Abstract
A spectroscopic assay for detection of extrahelical thymine residues in DNA heteroduplexes under their modification by potassium permanganate has been developed. The assay is based on increase in absorbance at 420 nm due to accumulation of thymidine oxidation intermediates and soluble manganese dioxide. The analysis was carried out using a set of 19-bp DNA duplexes containing unpaired thymidines opposite tetrahydrofuranyl derivatives mimicking a widespread DNA damage (apurinic (AP) sites) and a library of 50-bp DNA duplexes containing all types of base mismatches in different surroundings. The relation between the selectivity of unpaired T oxidation and the thermal stability of DNA double helix was investigated. The method described here was shown to discriminate between DNA duplexes with one or two AP sites and to reveal thymine-containing mismatches and all noncanonical base pairs in AT-surroundings. Comparative results of CCM analysis and the rapid photometric assay for mismatch detection are demonstrated for the first time in the same model system. The chemical reactivity of target thymines was shown to correlate with local disturbance of double helix at the mismatch site. As the spectroscopic assay does not require the DNA cleavage reaction and gel electrophoresis, it can be easily automated and used for primary screening of somatic mutations.
Similar content being viewed by others
Abbreviations
- AP:
-
apurinic site
- CCM:
-
Chemical Cleavage of Mismatches
- TEAC:
-
tetraethylammonium chloride
- Tml :
-
melting temperature; prefix “d” in designation of sequences of oligodeoxyribonucleotides is omitted
References
Nakatani, K. (2004) Chem. Bio. Chem., 5, 1623–1633.
Latorra, D., Campbell, K., Wolter, A., and Hurley, J. M. (2003) Human Mutation, 22, 79–85.
Brenner, E. V., Ivanova, E. M., Pyshny, D. V., and Morozov, I. V. (2005) Bioorg. Khim., 31, 213–215.
Karaman, M. W., Groshen, S., Lee, Ch.-Ch., Pike, B. L., and Hacia, J. G. (2005) Nucleic Acids Res., 33, e33.
Fan, X., Furnari, F. B., Cavenee, W. K., and Castresana, J. S. (2001) Int. J. Oncol., 18, 1023–1026.
Chan, E. Y. (2005) Mutat. Res., 573, 13–40.
Hongyo, T., Buzard, G. S., Calvert, R. J., and Meghorst, C. M. (1993) Nucleic Acids Res., 21, 3637–3642.
Cotton, R. G., Rodrigues, N. R., and Campbell, R. D. (1988) Proc. Natl. Acad. Sci. USA, 85, 4397–4401.
Lambrinakos, A., Yakubovskaya, M., Babon, J. J., Neschastnova, A. A., Vishnevskaya, Y. V., Belitsky, G. A., D’Cunha, G., Horaitis, O., and Cotton, R. G. H. (2004) Human Mutation, 23, 186–192.
Cotton, R. G. H., and Campbell, R. D. (1989) Nucleic Acids Res., 17, 4223–4233.
Roberts, E., Deeble, V. J., Woods, C. G., and Taylor, G. R. (1997) Nucleic Acids Res., 25, 3377–3378.
Tessitore, A., Di Rocco, Z. C., Cannita, K., Ricevuto, E., Toniato, E., Tosi, M., Ficorella, C., Frati, L., Gulino, A., Marchetti, P., and Martinotti, S. (2002) Genes, Chromosomes & Cancer, 35, 86–91.
Neschastnova, A. A., Gasanova, V. K., Belitsky, G. A., Yakubovskaya, M. G., and Dolinnaya, N. G. (2007) Mol. Biol. (Moscow), 41, 535–543.
Yakubovskaya, M. G., Belyakova, A. A., Gasanova, V. K., Belitsky, G. A., and Dolinnaya, N. G. (2010) Biochimie, 92, 762–771.
Bui, C. T., Lambrinakos, A., and Cotton, R. G. H. (2003) Biopolymers, 70, 628–636.
Tabone, T., Sallmann, G., Webb, E., and Cotton, R. G. H. (2006) Nucleic Acids Res., 34, e45.
Volkov, E. M., Kubareva, E. A., Sergeev, V. N., and Oretskaya, T. S. (1990) Khim. Prirod. Soedin., 3, 417–419.
Dolinnaya, N. G., Jan, M. R., Kawde, A.-N., Oretskaya, T. S., Tashlitsky, V. N., and Wang, J. (2006) Electroanalysis, 18, 399–404.
Gelfand, C. A., Plum, G. E., Grollman, A. P., Johnson, F., and Breslauer, K. J. (1998) Biochemistry, 37, 7321–7327.
Hianik, T., Wang, X., Andreev, S., Dolinnaya, N., Oretskaya, T., and Thompson, M. (2006) Analyst, 131, 1161–1166.
Simandi, L. I., and Jaky, M. (1976) J. Am. Chem. Soc., 98, 1995–1997.
Hayatsu, H., and Iida, S. (1969) Tetrahedron Lett., 1031–1034.
Bui, C. T., Sam, L. A., and Cotton, R. G. (2004) Bioorg. Med. Chem. Lett., 14, 1313–1315.
Bui, C. T., and Cotton, R. G. H. (2002) Bioorg. Chem., 30, 133–137.
Zhang, F., and Zhao, Z. (2004) Genomics, 84, 785–795.
Loeb, L. A., and Preston, B. D. (1986) Ann. Rev. Genet., 20, 201–230.
Lindahl, T. (1982) Annu. Rev. Biochem., 51, 61–87.
Weiss, B., and Grossman, L. (1987) Adv. Enzymol. Relat. Areas Mol. Biol., 60, 1–34.
Wu, X., and Wang, Z. (1999) Nucleic Acids Res., 27, 956–962.
Sudyina, A. E., Volkov, E. M., Oretskaya, T. S., Degtyarev, S. Kh., Gonchar, D. A., and Kubareva, E. A. (2000) Bioorg. Khim., 26, 442–447.
Demole, B., and Harrison, L. (1994) Annu. Rev. Biochem., 63, 915–948.
Cappelli, E., Degan, P., and Frosina, G. (2000) Carcinogenesis, 21, 1135–1141.
Bui, C. T., Rees, K., and Cotton, R. G. H. (2003) Nucleosides, Nucleotides & Nucleic Acids, 22, 1835–1855.
Chen, J., Dupradeau, F.-Y., Case, D. A., Turner, C. J., and Stubbe, J. (2008) Nucleic Acids Res., 36, 253–262.
Peyret, N., Seneviratne, P. A., Allawi, H. T., and SantaLucia, J., Jr. (1999) Biochemistry, 38, 3468–3477.
Tanaka, F., Kameda, A., Yamamoto, M., and Ohuchi, A. (2004) Biochemistry, 43, 7143–7150.
Tikhomirova, A., Beletskaya, I. V., and Chalikian, T. V. (2006) Biochemistry, 45, 10563–10571.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © N. A. Logvina, M. G. Yakubovskaya, N. G. Dolinnaya, 2011, published in Biokhimiya, 2011, Vol. 76, No. 2, pp. 297–306.
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Logvina, N.A., Yakubovskaya, M.G. & Dolinnaya, N.G. Rapid photometric detection of thymine residues partially flipped out of double helix as a method for direct scanning of point mutations and apurinic DNA sites. Biochemistry Moscow 76, 245–252 (2011). https://doi.org/10.1134/S0006297911020118
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297911020118