Thursday, October 7, 2010

Examining blocking lesions in ancient DNA

The characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions (chemical alterations that cannot be bypassed by DNA polymerases). Blocking lesions prevent amplification and sequencing of affected molecules, thus limiting the analysis of DNA derived from ancient samples. Heyn et al. recently developed a new method--polymerase extension profiling (PEP)--that reveals occurrences of polymerase stalling on DNA templates. This sequencing-based technology allows detection of damage on a single-molecule level. The technique used CircLigase™ ssDNA Ligase for high-efficiency ligation of single-stranded adaptors (containing the Roche 454 A sequence) to the 3’ ends of primer-extension products.

The authors found evidence of blocking lesions in three out of four ancient samples, but no more than 40% of the molecules were affected, indicating that such modifications are far less frequent than previously thought.

ResearchBlogging.orgHeyn, P. et al. (2010). Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA Nucleic Acids Research, 38 (16) DOI: 10.1093/nar/gkq572

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