UV-Induced Nucleic Acid-Protein Cross-Linking: Manual on Planning of Irradiation Experiments and Calculation of Absorbed Dose and Quantum Yield

Photochemistry and Photobiology

Volumn 67, Issue 3, 1998, Pages 269-275

  Dobrov, Eugene N ^a   Nikogosyan, David N ^b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0012709945     PISSN: 00318655     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1751-1097.1998.tb05198.x     Document Type: Article

References (49)

1. Alexander, P. and H. Moroson (1962) Cross-linking of deoxyribonucleic acid to protein following ultraviolet irradiation of different cells. Nature 194, 882-883.
2. Schoemaker, H. J. P. and P. R. Schimmel (1974) Photoinduced joining of a transfer RNA with its cognate aminoacyl-transfer RNA synthetase. J. Mol. Biol. 84, 503-513.
3. Budzyk, G. P., S. S. M. Lam, H. J. P. Schoemaker and P. R. Schimmel (1975) Two photo-cross-linked complexes of isoleucine specific transfer ribonucleic acid with aminoacyl transfer ribonucleic acid synthetases. J. Biol. Chem. 250, 4433-4439.
4. Schoemaker, H. J. P., G. P. Budzyk, R. Giege and P. R. Schimmel (1975) Three photo-cross-linked complexes of yeast phenylalanine specific transfer ribonucleic acid with aminoacyl transfer ribonucleic acid synthetases. J. Biol. Chem. 250, 4440-4444.
5. Schimmel, P. R. and G. P. Budzyk (1977) Photo-crosslinking of protein-nucleic acid complexes. Methods Enzymol. 46, 168-180.
6. Möller, K., C. Zwieb and R. Brimacombe (1978) Identification of the oligonucleotide and oligopeptide involved in an RNA-protein crosslink induced by ultraviolet irradiation of Escherichia coli 30 S ribosomal subunits. J. Mol. Biol. 126, 489-506.
7. Met in complexes with Escherichia coli methionine : tRNA ligase. Biochemistry 18, 637-647.
8. Ehresmann, B., C. Backendorf, C. Ehresmann, R. Millon and J. P. Ebel (1980) Effect of ultraviolet irradiation on 30S ribosomal subunits. Identification of the RNA region cross-linked to protein S7. Eur. J. Biochem. 104, 255-262.
9. Hajnsdorf, E., Y. L. Dubreuil, R. Bezerra, A. Favre and A. Expert-Besancon (1987) RNA-protein crosslinks introduced into E. coli ribosomes by use of the intrinsic probe 4-thiouridine. Photochem. Photobiol. 45, 445-451.
10. Budowsky, E. I. and G. G. Abdurashidova (1989) Polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins. In Progress in Nucleic Acid Research and Molecular Biology, Vol. 37 (Edited by W. E. Cohn and K. Moldave), pp. 1-65. Academic Press, San Diego.
11. Timofeeva, E. K., S. V. Kust and E. N. Dobrov (1992) Estimation of the UV-induced RNA-protein cross-linking efficiency in the potato virus X particles. Mol. Genet. Mikrobiol. Virusol. 2, 6-8. [In Russian]
12. Dobrov, E. N., Z. Kh. Arbieva, I. S. Khromov and S. V. Kust (1986) RNA-protein crosslink and RNA chain break formation on UV irradiation of tobacco mosaic virus. Photochem. Photobiol. 43, 493-498.
13. Harrison, C. A., D. H. Turner and D. C. Hinkle (1982) Laser crosslinking of E. coli RNA polymerase and T7 DNA. Nucleic Acids Res. 10, 2399-2414.
14. Budowsky, E. I., M. S. Axentyeva, G. G. Abdurashidova, N. A. Simukova and L. B. Rubin (1986) Induction of polynucleotide-protein cross-linkages by ultraviolet irradiation. Peculiarities of the high-intensity laser pulse irradiation. Eur. J. Biochem. 159, 95-101.
15. Hockensmith, J. W., W. L. Kubasek, W. R. Vorachek and P. H. von Hippel (1986) Laser cross-linking of nucleic acids to proteins. J. Biol. Chem. 261, 3512-3518.
16. Arbieva, Z. Kh., P. V. Kalmykov, E. N. Dobrov, R. O. Esenaliev, P. G. Morev and D. N. Nikogosyan (1987) Formation of cross-links with protein and polynucleotide chain breaks in TMV RNA in situ under high-intensity picosecond laser UV irradiation. Dokl. Akad. Nauk SSSR 292, 227-230. [In Russian]
17. Angelov, D., V. Yu. Stefanovsky, S. I. Dimitrov, V. R. Russanova, E. Keskinova and I. G. Pashev (1988) Protein-DNA crosslinking in reconstituted nucleohistone, nuclei and whole cells by picosecond UV laser irradiation. Nucleic Acids Res. 16, 4528-4538.
18. Stefanovsky, V. Y., S. I. Dimitrov, V. R. Russanova, D. Angelov and I. G. Pashev (1989) Laser-induced crosslinking of histones to DNA in chromatin: implications in studying histone-DNA interactions. Nucleic Acids Res. 17, 10069-10081.
19. Dobrov, E. N., Z. Kh. Arbieva, E. K. Timofeeva, R. O. Esenaliev, A. A. Oraevsky and D. N. Nikogosyan (1989) UV laser induced RNA-protein cross-links and RNA chain breaks in tobacco mosaic virus in situ. Photochem. Photobiol. 49, 595-599.
20. Hockensmith, J. W., W. L. Kubasek, W. R. Vorachek, E. M. Evertsz and P. H. von Hippel (1991) Laser cross-linking of protein-nucleic acid complexes. Methods Enzymol. 208, 211-236.
21. Hockensmith, J. W., W. L. Kubasek, W. R. Vorachek and P. H. von Hippel (1993) Laser cross-linking of proteins to nucleic acids. I. Examining physical parameters of protein-nucleic acid complexes. J. Biol. Chem. 268, 15712-15720.
22. Hockensmith, J. W., W. L. Kubasek, E. M. Evertsz, L. D. Mesner and P. H. von Hippel (1993) Laser cross-linking of proteins to nucleic acids. II. Interactions of the bacteriophage T4 DNA replication polymerase accessory proteins complex with DNA. J. Biol. Chem. 268, 15721-15730.
23. Barritault, D., R. H. Buckingham, A. Favre and G. Thomas (1981) Photocrosslinking of thiolated aminoacyl-tRNA to ribosomal RNA and proteins. Biochimie 63, 587-593.
24. Phe to protein S10 in the ribosomal P site. Eur. J. Biochem. 128, 427-433.
25. Tanner, N. K., M. M. Hanna and J. Abelson (1988) Binding interactions between yeast tRNA ligase and a precursor transfer RNA containing two photoreactive uridine analogues. Biochemistry 27, 8852-8861.
26. Hajnsdorf, E., A. Favre and A. Expert-Besancon (1989) New RNA-protein crosslinks in domains 1 and 2 of E. coli 30S ribosomal subunits obtained by means of intrinsic photoaffinity probe. Nucleic Acids Res. 17, 1475-1485.
27. Dontsova, O., A. Kopylov and R. Brimacombe (1991) The location of mRNA in the ribosomal 30S initiation complex; site-directed cross-linking of mRNA analogues carrying several photo-reactive labels simultaneously on either side of the AUG start codon. EMBO J. 10, 2613-2620.
28. Dokudovskaya, S., O. Dontsova, S. Bogdanova, A. Bogdanov and R. Brimacombe (1993) mRNA-ribosome interactions. Biotechnol. Appl. Biochem. 18, 149-155.
29. Dontsova, O., V. Tishkov, S. Dokudovskaya, A. Bogdanov, T. Doring, J. Rinke-Appel, S. Tamm, B. Gruer and R. Brimacombe (1994) Stem-loop IY of 5S ribosomal RNA lies close to the peptidile transferase center. Proc. Natl. Acad. Sci. USA 91, 4125-4129.
30. Nolan-Sorden, N. L., K. Lesiak, B. Bayard, P. F. Torrance and R. S. Silverman (1990) Photochemical crosslinking in oligonucleotide-protein complexes between a Br-substituted 2-5A analogue and 2-5A-dependent RNase by UV-lamp or laser. Anal. Biochem. 184, 298-304.
31. Willis, M. C., B. J. Hicke, O. C. Uhlenbeck, T. C. Cech and T. H. Koch (1993) Photocrosslinking of 5-iodouracil-substituted RNA and RNA to proteins. Science 262, 1255-1257.
32. Willis, M. C., K. A. Le Cuyer, K. M. Meisenheimer and O. C. Uhlenbeck (1994) An RNA-protein contact determined by 5-bromouridine substitution, photocrosslinking and sequencing. Nucleic Acids Res. 22, 4947-4952.
33. Wang, Y. and K. Adzuma (1996) Differential proximity probing of two DNA binding sites in the E. coli recA protein using photo-cross-linking methods. Biochemistry 35, 3563-3571.
34. Kubasek, W. L., D. Spann and J. W. Hockensmith (1993) Laser cross-linking of proteins to nucleic acids: photodegradation and alternative photoproducts of the bacteriophage T4 gene 32 protein. Photochem. Photobiol. 58, 1-10.
35. Nikogosyan, D. N. (1990) Two-quantum UV photochemistry of nucleic acids: comparison with conventional low-intensity UV photochemistry and radiation chemistry. Int. J. Radiat. Biol. 57, 233-299.
36. Borodavkin, A. V., E. I. Budowsky, Y. V. Morozov, F. A. Savin and N. A. Simukova (1977) Electronic Structure, UV Absorption Spectra and Reactivity of Nucleic Acids Components. VINITI, Moscow. [In Russian]
37. Reuther, A., D. N. Nikogosyan and A. Laubereau (1996) Primary photochemical processes in thymine in concentrated aqueous solution studied by femtosecond UV spectroscopy. J. Phys. Chem. 100, 5570-5577.
38. Salet, C. and R. Bensasson (1975) Studies on thymine and uracil triplet excited state in acetonitrile and water. Photochem. Photobiol. 22, 231-235.
39. Salet, C., R. Bensasson and R. S. Becker (1979) Triplet excited states of pyrimidine nucleosides and nucleotides. Photochem. Photobiol. 30, 325-329.
40. Fielden, E. M. and E. J. Hart (1967) Activation energy of the hydrated electron + water reaction and the ultraviolet absorption spectrum of the hydrated electron. Trans. Faraday Soc. 63, 2975-2982.
41. .. J. Phys. Chem. 73, 1029-1038.
42. Khoroshilova, E. V., Yu. A. Repeyev and D. N. Nikogosyan (1990) UV photolysis of aromatic amino acids and related dipeptides and tripeptides. J. Photochem. Photobiol. B Biol. 7, 159-172.
43. Nikogosyan, D. N., D. Angelov, B. Soep and L. Lindqvist (1996) Direct measurement of excited state lifetime in the homologous sequence adenine, adenosine, adenosine-5′-monophosphate and in calf thymus DNA. Chem. Phys. Lett. 252, 322-326.
44. Morev, P. G., A. A. Oraevsky and D. N. Nikogosyan (1988) Photophysics of highly excited states of nucleic acid constituents. Khim. Fiz. 7. 485-491. [English translation: Sov. J. Chem. Phys. 7, 778-790.]
45. Morev, P. G., A. A. Oraevsky and D. N. Nikogosyan (1988) Photophysics of highly excited states of nucleic acid constituents. Khim. Fiz. 7. 485-491. [English translation: Sov. J. Chem. Phys. 7, 778-790.]
46. Oraevsky, A. A., A. V. Sharkov and D. N. Nikogosyan (1981) Picosecond study of electronically excited singlet states of nucleic acid components. Chem. Phys. Lett. 83, 276-280.
47. Wang, S. Y. (1962) Analysis of the rate of the ultraviolet irradiation and reconstitution reactions of 1,3-dimethyluracil and uridine. Photochem. Photobiol. 1, 135-145.
48. Rahn, R. O. and H. G. Selin (1982) Action spectra for the photolysis of 5-iododeoxyuridine in DNA and related model systems: evidence for short-range energy transfer. Photochem. Photobiol. 35, 459-465.
49. Favre, A. (1993) 4-Thiouridine as an intrinsic photoaffinity probe of nucleic acid structure and interactions. In Biorganic Photochemistry, Vol. 1 (Edited by H. Morrison), pp. 380-425. John Wiley & Sons, New York.