Technical note: Improved ancient DNA purification for PCR using ion-exchange columns

American Journal of Physical Anthropology

Volumn 136, Issue 1, 2008, Pages 114-121

  Kim, Kijeong ^a   Kim, Kyung Yong ^a   Jeon, Eunhee ^a   Togloom, Ariunaa ^a   Cho, Youn Ock ^a   Lee, Min Soo ^a   Lkhagvasuren, Gavaachimed ^a   Choi, Jee Hye ^a   Tumen, Dashtseveg ^b   Ae, Ja Park ^c   Kim, Keun Cheol ^d   Park, Ki Won ^e   Kim, Jae Hyun ^f   Noh, Maengseok ^g   Yoo, Kwon Jong ^a   Lee, Kwang Ho ^a  

^a Chung Ang University   (South Korea)

^b NATIONAL UNIVERSITY OF MONGOLIA   (Mongolia)

^c Chung Ang University College of Medicine   (South Korea)

^d Kangwon National University   (South Korea)

^e National Institute of Scientific Investigation   (South Korea)

^f Dong A University   (South Korea)

^g Pukyong National University   (South Korea)

Author keywords

Ancient bone; DNA purification; Ion exchange columns; PCR amplification; PCR inhibitors

Indexed keywords

AMELOGENIN; MITOCHONDRIAL DNA; DNA;

ARTICLE; BONE; DNA EXTRACTION; DNA PURIFICATION; FEMALE; HUMAN; HUMAN TISSUE; MALE; MEDICAL INSTRUMENTATION; POLYMERASE CHAIN REACTION; ION EXCHANGE CHROMATOGRAPHY; ISOLATION AND PURIFICATION; METHODOLOGY; PHYSICAL ANTHROPOLOGY;

BONE AND BONES; CHROMATOGRAPHY, ION EXCHANGE; DNA; FORENSIC ANTHROPOLOGY; HUMANS; POLYMERASE CHAIN REACTION;

EID: 42149168520     PISSN: 00029483     EISSN: 10968644     Source Type: Journal    
DOI: 10.1002/ajpa.20782     Document Type: Article

References (42)

1. Abu-Amero KK, Gonzalez AM, Larruga JM, Bosley TM, Cabrera VM. 2007. Eurasian and African mitochondrial DNA influences in the Saudi Arabian population. BMC Evol Biol 7:32.
2. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147.
3. Blake E, Mihalovich J, Higuchi R, Walsh PS, Erlich H. 1992. Polymerase chain reaction (PCR) amplification and human leukocyte antigen (HLA)-DQ alpha oligonucleotide typing on biological evidence samples: casework experience. J Forensic Sci 37:700-726.
4. Calacal GC, De Ungria MC. 2005. Fungal DNA challenge in human STR typing of bone samples. J Forensic Sci 50:1394-1401.
5. Cattaneo C, Craig OE, James NT, Sokol RJ. 1997. Comparison of three DNA extraction methods on bone and blood stains up to 43 years old and amplification of three different gene sequences. J Forensic Sci 42:1126-1135.
6. Cattaneo C, Smillie DM, Gelsthorpe K, Piccinini A, Gelsthorpe AR, Sokol RJ. 1995. A simple method for extracting DNA from old skeletal material. Forensic Sci Int 74:167-174.
7. Edson SM, Ross JR, Coble MD, Parsons TJ, Barritt SM. 2004. Naming the dead - confronting the realities of rapid identification of degraded skeletal remains. Forensic Sci Rev 16:64-89.
8. Evison MP, Smillie DM, Chamberlain AT. 1997. Extraction of single-copy nuclear DNA from forensic specimens with a variety of postmortem histories. J Forensic Sci 42:1032-1038.
9. Faerman M, Filon D, Kahila G, Greenblatt CL, Smith P, Oppenheim A. 1995. Sex identification of archaeological human remains based on amplification of the X and Y amelogenin alleles. Gene 167:327-332.
10. Fischer GF, Fae I, Mann D, Kriks D, Jager W, Platzer W, Mayr WR, Volc-Platzer B. 2001. An HLA class-II allele frequent in Eskimos and Amerindians is found in the Tyrolean Ice Man. Ann Hum Genet 65:363-369.
11. Hagelberg E, Clegg JB. 1991. Isolation and characterization of DNA from archaeological bone. Proc Biol Sci 244:45-50.
12. Handt O, Höss M, Krings M, Pääbo S. 1994. Ancient DNA: methodological challenges. Experientia 50:524-529.
13. Hänni C, Brousseau T, Laudet V, Stehelin D. 1995. Isopropanol precipitation removes PCR inhibitors from ancient bone extracts. Nucleic Acids Res 23:881-882.
14. Höss M, Jaruga P, Zastawny TH, Dizdaroglu M, Pääbo S. 1996. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res 24:1304-1307.
15. Höss M, Pääbo S. 1993. DNA extraction from Pleistocene bones by a silica-based purification method. Nucleic Acids Res 21: 3913-3914.
16. Hunter P. 2006. Ancient DNA research goes nuclear. A new technique to extract sequence data from nuclear DNA may reveal exciting new insights into evolution and phylogeny. EMBO Rep 7:136-139.
17. Kalmar T, Bachrati CZ, Marcsik A, Rasko I. 2000. A simple and efficient method for PCR amplifiable DNA extraction from ancient bones. Nucleic Acids Res 28:E67.
18. Kemp BM, Monroe C, Smith DG. 2006. Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts. J Archaeol Sci 33:1680-1689.
19. Kemp BM, Smith DG. 2005. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int 154:53-61.
20. Keyser-Tracqui C, Crubezy E, Ludes B. 2003. Nuclear and mitochondrial DNA analysis of a 2,000-year-old necropolis in the Egyin Gol Valley of Mongolia. Am J Hum Genet 73:247-260.
21. Keyser-Tracqui C, Ludes B. 2005. Methods for the study of ancient DNA. Methods Mol Biol 297:253-264.
22. Kim J-H. 1994. The burial process of the Chuam-Dong tumuli, Dong-Hae city, Korea: in the case of the KA-31 location B tomb. J Soc Kyushu Prehist Ancient Cultur Stud (ROBUNKA DANSO. JAPAN) 33:205-221.
23. Kolman CJ, Tuross N. 2000. Ancient DNA analysis of human populations. Am J Phys Anthropol 111:5-23.
24. Kumar SS, Nasidze I, Walimbe SR, Stoneking M. 2000. Brief communication: discouraging prospects for ancient DNA from India. Am J Phys Anthropol 113:129-133.
25. Kurosaki K, Matsushita T, Ueda S. 1993. Individual DNA identification from ancient human remains. Am J Hum Genet 53:638-643.
26. Mulligan CJ. 2005. Isolation and analysis of DNA from archaeological, clinical, and natural history specimens. Methods Enzymol 395:87-103.
27. O'Rourke DH, Carlyle SW, Parr RL. 1996. Ancient DNA: methods, progress, and perspectives. Am J Hum Biol 8:557-571.
28. Pääbo S. 1989. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 86:1939-1943.
29. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. 2004. Genetic analyses from ancient DNA. Annu Rev Genet 38:645-679.
30. Poinar HN, Höss M, Bada JL, Pääbo S. 1996. Amino acid racemization and the preservation of ancient DNA. Science 272:864-866.
31. Prado VF, Castro AK, Oliveira CL, Souza RT, Pena SD. 1997. Extraction of DNA from human skeletal remains: practical applications in forensic sciences. Genet Anal 14:41-44.
32. Richards MB, Macaulay VA, Bandelt H-J, Sykes BC. 1998. Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet 62:241-260
33. Rohland N, Hofreiter M. 2007. Comparison and optimization of ancient DNA extraction. Biotechniques 42:343-352.
34. Shim B-K, Kim, J-H. 2001. A Significance of Nuk-Do Site, SaCheon. The Research report of Graduate School of Kyushu University, Japan. p 139-153.
35. Tebbe CC, Vahjen W. 1993. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59:2657-2665.
36. Tumen D. 1978. Paleoanthropology of western Mongolia. Studia Archeologica, Institute Historiae Academiae Scientiarum, Mongolia. T-VII (in Russian).
37. Tumen D. 1982. Paleoanthropological study of human remains from Kara Korum (Mongolian Period - 13-15th c). Studia Archeologica, Institute Historiae Academiae Scientiarum, Mongolia. T-XI (in Russian).
38. Tumen D. 2006. Paleoanthropology of ancient popultion of Mongolia. Mongolian J Archaeol Anthropol Ethnol 2. p 90-108.
39. Tumen D. 2007. Anthropology of human remains from Mongolian Period in Sharga mountain site, Asgat sum, Sukhbaatar aimag. Research report of eastern Mongolia: Archaeology and Anthropolog Perspective. p 15-16.
40. Walsh PS, Metzger DA, Higuchi R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506-513.
41. Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR. 1998. Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am J Phys Anthropol 105:539-543.
42. Zaporozhenko EV, Slobodova NV, Bulygina ES, Kravchenko IK, Kuznetsov BB. 2006. Method for rapid DNA extraction from bacterial communities of different soils. Mikrobiologiia 75: 127-134.