Amino Acid Racemization and the Preservation of Ancient DNA

Abstract

The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.

Taxonomic heterogeneity within the Planctomycetales as derived by DNA–DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula

“…The problem is compounded by the fact that calibration rates are ultimately based on a known fossil record (Doolittle, 1997;Doolittle et al, 1996;Feng et al, 1997;Lee, 1999), and even then rates may vary between lineages (Ochman et al, 1999;Soltis et al, 2002). In addition, there are no reliable reports of 'molecular fossils' that are more than 50-100 million years old (Poinar et al, 1996;Willerslev et al, 2003). Such problems have been highlighted by Sneath (1974) and are beginning to be discussed again.…”

Analysis of one million base pairs of Neanderthal DNA

“…The vast majority of these samples had low overall contents of amino acids and/or high levels of amino acid racemization, a stereoisomeric structural change that affects amino acids in fossils, indicating that they are unlikely to contain retrievable endogenous DNA 26 . However, some of the samples are better preserved in that they contain high levels of amino acids (more than 20,000 p.p.m.…”

Techniques of DNA-studies on prehispanic ectoparasites (Pulex sp., Pulicidae, Siphonaptera) from animal mummies of the Chiribaya Culture, Southern Peru

“…Initially, the screening for the D/L ratio was mainly used for age assessments of geological and paleobiological material (Robins et al 2001). Recently though, researchers have found a connection between the D/L ratio of aspartic acid and the preservation of aDNA (Poinar et al 1996). Poinar et al (1996) state that ratios above 0.08-0.10 usually yield no DNA.…”

“…Recently though, researchers have found a connection between the D/L ratio of aspartic acid and the preservation of aDNA (Poinar et al 1996). Poinar et al (1996) state that ratios above 0.08-0.10 usually yield no DNA. The contemporary samples all showed a ratio of 0.0.…”

“…Environments of great aridity, like deserts, are known to provide extraordinarily favorable conditions for the preservation of organic material. However, recent research has shown that nearly no reproducible aDNA could be extracted from organic archaeological material of this origin (Poinar et al 1996, Hofreiter et al 2001. Heat, direct exposure to the sun and a constantly changing pH are especially unfavorable for the conservation of DNA.…”