Molecular beacon probes of photodamage in thymine and uracil oligonucleotides

Photochemistry and Photobiology

Volumn 81, Issue 2, 2005, Pages 467-473

  Yarasi, Soujanya ^a   McConachie, Cheryl ^a   Loppnow, Glen R ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM CHLORIDE; OLIGONUCLEOTIDE; PYRIMIDINE DIMER; THYMINE; URACIL;

ARTICLE; CHEMISTRY; GENETIC PROCEDURES; KINETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID PROBE; RADIATION EXPOSURE; SENSITIVITY AND SPECIFICITY; SPECTROFLUOROMETRY; TEMPERATURE; TIME; ULTRAVIOLET RADIATION;

KINETICS; MAGNESIUM CHLORIDE; MOLECULAR PROBE TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID PROBES; OLIGONUCLEOTIDES; PYRIMIDINE DIMERS; SENSITIVITY AND SPECIFICITY; SPECTROMETRY, FLUORESCENCE; TEMPERATURE; THYMINE; TIME FACTORS; ULTRAVIOLET RAYS; URACIL;

EID: 17444429234     PISSN: 00318655     EISSN: None     Source Type: Journal    
DOI: 10.1562/2004-09-02-RA-301.1     Document Type: Article

References (36)

1. Ruzsicska, B. P. and D. G. E. Lemaire (1995) DNA photochemistry. In CRC Handbook of Organic Photochemistry and Photobiology (Edited by W. H. Hoispool and P.-S. Song), pp. 1289-1317. CRC Press, New York.
2. Coohill, T. P., M. J. Peak and J. G. Peak (1987) The effects of the ultraviolet wavelengths of radiation present in sunlight on human cells in vitro. Photochem. Photobiol. 46, 1043-1050.
3. Cicerone, R. J. (1987) Changes in stratospheric ozone. Science 237, 35-42.
4. 32P-Postlabeling detection of radiation-induced DNA damage: identification and estimation of thymine glycols and phosphoglycolate termini. Biochemistry 30, 1091-1097.
5. Haab, B. B. and R. A. Mathies (1995) Single molecule fluorescence burst detection of DNA fragments separated by capillary electrophoresis. Anal. Chem. 67, 3253-3260.
6. Le, X. C., J. Z. Xing, J. Lee, S. A. Leadom and M. Weinfeld (1998) Inducible repair of thymine glycol detected by an ultrasensitive assay for DNA damage. Science 280, 1066-1069.
7. Wang, J., G. Rivas, M. Ozsoz, H. G. Douglas, X. Cai and C. Parrado (1997) Microfabricated electrochemical sensor for the detection of radiation-induced DNA damage. Anal. Chem. 69, 1457-1460.
8. Kaur, H. and B. Halliwell (1996) Measurement of oxidized and methylated DNA bases by HPLC with electrochemical detection. Biochem. J. 318, 21-23.
9. Dizdaroglu, M. (1994) Chemical determination of oxidative DNA damage by gas chromatography-mass spectrometry. Methods Enzymol. 234, 3-16.
10. Douki, T., M. Court, S. Sauvaigo, F. Odin and J. Cadet (2000) Formation of the main UV-induced thymine dimeric lesions within isolated and cellular DNA as measured by high performance liquid chromatography-tandem mass spectrometry. J. Biol. Chem. 275, 11678-11685.
11. Douki, T. and J. Cadet (2001) Individual determination of the yield of the main UV-induced dimeric pyrimidine photoproducts in DNA suggests a high mutagenicity of CC photolesions. Biochemistry 40, 2495-2501.
12. Ravanat, J.-L., T. Douki and J. Cadet (2001) Direct and indirect effects of UV radiation on DNA and its components. J. Photochem. Photobiol. B: Biol. 63, 88-102.
13. Kumar, A., M. B. Tyagi and P. N. Jha (2004) Evidences showing ultraviolet-B radiation-induced damage of DNA in cyanobacteria and its detection by PCR assay. Biochem. Biophys. Res. Commun. 318, 1025-1030.
14. Ramanathan, K., R. K. Gary, A. Apostol and K. R. Rogers (2003) A fluorescence based assay for DNA damage induced by radiation, chemical mutagens and enzymes. Curr. Appl. Phys. 3, 99-106.
15. Cosa, G., A. L. Vinette, J. R. N. McLean and J. C. Scaiano (2002) DNA damage detection technique applying time-resolved fluorescence measurements. Anal. Chem. 74, 6163-6169.
16. Tyagi, S. and F. R. Kramer (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303-308.
17. Bonnet, G., S. Tyagi, A. Libchaber and F. R. Kramer (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA 96, 6171-6176.
18. Yang, J.-H., J.-P. Lai, S. D. Douglas, D. Metzger, X.-H. Zhu and W.-Z. Ho (2002) Real-time RT-PCR for quantitation of hepatitis C virus RNA. J. Virot. Methods 102, 119-128.
19. Lai, J.-P., S. D. Douglas, F. Shaheen, D. E. Pleasure and W.-Z. Ho (2002) Quantification of substance P mRNA in human immune cells by real-time reverse transcriptase PCR assay. Clin. Diagn. Lab. Immunol. 9, 138-143.
20. Leone, G., H. van Schijndel, B. van Gemen, F. R. Kramer and C. D. Shoen (1998) Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res. 26, 2150-2155.
21. Matsuo, T. (1998) In situ visualization of messenger RNA for basic fibroblast growth factor in living cells. Biochim. Blophys. Acta 1379, 178-184.
22. Sokol, D. L., X. Zhang, P. Lu and A. M. Gewirtz (1998) Real time detection of DNA-RNA hybridization in living cells. Proc. Natl. Acad. Sci. USA 95, 11538-11543.
23. Kundu, L. M., L. T. Burgdorf, O. Kleiner, A. Batschauer and T. Carell (2002) Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity. ChemBioChem 3, 1053-1060.
24. Warshaw, M. M. and I. Tinoco (1966) Optical properties of sixteen dinucleoside phosphates. J. Mol. Biol. 20, 29-38.
25. Warshaw, M. M. and I. Tinoco (1965) Absorption and optical rotatory dispersion of sixteen dinucleoside phosphates. J. Mol. Biol. 13, 54-64.
26. Mitchell, D. L. (1995) DNA damage and repair. In CRC Handbook of Organic Photochemistry and Photobiology (Edited by W. H. Horspool and P.-S. Song), pp. 1326-1331. CRC Press, New York.
27. Helleiner, C. W., M. N. Pearson and H. E. Johns (1963) The ultraviolet photochemistry of deoxyuridylyl (3′→5′) deoxyuridine. Biochemistry 50, 761-767.
28. Brown, I. H., K. B. Freeman and H. E. Johns (1966) Photochemistry of uridylyl-(3′→5′)-uridine. J. Mol. Biol. 15, 640-662.
29. Johns, H. E., S. A. Rapaport and M. Delbrück (1962) Photochemistry of thymine dimers. J. Mol. Biol. 4, 104-114.
30. Johns, H. E., M. L. Pearson, J. C. LeBlanc and C. W. Helleiner (1964) The ultraviolet photochemistry of thymidylyl-(3′→5′)-thymidine. J. Mol. Biol. 9, 503-524.
31. De Bont, R. and N. van Larebeke (2004) Endogenous DNA damage in humans: a review of quantitative data. Mutagenesis 19, 169-185.
32. Taylor, J.-S. (1994) Unraveling the molecular pathway from sunlight to skin cancer. Acc. Chem. Res. 27, 76-82.
33. Cantor, C. R., M. M. Warshaw and H. Shapiro (1970) Oligonucleotide interactions III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9, 1059-1077.
34. Warshaw, M. M. and C. R. Cantor (1970) Oligonucleotide interactions IV. Conformational differences between deoxy-and ribodinucleoside phosphates. Bioploymers 9, 1079-1103.
35. Lipsett, M. N. (1960) Evidence for helical structure in polyuridylic acid. Proc. Natl. Acad. Sci. USA 46, 445-446.
36. n tract bending and its biological implications. Proc. Natl. Acad. Sci. USA 88, 9072-9076.