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ANIMAL DNA IN PCR REAGENTS PLAGUES ANCIENT DNA RESEARCH
Citation:
LEONARD, J. A., O. C. SHANKS, M. HOFREITER, E. KREUZ, L. HODGES, W. REAM, R. K. WAYNE, AND R. C. FLEISCHER. ANIMAL DNA IN PCR REAGENTS PLAGUES ANCIENT DNA RESEARCH. JOURNAL OF ARCHAEOLOGICAL SCIENCE. Elsevier Science Ltd, New York, NY, 34(9):1361-1366, (2007).
Description:
Ancient DNA analysis is becoming widespread. These studies use polymerase chain reaction (PCR) to amplify minute quantities of heavily damaged template. Unusual steps are taken to achieve the sensitivity necessary to detect ancient DNA, including high-cycle PCR amplification targeting short (<300 bp), high-copy templates. Often, primers are used that anneal to target sequences from multiple species. These factors increase the likelihood that PCR will amplify traces of highly fragmented DNA, including ancient DNA and extraneous DNA that may contaminate PCR reagents. We have found, in four independent laboratories, that extraneous DNA molecules are regularly amplified under a wide variety of PCR conditions. Using different protocols, we amplified extraneous sequences from either negative controls or extracts of other species. The most pervasive non-human vertebrate contamination was from cow, pig and chicken. Six other species associated with humans, including mouse, rabbit, guinea pig, domestic cat, dog, and goat, were detected occasionally. Deoxynucleoside triphosphates (dNTPs) are the only source with a known connection to these animals. Deoxynucleoside monophosphates are obtained by hydrolysis of animal DNA and then phosphorylated chemically to produce triphosphates. Incomplete hydrolysis of animal DNA during dNTP production may lead to dNTP contamination.