Stability of Synthetic Single-Strand DNA as a Criterion for the Usage as Marking System
DOI:
https://doi.org/10.12970/2311-1755.2014.02.01.5Keywords:
DNA stability, DNA damage, amplification ratio, rate constant, half-life, Real-time PCR.Abstract
DNA is a carrier of genetic information and can be used as an invisible barcode. For its successful application, stability is one important criterion. This report describes the investigation of synthetic single-strand DNA (ssDNA) damage under several environmental conditions with Real-time PCR. We measured the amplification ratio of amplifiable ssDNA against time and calculated the half-life. Comparing the half-life of all DNA degradations, ultraviolet irradiation leads to the fastest ssDNA decay, followed by ssDNA treatment at 80°C in the presence of water and acidic ssDNA incubation. However, ssDNA is protected against high temperatures by complexation to hydroxyapatite. This study shows for the first time half-life values for ssDNA, which are important for technical applications such as the usage as a marking system. Also this study is of crucial importance for all other applications, in which DNA damage can lead to misinterpretations in PCR results.
References
Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993; 362: 709-15. http://dx.doi.org/10.1038/362709a0
Sinha RP, Häder DP. UV-induced DNA damage and repair: a review. Photochem Photobiol Sci 2002; 1: 225-36. http://dx.doi.org/10.1039/b201230h
Takeshita M, Chang CN, Johnson F, Will S, Grollman AP. J Biol Chem 1987; 262: 10171-9.
Shibutani S, Takeshita M, Grollman AP. Nature 1991; 349: 431-4. http://dx.doi.org/10.1038/349431a0
Yakes FM, Chen Y, Van Houten B. In Technologies for Detection of DNA Damage and Mutations, Plenum Press: New York 1996; pp. 169-82.
Swango KL, Timken MD, Chong MD, Buoncristiani MR. A quantitative PCR assay for the assessment of DNA degradation in forensic samples. Forensic Sci Int 2006; 158: 14-26. http://dx.doi.org/10.1016/j.forsciint.2005.04.034
Reynolds R, Saiki R, Grow M, et al. in Advantages in Forensic Haemogenetics, Springer: Heidelberg 1992; pp. 29-31. http://dx.doi.org/10.1007/978-3-642-77324-2_5
Alonso A, Martín P, Albarrán C, et al. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci Int 2004; 139: 141-9. http://dx.doi.org/10.1016/j.forsciint.2003.10.008
Timken MD, Swango KL, Orrego C, Buoncristiani MR. A duplex real-time qPCR assay for the quantification of human nuclear and mitochondrial DNA in forensic samples: implications for quantifying DNA in degraded samples. J Forensic Sci 2005; 50: 1044-60. http://dx.doi.org/10.1520/JFS2004423
Shibutani S, Bodepudi V, Johnson F, Grollman AP. Trans-lesional synthesis on DNA templates containing 8-oxo-7,8-dihydrodeoxyadenosine. Biochemistry 1993; 32: 4615-21. http://dx.doi.org/10.1021/bi00068a019
Shibutani S, Takeshita M, Grollman AP. Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the "A rule". J Biol Chem 1997; 272: 13916-22. http://dx.doi.org/10.1074/jbc.272.21.13916
Smith CA, Baeten J, Taylor JS. The ability of a variety of polymerases to synthesize past site-specific cis-syn, trans-syn-II, (6-4), and Dewar photoproducts of thymidylyl-(3'-->5')-thymidine. J Biol Chem 1998; 273: 21933-40. http://dx.doi.org/10.1074/jbc.273.34.21933
Asagoshi K, Terato H, Ohyama Y, Ide H. Effects of a guanine-derived formamidopyrimidine lesion on DNA replication: translesion DNA synthesis, nucleotide insertion, and extension kinetics. J Biol Chem 2002; 277: 14589-97. http://dx.doi.org/10.1074/jbc.M200316200
Sikorsky JA, Primerano DA, Fenger TW, Denvir J. Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method. Biochem Biophy Res Commun 2004; 323: 823-30. http://dx.doi.org/10.1016/j.bbrc.2004.08.168
Sikorsky JA, Primerano DA, Fenger TW, Denvir J. DNA damage reduces Taq DNA polymerase fidelity and PCR amplification efficiency. Biochem Biophy Res Commun 2007; 355: 431-7. http://dx.doi.org/10.1016/j.bbrc.2007.01.169
Pruvost M, Geigl EM. Real-time quantitative PCR to assess the authenticity of ancient DNA amplification. J Archaeol Sci 2004; 31: 1191-7. http://dx.doi.org/10.1016/j.jas.2002.05.002
Swango KL, Hudlow WR, Timken MD, Buoncristiani MR. Developmental validation of a multiplex qPCR assay for assessing the quantity and quality of nuclear DNA in forensic samples. Forensic Sci Int 2007; 170: 35-45. http://dx.doi.org/10.1016/j.forsciint.2006.09.002
Yoshida H, Regan JD. Solar UVB dosimetry by amplification of short and long segments in phage lambda DNA. Photochem Photobiol 1997; 66: 672-5. http://dx.doi.org/10.1111/j.1751-1097.1997.tb03205.x
Yakes FM, van Houten B. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc Natl Acad Sci USA 1997; 94: 514-9. http://dx.doi.org/10.1073/pnas.94.2.514
Bernardi G. Chromatography of nucleic acids on hydroxyapatite. Nature 1965; 206: 779-83. http://dx.doi.org/10.1038/206779a0
Bustin SA, Nolan T. In Real-time PCR: Current technology and applications, Caister Academic Press: Norfolk 2009; pp. 111-35.
Muller PY, Janovjak H, Miserez AR, Dobbie Z. Processing of gene expression data generated by quantitative real-time RT-PCR 2002; 32: 1372-4.
Loeb LA, Preston BD. Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet 1986; 20: 201-30. http://dx.doi.org/10.1146/annurev.ge.20.120186.001221
Lindahl T, Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 1972; 11: 3610-8. http://dx.doi.org/10.1021/bi00769a018
Lindahl T, Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 1972; 11: 3618-23. http://dx.doi.org/10.1021/bi00769a019
Lawley PD, Lethbridge JH, Edwards PA, Shooter KV. Inactivation of bacteriophage T7 by mono- and difunctional sulphur mustards in relation to cross-linking and depurination of bacteriophage DNA. J Mol Biol 1969; 39: 181-98. http://dx.doi.org/10.1016/0022-2836(69)90341-6
Lindahl T, Karlstrom O. Heat-induced depyrimidination of deoxyribonucleic acid in neutral solution. Biochemistry 1973; 12: 5151-4. http://dx.doi.org/10.1021/bi00749a020
Sugiyama H, Fujiwara T, Ura A, et al. Chemistry of thermal degradation of abasic sites in DNA. Mechanistic investigation on thermal DNA strand cleavage of alkylated DNA. Chem Res Toxicol 1994; 7: 673-83. http://dx.doi.org/10.1021/tx00041a013
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S. Neandertal DNA sequences and the origin of modern humans. Cell 1997; 90: 19-30. http://dx.doi.org/10.1016/S0092-8674(00)80310-4
Krause J, Dear PH, Pollack JL, et al. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 2006; 439: 724-7. http://dx.doi.org/10.1038/nature04432
Yamauchi E, Watanabe R, Oikawa M, et al. Application of real time PCR for the quantitative detection of radiation-induced genomic DNA strand breaks. J Insect Biotechnol Sericol 2008, 77, 1_17-1_24.
