Date Published: January 8, 2010
Publisher: Public Library of Science
Author(s): Cristina Olivieri, Luca Ermini, Ermanno Rizzi, Giorgio Corti, Raoul Bonnal, Stefania Luciani, Isolina Marota, Gianluca De Bellis, Franco Rollo, M. Thomas P. Gilbert. http://doi.org/10.1371/journal.pone.0008629
Abstract: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation (“miscoding lesions”) has been the object of extensive investigations.
Partial Text: Within living cells, the integrity of DNA molecules is continually maintained by enzymatic repair processes . After the death of an organism, cellular compartments that normally sequester catabolic enzymes break down and, as a consequence, DNA is rapidly degraded by cellular enzymes. A further source of degradation is represented by bacteria, fungi, and soil invertebrates that, overtime, feed on and degrade macromolecules . According to the studies of Tomas Lindahl , spontaneous chemical reactions can arise and lead to a partial or total degradation of the DNA molecule. These studies have shown that, for DNA in aqueous solution, hydrolytic cleavage of the base-sugar bond (N-glycosidic bond) leads to the loss of nucleotidic bases and induces the formation of apurinic/apyrimidinic (AP) sites . These baseless sites strongly destabilize the DNA structure and, consequently, strands of the double helix are broken down by a β-elimination reaction . As time goes on, this mechanism leads to a progressive fragmentation of the whole molecule into tiny fragments. Hydrolysis is also responsible for base deamination reactions which produce damage in ancient DNA templates. Cytosine (C) and its homologue 5-methylcytosine are the main targets for the hydrolytic deamination and as a result of this reaction the two bases are converted to either uracil (U) or thymine (T), respectively . In the experimental system used by Lindahl, deamination of DNA purines such as adenine (A) and guanine (G) is less frequent (deamination rate of C is ∼30–50 times higher than that of A; ) and generates hypoxanthine (H) and xanthine (X) from adenine and guanine respectively.
Tables S1, S2 and S3 report misincorporations observed in each clonal group of ancient, modern and contaminant sequences respectively.