Crosslinks rather than Strand Breaks Determine Access to Ancient DNA Sequences from Frozen Sediments

• Published in: Genetics
• Main Authors: Hansen, AJ, Mitchell, D, Wiuf, Carsten, Paniker, L, Brand, TB, Binladen, J, Gilichinsky, DA, Rønn, R, Willerslev, E
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2006
• Subjects: Ancient DNA; Crosslinks; DNA Damage; Permafrost; Single strand breaks; permafrost
• Online Access: https://pure.au.dk/portal/da/publications/crosslinks-rather-than-strand-breaks-determine-access-to-ancient-dna-sequences-from-frozen-sediments(a4f88ef0-afa1-11db-bee9-02004c4f4f50).html; https://doi.org/10.1534/genetics.106.057349

Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10 to 400 thousand 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 about hundred 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 base pair fragments of bacterial 16S ribosomal DNA was estimated to be about 400 thousand 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.