Is amino acid racemization a useful tool for screening for ancient DNA in bone?

TY - JOUR

T1 - Is amino acid racemization a useful tool for screening for ancient DNA in bone?

AU - Collins, Matthew J.

AU - Penkman, Kirsty E.H.

AU - Rohland, Nadin

AU - Shapiro, Beth

AU - Dobberstein, Reimer C.

AU - Ritz-Timme, Stefanie

AU - Hofreiter, Michael

PY - 2009/8/22

Y1 - 2009/8/22

N2 - Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02-0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that D/L Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx D/L is not a useful screening technique for ancient DNA from bone.

AB - Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02-0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that D/L Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx D/L is not a useful screening technique for ancient DNA from bone.

KW - Ancient DNA

KW - Aspartic acid racemization

KW - Bone

KW - Collagen

KW - Screening

UR - http://www.scopus.com/inward/record.url?scp=68249101253&partnerID=8YFLogxK

U2 - 10.1098/rspb.2009.0563

DO - 10.1098/rspb.2009.0563

M3 - Journal article

C2 - 19493899

AN - SCOPUS:68249101253

SN - 0962-8452

VL - 276

SP - 2971

EP - 2977

JO - Proceedings of the Royal Society B: Biological Sciences

JF - Proceedings of the Royal Society B: Biological Sciences

IS - 1669

ER -