18:29:40+00:00 Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments Hansen, Anders J Mitchell, David L Wiuf, Carsten Paniker, Lakshmi Brand, Tina B Binladen, Jonas Gilichinsky, David A Rønn, Regin Willerslev, Eske 2006 http://dx.doi.org/10.1534/genetics.106.057349 https://academic.oup.com/genetics/article-pdf/173/2/1175/42067708/genetics1175.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model Genetics volume 173, issue 2, page 1175-1179 ISSN 1943-2631 journal-article 2006 croxfordunivpr https://doi.org/10.1534/genetics.106.057349 2024-07-08T04:23:12Z Abstract Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10,000 to 400,000 years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks; single- and double-stranded breaks; and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate ∼100 times faster than single-stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost sediments is to be significantly increased. Using the obtained rate constant for interstrand crosslinks the maximal survival time of amplifiable 120-bp fragments of bacterial 16S ribosomal DNA was estimated to be ∼400,000 years. Additionally, a clear relationship was found between DNA damage and sample age, contradicting previously raised concerns about the possible leaching of free DNA molecules between permafrost layers. Article in Journal/Newspaper permafrost Oxford University Press Genetics 173 2 1175 1179 |
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Oxford University Press |
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English |
description |
Abstract Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10,000 to 400,000 years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks; single- and double-stranded breaks; and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate ∼100 times faster than single-stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost sediments is to be significantly increased. Using the obtained rate constant for interstrand crosslinks the maximal survival time of amplifiable 120-bp fragments of bacterial 16S ribosomal DNA was estimated to be ∼400,000 years. Additionally, a clear relationship was found between DNA damage and sample age, contradicting previously raised concerns about the possible leaching of free DNA molecules between permafrost layers. |
format |
Article in Journal/Newspaper |
author |
Hansen, Anders J Mitchell, David L Wiuf, Carsten Paniker, Lakshmi Brand, Tina B Binladen, Jonas Gilichinsky, David A Rønn, Regin Willerslev, Eske |
spellingShingle |
Hansen, Anders J Mitchell, David L Wiuf, Carsten Paniker, Lakshmi Brand, Tina B Binladen, Jonas Gilichinsky, David A Rønn, Regin Willerslev, Eske Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments |
author_facet |
Hansen, Anders J Mitchell, David L Wiuf, Carsten Paniker, Lakshmi Brand, Tina B Binladen, Jonas Gilichinsky, David A Rønn, Regin Willerslev, Eske |
author_sort |
Hansen, Anders J |
title |
Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments |
title_short |
Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments |
title_full |
Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments |
title_fullStr |
Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments |
title_full_unstemmed |
Crosslinks Rather Than Strand Breaks Determine Access to Ancient DNA Sequences From Frozen Sediments |
title_sort |
crosslinks rather than strand breaks determine access to ancient dna sequences from frozen sediments |
publisher |
Oxford University Press (OUP) |
publishDate |
2006 |
url |
http://dx.doi.org/10.1534/genetics.106.057349 https://academic.oup.com/genetics/article-pdf/173/2/1175/42067708/genetics1175.pdf |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
Genetics volume 173, issue 2, page 1175-1179 ISSN 1943-2631 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/genetics.106.057349 |
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Genetics |
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173 |
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2 |
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1175 |
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1179 |
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1810471084866142208 |