BMB Reports

Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
권호 표지
DOI QR코드

DOI QR Code

DNA·RNA Heteroduplex Containing 8-Oxo-7,8-dihydroguanosine: Base Pairing, Structures, and Thermodynamic Stability

  • Kim, Sang-Kook (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Lee, Sung-Hwa (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Kwon, Oh-Shin (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Moon, Byung-Jo (Department of Biochemistry, College of Natural Sciences, Kyungpook National University)
  • Published : 2004.11.30
Download PDF
⟨ Previous Next ⟩

Abstract

Oligoribonucleotides containing 8-oxo-7,8-dihydroguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2'-O-methylguanosine (8-oxoG-Me) were synthesized. The base pairing properties of 8-oxoG and 8-oxoG-Me in oligoribonucleotide in cDNA synthesis by reverse transcriptases were studied. dCMP was preferentially incorporated into the site opposite 8-oxoG or 8-oxoG-Me than into other dNMPs. TMP and dCMP were inserted preferentially into sites opposite 8-oxoG or 8-oxoG by reverse transcriptases. HIV-RT did not incorporate TMP, but RAV2-RT incorporated 50% more TMP than dCMP into the site opposite 8-oxoG. In the site opposite 8-oxoG-Me TMP was substantially incorporated by HIV-RT or RAV2-RT. Thermodynamic analysis of the DNA. RNA heteroduplex containing 8-oxoG revealed that 8-oxoG and 8-oxoG-Me formed base pairs with cytidine and thymidine with similar stability. The thermodynamic parameter (${\Delta}G^{\circ}$) demonstrated that the formation of duplexes between 8-oxoG or 8-oxoG-Me and cytidine or thymidine is more thermodynamically favorable than with adenosine and guanosine. However, differences in the melting temperature and ${\Delta}G^{\circ}$'s of 8-oxoG/dC and 8-oxoG/T were much smaller than between G/dC and G/T. CD spectra showed that DNA . RNA containing 8-oxoG or 8-oxoG-Me duplexes showed similarities between the A-type RNA and B-type DNA conformations.

Keywords

References

  1. Aboul-ela, F., Koh, D., Tinoco, I. Jr. and Martin, F. H. (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCTsYT3G (X, Y = A, C, G, T), Nucleic Acids Res. 13, 4811-4824. https://doi.org/10.1093/nar/13.13.4811
  2. Ames, B. N. (1983) Dietary Carcinogens and Anticarcinogens. Science 221, 1256-1264. https://doi.org/10.1126/science.6351251
  3. Atkinson, T. and Smith, M. (1984) Solid-phase synthesis of oligonucleotides by the phosphite-trieser method; in Oligonucleotide Synthesis: A Practical Approach, Gait, M. J. (ed.), pp. 41-45, IRL Press, Oxford, UK.
  4. Cummins, L. L., Owens, S. R., Risen, L. M., Lesnik, E. A., Freier, S. M., McGee, D., Guinosso, C. J. and Cook, P. D. (1995) Characterization of fully 2'-modified oligonucleotide hetero- and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res. 23, 2019-2024. https://doi.org/10.1093/nar/23.11.2019
  5. Duarte, V., Muller, J. G. and Burrows, C. J. (1998) Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine. Nucleic Acids Res. 27, 496-502.
  6. Fraga, C. G., Shigenaga, M. K., Park, J. W., Degan, P. and Ames, B. N. (1990) Oxidative Damage to DNA During Aging: 8-Hydroxy-2'-Deoxyguanosine in Rat Organ DNA and Urine. Proc. Natl. Acad. Sci. USA 87, 4533-4537. https://doi.org/10.1073/pnas.87.12.4533
  7. Gannett, P. and Sura, T. (1993) Base pairing of 8-oxoguanosine and 8-oxo-2'-deoxyguanosine with 2'-Deoxyadenosine, 2'- Deoxycytosine, 2'- Deoxyguanosine, and Thymidine. Chem. Res. Toxicol. 6, 690-700. https://doi.org/10.1021/tx00035a015
  8. Kamiya, H., Miura, H., Murata-Kamiya, N., Ishikawa, H., Sakaguchi, T., Inoue, H., Sasaki, T., Masutani, C., Hanaoka, F., Nishimura, S. and Ohtsuka, E. (1995) 8-Hydroxyadenin (7,8- dihydro-8-oso-adenine) induces misincorporation in in vitro DNA synthesis and mutations in NIH 3T3 cells. Nucleic Acids Res. 23, 2893-2899. https://doi.org/10.1093/nar/23.15.2893
  9. Kasai, H. and Nishimura, S. (1984) Hydroxylation of deoxyguanosine at the C-8 position by ascorbic acid and other reducing agents. Nucleic Acids Res. 12, 2137-2145. https://doi.org/10.1093/nar/12.4.2137
  10. Kim, S. K., Kim, J. Y., Kim A. K. and Moon, B. J. (2002) Base pairing properties of 8-oxo-7,8-dihydroadenosine in cDNA synthesis by reverse transcriptases. Bioorg. Med. Chem. Lett. 12, 1977-1980. https://doi.org/10.1016/S0960-894X(02)00297-4
  11. Kim, S. K., Kim, J. Y., Yokoyama, S., Takaku, H. and Moon, B. J. (1999) Misreading of RNA templates containing 8-oxo-7,8- dihydroguanosine and 8-oxo-7,8-dihydro-2-O-methylguanosine in cDNA synthesis by reverse transcriptases. Nucleosides Nucleotides 18, 1335-1337. https://doi.org/10.1080/07328319908044709
  12. Kim, S. K., Yokoyama, S., Takaku, H. and Moon, B. J. (1998) Oligoribonucleotides containing 8-oxo-7,8-dihydroguanosine and 8-oxo-7,8-dihydro-2-O-methylguanosine: synthesis and base pairing properties. Bioorg. Med. Chem. Lett. 8, 939-944. https://doi.org/10.1016/S0960-894X(98)00150-4
  13. Koizumi, S., Kamiyama, H., Inoue, H. and Ohtsuka, E. (1994) Synthesis and thermodynamic stabilities of damaged DNA involving 8-hydroxyguanine (7,8-dihydro-8-oxoguanine) in a ras-gene fragment. Nucleosides Nucleotides 13, 1517-1534. https://doi.org/10.1080/15257779408012168
  14. Kuchino, M. L., Mori, F., Kasai, H., Iwai, S., Miura, K., Ohtsuka, E. and Nishimura, S. (1987) Misreading of DNA templates containing 8-hydroxyguanosine at the site modified base and at adjacent residues. Nature 327, 77-79. https://doi.org/10.1038/327077a0
  15. Lee, S.-H. (2001) Recognition of DNA damage in mammals. J. Biochem. Mol. Biol. 34, 489-495.
  16. Lin, T.-S., Cheng, J.-C., Ishiguro, K. and Sartorelli, A. C. (1985) 8-Substitude guanosine and 2'-deoxyguanosine derivatives as potential inducers of the differentiation of friend erythroleukemia cells. J. Med. Chem. 28, 1194-1198. https://doi.org/10.1021/jm00147a012
  17. Oda, Y., Uesugi, S., Ikehara, M., Nishimura, S., Kawase, Y., Ishikawa, J. H., Inoue, H. and Ohtsuka, E. (1991) NMR studies of DNA containing 8-hydroxydeoxyguanosine. Nucleic Acids Res. 19, 1407-1412. https://doi.org/10.1093/nar/19.7.1407
  18. Rhee, Y. S., Valentine, M. R. and Termini, J. (1995) Oxidative base damage in RNA detected by reverse transcriptase. Nucleic Acids Res. 23, 3275-3282. https://doi.org/10.1093/nar/23.16.3275
  19. Schneider, J. E. Jr., Phillips, J. R., Pye, Q., Maidt, M. L., Price, S. and Floyd, R. A. (1993) Methylene blue and rose bangal photo inactivation of RNA bacteriophage: comparative studies of 8-oxoguanine formation in isolated RNA. Arch. Biochem. Biophys. 301, 91-97. https://doi.org/10.1006/abbi.1993.1119
  20. Shibutani, S., Bodepudi, V., Johnson, F. and Grollman, A. P. (1993) Translational synthesis on DNA templates containing 8- oxo-7,8-dihydroadenosine. Biochemistry 32, 4615-4621. https://doi.org/10.1021/bi00068a019
  21. Shibutani, S., Takesita, M. and Grollman, A. P. (1991) Insertion of specific bases during DNA synthesis past the oxidationdamaged base 8-oxodG. Nature 349, 431-434. https://doi.org/10.1038/349431a0
  22. Tudek, B. (2003) Imidazole ring-opend DNA purines and their biological significance. J. Biochem. Mol. Biol. 33, 126-132.
  23. Wang, L. and Keiderling, T. A. (1992) Vibrational circular dichroism studies of the A-to-B conformational translation in DNA. Biochemistry 31, 10265-10271. https://doi.org/10.1021/bi00157a013
  24. Yanagawa, H., Ogawa, Y. and Ueno, M. (1992) Redox ribonucleosides: Isolation and characterization of 5- hydroxyuridine, 8-hydroxyguanosine, and 8-hydroxyadenosine from Torula yeast RNA. J. Biol. Chem. 267, 13320-13326.

Cited by

  1. Quantification of RNA damage by reverse transcription polymerase chain reactions vol.357, pp.1, 2006, https://doi.org/10.1016/j.ab.2006.06.025
  2. Synthesis and base pairing properties of DNA-RNA heteroduplex containing 5-hydroxyuridine vol.42, pp.6, 2009, https://doi.org/10.5483/BMBRep.2009.42.6.373
  3. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA—a study of duplex, hairpins and the aptamer for preQ1as models 2016, https://doi.org/10.1093/nar/gkw885
  4. Base Pairing and Miscoding Properties of 1,N6-Ethenoadenine- and 3,N4-Ethenocytosine-Containing RNA Oligonucleotides vol.52, pp.11, 2013, https://doi.org/10.1021/bi400116y
  5. The effect of RNA base lesions on mRNA translation vol.43, pp.9, 2015, https://doi.org/10.1093/nar/gkv377
  6. Synthesis of the Oligoribonucleotides Incorporating 8-Oxo-Guanosine and Evaluation of their Base Pairing Properties vol.32, pp.3, 2013, https://doi.org/10.1080/15257770.2013.767461
  7. 8-Oxoguanosine Switches Modulate the Activity of Alkylated siRNAs by Controlling Steric Effects in the Major versus Minor Grooves vol.133, pp.16, 2011, https://doi.org/10.1021/ja2003878