Dissolved oxygen alteration of the spectrophotometric analysis and quantification of nucleic acid solutions

Biochemical Society Transactions

Volumn 37, Issue 2, 2009, Pages 466-470

  Doshi, Rupak ^a,b   Day, Philip J R ^a   Tirelli, Nicola ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Dissolved oxygen nitrogen; DNA purity; DNA quantification; Nucleic acid measurement; Oxygen DNA interaction; UV spectrophotometry

Indexed keywords

DISSOLVED OXYGEN; DOUBLE STRANDED DNA; NITROGEN; ORGANIC COMPOUND; PHENOL; SINGLE STRANDED DNA; NUCLEIC ACID; OXYGEN;

AQUEOUS SOLUTION; CIRCULAR DICHROISM; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DNA DAMAGE; NUCLEIC ACID ANALYSIS; OXIDATIVE STRESS; OXYGENATION; PHYSICAL CHEMISTRY; PRESERVATION AND STORAGE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUANTITATIVE ANALYSIS; RAMAN SPECTROMETRY; REVIEW; ULTRAVIOLET SPECTROPHOTOMETRY; METHODOLOGY; SOLUTION AND SOLUBILITY;

NITROGEN; NUCLEIC ACIDS; OXYGEN; SOLUTIONS; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 65549124020     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370466     Document Type: Review

References (30)

1. Sambrook, J. and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual, 3rd, Cold Spring Harbor Laboratory Press, Cold Spring Harbor
2. Saunders, G.C., Parkes, H.C. and Primrose, S.B. (1999) Analytical Molecular Biology: Quality and Validation, Royal Society of Chemistry, Cambridge
3. Gallagher, S.R. (2004) Quantitation of DNA and RNA with absorption and fluorescence spectroscopy. In Current Protocols in Molecular Biology, Volume 5 (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K., eds), pp. A.3D.1-A.3D.12, John Wiley and Sons, New York
4. Kieleczawa, J. (2006) DNA Sequencing. II: Optimizing Preparation and Cleanup, Jones and Bartlett, Sudbury, MA
5. Tsanev, R. and Markov, G.G. (1960) Substances interfering with spectrophotometric estimation of nucleic acids and their elimination by the two-wavelength method. Biochim. Biophys. Acta 42, 442-452
6. Schy, W.E. and Plewa, M.J. (1989) Use of the diaminobenzoic acid fluorescence assay in conjunction with UV absorbance as a means of quantifying and ascertaining the purity of a DNA preparation. Anal. Biochem. 180, 314-318
7. Teare, J.M., Islam, R., Flanagan, R., Gallagher, S., Davies, M.G. and Grabau, C. (1997) Measurement of nucleic acid concentrations using the DyNA Quant and the GeneQuant. BioTechniques 22, 1170-1174
8. De Mey, M., Lequeux, G., Maertens, J., De Maeseneire, S., Soetaert, W. and Vandamme, E. (2006) Comparison of DNA and RNA quantification methods suitable for parameter estimation in metabolic modeling of microorganisms. Anal. Biochem. 353, 198-203
9. Leggate, J., Allain, R., Isaac, L. and Blais, B.W. (2006) Microplate fluorescence assay for the quantification of double stranded DNA using SYBR Green I dye. Biotechnol. Lett. 28, 1587-1594
10. García-Closas, M., Moore, L.E., Rabkin, C.S., Franklin, T., Struewing, J., Ginzinger, D., Alguacil, J. and Rothman, N. (2006) Quantitation of DNA in buccal cell samples collected in epidemiological studies. Biomarkers 11, 472-479
11. Haque, K.A., Pfeiffer, R.M., Beerman, M.B., Struewing, J.P., Chanock, S.J. and Bergen, A.W. (2003) Performance of high-throughput DNA quantification methods. BMC Biotechnol. 3, 20
12. Shokere, L.A., Holden, M.J. and Jenkins, G.R. (2009) Comparison of fluorometric and spectrophotometric DNA quantification for real-time quantitative PCR of degraded DNA. Food Control 20, 391-401
13. Nielsen, K., Mogensen, H.S., Hedman, J., Niederstätter, H., Parson, W. and Morling, N. (2008) Comparison of five DNA quantification methods. Forensic Sci. Int. 2, 226-230
14. Evans, D.F. (1953) Molecular association of oxygen and aromatic substances. J. Chem. Soc., 345-347
15. Munck, A.U. and Scott, J.F. (1956) Ultra-violet absorption of oxygen in organic solvents. Nature 177, 587
16. Tsubomura, H. and Mulliken, R.S. (1960) Molecular complexes and their spectra. XII. Ultraviolet absorption spectra caused by the interaction of oxygen with organic molecules. J. Am. Chem. Soc. 82, 5966-5974
17. Wilkinson, F., Helman, W.P. and Ross, A.B. (1995) Rate constants for the decay and reactions of the lowest electronically excited singlet state of molecular oxygen in solution: an expanded and revised compilation. J. Phys. Chem. Ref. Data 24, 663-677
18. Mikhalko, V.K., Zhidomirov, G.M. and Lebedev, O.L. (1984) Influence of oxygen on the electronic spectra of organic compounds. II. Calculations of the spectrum of the benzene-oxygen molecular complex. J. Struct. Chem. 25, 1-5
19. Choi, M.F. and Hawkins, P. (1995) Investigation of the contact charge transfer absorption organic solvents with oxygen for use in oxygen determination. Talanta 42, 987-997
20. Choi, M.F. and Hawkins, P. (1996) A fibre-optic oxygen sensor based on contact charge-transfer absorption. Sensors Actuators B 30, 167-171
21. Willson, R.L. (1970) The reaction of oxygen with radiation-induced free radicals in DNA and related compounds. Int. J. Radiat. Biol. 17, 349-358
22. Boon, P.J., Cullis, P.M., Symons, M.C.R. and Wren, B.W. (1984) Effects of ionizing radiation on deoxyribonucleic acid and related systems. Part 1. The role of oxygen. J. Chem. Soc. Perkin Trans. 2, 1393-1399
23. Udoviĉić, L., Mark, F. and Bothe, E. (1994) Yields of single-strand breaks in double-stranded calf thymus DNA irradiated in aqueous solution in the presence of oxygen and scavengers. Radiat. Res. 140, 166-171
24. Breen, A.P. and Murphy, J.A. (1995) Reactions of oxyl radicals with DNA. Free Radical Biol. Med. 18, 1033-1077
25. Valko, M., Izakovic, M., Mazur, M., Rhodes, C.J. and Telser, J. (2004) Role of oxygen radicals in DNA damage and cancer incidence. Mol. Cell. Biochem. 266, 37-56
26. Vaupel, P. and Harrison, L. (2004) Tumor hypoxia: causative factors, compensatory mechanisms, and cellular response. Oncologist 9, 4-9
27. Brown, J.M. and Wilson, W.R. (2004) Exploiting tumour hypoxia in cancer treatment. Nat. Rev. Cancer 4, 437-447
28. Haber, F. and Weiss, J. (1934) The catalytic decomposition of hydrogen peroxide by iron salts. Proc. R. Soc. London Ser. A 147, 332-351
29. Feng, X.D., Guo, X.Q. and Qiu, K.Y. (1988) Study of the initiation mechanism of the vinyl polymerization with the system persulfate/ N,N,N′,N′-tetramethylethylenediamine. Makromol. Chem. 189, 77-83
30. Miyamoto, S., Ronsein, G.E., Prado, F.M., Uemi, M., Corrêa, T.C., Toma, I.N., Bertolucci, A., Oliveira, M.C., Motta, F.D., Medeiros, M.H. and Mascio, P.D. (2007) Biological hydroperoxides and singlet molecular oxygen generation. IUBMB Life 59, 322-331