Hypersensitive PCR, Ancient Human mtDNA, and Contamination

Document Type

Article

Authors

Dongya Y. Yang, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
Barry Eng, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
Shelley R. Saunders, McMaster Paleogenetics Institute, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada.

Abstract

When highly efficient polymerase was used with high cycle numbers (50–60), strong amplifications were observed, but negative controls were also unexpectedly amplified in a study of ancient human mtDNA from 2000-year-old skeletons. The results of a series of tests revealed that the hypersensitive polymerase chain reaction (PCR) generated by higher cycles and the presence of contaminant DNA (though at extremely low levels) should be responsible for the amplification of negative controls. We suggest that PCR sensitivity be optimized to take advantage of highly efficient polymerase and at the same time prevent “background DNA” from becoming “contaminant DNA” and obscuring the analysis of authentic ancient DNA. We propose the use of multiple positive controls when amplifying ancient human mtDNA samples to indicate the sensitivity of individual PCR amplifications and to monitor the contamination levels of modern human DNA. This study provides some suggestions as to how to amplify and analyze ancient human mtDNA when unavoidable and extremely tiny amounts of modern human DNA exist.

Recommended Citation

Yang, Dongya Y.; Eng, Barry; and Saunders, Shelley R. (2003) "Hypersensitive PCR, Ancient Human mtDNA, and Contamination," Human Biology: Vol. 75: Iss. 3, Article 4.
Available at: https://digitalcommons.wayne.edu/humbiol/vol75/iss3/4