Reconstructing protein-coding sequences from ancient DNA
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Updated: Dec 11, 2025

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
Published on: September 3, 2009
Michael Hofreiter1, Stefanie Hartmann1
1Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
Abstract:
Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including miscoding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.
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