Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA
Year: 2006
Type: article
Abstract: Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation.
Institutions: Max Planck Institute for Evolutionary Anthropology, Max Planck Society, Siberian Branch of the Russian Academy of Sciences, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Institute of Archaeology, Zoological Institute, Pacific Institute of Geography, Far Eastern Branch of the Russian Academy of Sciences, Sakhalin State University, Beckman Research Institute
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W1974900938