DNA damage in preserved specimens and tissue samples: A molecular assessment

Frontiers in Zoology

Volumn 5, Issue , 2008, Pages

  Zimmermann, Juergen ^a   Hajibabaei, Mehrdad ^b   Blackburn, David C ^c   Hanken, James ^c   Cantin, Elizabeth ^a   Posfai, Janos ^a   Evans Jr , Thomas C ^a  

^a NEW ENGLAND BIOLABS   (United States)

^b UNIVERSITY OF GUELPH   (Canada)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; ANURA; LEPIDOPTERA;

EID: 55349105499     PISSN: None     EISSN: 17429994     Source Type: Journal    
DOI: 10.1186/1742-9994-5-18     Document Type: Article

References (37)

1. Back to the future: museum specimens in population genetics. P Wandeler PE Hoeck LF Keller, Trends Ecol Evol 2007 22 634 642 17988758
2. DNA Damage and Repair. JT Stivers RD Kuchta, Chemical Reviews 2006 106 2 16895336
3. Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. U Lehmann H Kreipe, Methods 2001 25 409 418 11846610
4. Instability and decay of the primary structure of DNA. T Lindahl, Nature 1993 362 709 715 8469282
5. Genetic analyses from ancient DNA. S Paabo H Poinar D Serre V Jaenicke-Despres J Hebler N Rohland M Kuch J Krause L Vigilant M Hofreiter, Annu Rev Genet 2004 38 645 679 15568989
6. Patterns of nuclear DNA degeneration over time-a case study in historic teeth samples. P Wandeler S Smith PA Morin RA Pettifor SM Funk, Mol Ecol 2003 12 1087 1093 12753226
7. Antediluvian DNA research. EM Golenberg, Nature 1994 367 692 8107863
8. DNA from ancient mammoth bones. E Hagelberg MG Thomas CE Cook Jr AV Sher GF Baryshnikov AM Lister, Nature 1994 370 333 334 8047136
9. Histologic fixatives suitable for diagnostic light and electron microscopy. EM McDowell BF Trump, Arch Pathol Lab Med 1976 100 405 414 60092
10. On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions. H Puchtler SN Meloan, Histochemistry 1985 82 201 204 3997553
11. Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR. V Zsikla M Baumann G Cathomas, J Clin Pathol 2004 57 654 656 15166276
12. Reactions of nucleic acids and nucleoproteins with formaldehyde. MY Feldmann, Prog Nucleic Acid Res Mol Biol 1973 13 1 49 4573489
13. Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. JD McGhee PH von Hippel, Biochemistry 1975 14 1281 1296 235285
14. Formaldehyde as a probe of DNA structure. II. Reaction with endocyclic imino groups of DNA bases. JD McGhee PH von Hippel, Biochemistry 1975 14 1297 1303 235286
15. Formaldehyde as a probe of DNA structure. 3. Equilibrium denaturation of DNA and synthetic polynucleotides. JD McGhee PH von Hippel, Biochemistry 1977 16 3267 3276 560859
16. Formaldehyde as a probe of DNA structure. 4. Mechanism of the initial reaction of Formaldehyde with DNA. JD McGhee PH von Hippel, Biochemistry 1977 16 3276 3293 19043
17. Reaction Mechanisms of Formaldehyde with Endocyclic Imino Groups of Nucleic Acid Bases. Y-T Chang GH Loew, J Am Chem Soc 1994 116 3548 3555
18. Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. NJ Coombs AC Gough JN Primrose, Nucleic Acids Res 1999 27 e12 10454649
19. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. M Srinivasan D Sedmak S Jewell, Am J Pathol 2002 161 1961 1971 12466110
20. Fundamental study on the mechanism of DNA degradation in tissues fixed in formaldehyde. Y Tokuda T Nakamura K Satonaka S Maeda K Doi S Baba T Sugiyama, J Clin Pathol 1990 43 748 751 2120290
21. A high frequency of sequence alterations is due to formalin fixation of archival specimens. C Williams F Ponten C Moberg P Soderkvist M Uhlen J Ponten G Sitbon J Lundeberg, Am J Pathol 1999 155 1467 1471 10550302
22. Collection and storage of invertebrate samples. M Dick DM Bridge WC Wheeler R DeSalle, Methods Enzymol 1993 224 51 65 8264406
23. Factors affecting mitochondrial DNA quality from museum preserved Drosophila simulans. MD Dean JW Ballard, Entomologia Experimentalis et Applicata 2001 98 279 283
24. Damage and repair of ancient DNA. D Mitchell E Willerslev A Hansen, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2005 571 265 276
25. JE Simmons, Herpetological collecting and collections management Society for the Study of Amphibians and Reptiles 2002
26. Labeling of double-stranded DNA by ROX-dideoxycytosine triphosphate using terminal deoxynucleotidyl transferase and separation by capillary electrophoresis. D Figeys A Renborg NJ Dovichi, Anal Chem 1994 66 4382 4383 7847633
27. Complete release of (5'S)-8,5'-cyclo-2'-deoxyadenosine from dinucleotides, oligodeoxynucleotides and DNA, and direct comparison of its levels in cellular DNA with other oxidatively induced DNA lesions. P Jaruga J Theruvathu M Dizdaroglu PJ Brooks, Nucleic Acids Res 2004 32 e87 15215337
28. Novel relationships among hyloid frogs inferred from 12S and 16S mitochondrial DNA sequences. CR Darst DC Cannatella, Mol Phylogenet Evol 2004 31 462 475 15062788
29. Nucleic acids. DM Brown AR Todd, Annu Rev Biochem 1955 24 311 338 13249358
30. Physical and chemical properties of the apurinic acid of calf thymus. C Tamm E Chargaff, J Biol Chem 1953 203 689 694 13084638
31. 368. The nucleotide sequence in deoxyribonucleic acids. Part V. The alkaline degradation of apurinic acids. CR Bayley KW Brammer AS Jones, J Chem Soc 1961 1903 1907
32. Self-catalyzed site-specific depurination of guanine residues within gene sequences. O Amosova R Coulter JR Fresco, Proc Natl Acad Sci USA 2006 103 4392 4397 16537362
33. Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. N Masuda T Ohnishi S Kawamoto M Monden K Okubo, Nucleic Acids Res 1999 27 4436 4443 10536153
34. DNA interstrand cross-linking by formaldehyde: nucleotide sequence preference and covalent structure of the predominant cross-link formed in synthetic oligonucleotides. H Huang PB Hopkins, J Am Chem Soc 1993 115 9402 9408
35. Formaldehyde preferentially interstrand cross-links duplex DNA through deoxyadenosine residues at the sequence 5'-d(AT). H Huang MS Solomon PB Hopkins, J Am Chem Soc 1992 114 9240 9241
36. Development of Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry Methods for Analysis of DNA Adducts of Formaldehyde and Their Application to Rats Treated with N-Nitrosodimethylamine or 4-(Methylnitrosamino) -1-(3-pyridyl)-1-butanone. M Wang G Cheng PW Villalta SS Hecht, Chem Res Toxicol 2007 20 1141 1148 17676814
37. Rate of depurination of native deoxyribonucleic acid. T Lindahl B Nyberg, Biochemistry 1972 11 3610 3618 4626532