Azidoethidium derivatives as photoaffinity labels: Study of the photochemistry of the monoazidoethidium derivatives in water

Journal of Photochemistry and Photobiology B: Biology

Volumn 37, Issue 1-2, 1997, Pages 40-51

  Gritsan, N P ^a   Koshkin, A A ^b   Denisov, A Yu ^b   Markushin, Yu Ya ^b   Cherepanova, E V ^a   Lebedev, A V ^c  

^a NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^b INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

^c Genta Inc   (United States)

Author keywords

Monoazidoethidium derivatives; Oligonucleotide derivatives; Photolysis; Quantum chemical calculations; Quantum yield

Indexed keywords

AZIDE; DISSOLVED OXYGEN; ETHIDIUM; WATER;

ARTICLE; ENTHALPY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IRRADIATION; PHOTOAFFINITY LABELING; PHOTOCHEMISTRY; PHOTODEGRADATION; PHOTOLYSIS; PRIORITY JOURNAL; QUANTUM CHEMISTRY; THERMODYNAMICS;

EID: 0031027326     PISSN: 10111344     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1011-1344(96)07341-1     Document Type: Article

References (58)

1. [1] T. Le Doan, L. Perrousult, D. Praseuth, N. Habboub, J. Decout, N. Thuong and C. Helene, Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[a]-thymidine covalently linked to an azidoproflavine derivative, Nucleic Acids Res., 15 (1987) 7749-7760.
2. [2] C. Helene, T. Montenay-Garestier, T. Saison, M. Tacasugi, J.J. Toulme, U. Asseline, G. Lancelot, J.C. Maurizot, F. Toulme and N.T. Thong, Oligonucleotides covalently linked to intercalating agents: a new class of gene regulatory substances, Biochimie, 67 (1985) 777-788.
3. [3] D. Praseuth, T. Le Doan, M. Chassignal, J. Decout, N. Habboub, N. Thuong and C. Helene, Sequence-targeted photosensitized reactions in nucleic acids by oligodeoxynucleotides and oligodeoxynucleotides covalently linked to proflavine, Biochemistry, 27 (1988) 3031-3038.
4. [4] N.T. Thuong, U. Asseline, V. Roig, M. Takasugi and C. Helene, Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[a]-thymidilate covalently linked to intercalating agents: differential binding to ribo- and deoxyribonucleotides and stability towards nuclease digestion, Proc. Natl. Acad. Sci. USA, 84 (1987) 5129-5133.
5. [5] D.R. Tabatadse, M.I. Dobrikov, A.S. Levina, T.A. Prikhodko, J.V. Shishkin and V.F. Zarytova, Effective sequence-specific photomodification of nucleic acids by oligonucleotide derivatives bearing aromatic azido groups, Nucleic Acids Res. Symp. Ser., 24 (1991) 247.
6. [6] A.S. Levina, M.V. Berezovskii, A.G. Venjaminova, M.I. Dobrikov, M.N. Repkova and V.F. Zarytova, Photomodification of RNA and DNA fragments by oligonucleotide reagents bearing arilazide groups, Biochimie, 75 (1993) 25-27.
7. [7] V.F. Zarytova, I.V. Kutyavin, A.S. Levina, S.V. Mamaev and V.P. Maltsev, Photomodification of nucleic acids with N-(2-hydroxyethyl)phenazinium oligonucleotide derivatives, Dokl. Akad. Nauk SSSR, 302 (1988) 102-104.
8. [8] V.F. Zarytova, I.V. Kutyavin, T.V. Maltseva, S.V. Mamaev and V.P. Maltsev, Photomodification of nucleic acids with N-(2-hydroxyethyl)phenazinium oligonucleotide derivatives, Bioorg. Khim., 16(1990) 595-602.
9. [9] Y. Sci and J.E. Hearst, Wavelength dependence for the photoreactions of DNA-psoralene monoadducts, Biochemistry, 27 (1987) 3786-3798.
10. [10] L.Z. Benimetskaya, N.V. Bulychev, A.L. Kozionov, A.V. Lebedev, Yu.E. Nesterikhin, S.Yu. Novozhilov, S.G. Rautian and M.I. Stockman, Two-quantum selective laser scission of polyadenylic acid in the complementary complex with a dansyl derivative of oligothymidylate, FEBS Lett., 163 (1983) 144-149.
11. [11] D.G Knorre and V. V. Vlassov, Affinity Modification of Biopolymers, CRC Press, Boca Raton, FL, 1989.
12. [12] E. Wickstrom (ed.), Prospects for Antisense Nucleic Acid Therapy of Cancer and AIDS, Wiley-Liss, New York, 1991.
13. [13] J.S. Cohen (ed.), Oligonucleotides: Antisense Inhibitors of Gene Expression, Macmillan, London, 1989.
14. [14] A.A. Koshkin, A.V. Lebedev, A.S. Ryte and V.V. Vlassov, Ethidium oligonucleotide derivatives. Stability against cellular nuclear hydrolysis and photochemical modification of cellular proteins in the living cells, Nucleosides Nucleotides, 10 (1991) 541-542.
15. [15] L.Z. Benimetskaya, N.V. Bulychev, A.L. Kozionov, A.V. Lebedev, S.Yu. Novozhilov and M.I. Stockman, Site-specific laser modification (cleavage) of oligodeoxynucleotides, Biopolymers, 28 (1991) 1129-1147.
16. [16] A.A. Koshkin, T.M. Ivanova, N.V. Bulychev, M.I. Dobrykov and A. V. Lebedev, Photoreactive ethidium and azidoethidium dyes. Synthesis, properties, and covalent attachment to oligonucleotides, Bioorg. Khim., 19 (1993) 570-581.
17. [17] A.A. Koshkin, K.Yu. Kropachev, S.V. Mamaev, N.V. Bulychev, S.G. Lokhov, V.V. Vlasov and A.V. Lebedev, Ethidium and azidoethidium oligonucleotide derivatives. Synthesis, complementary complex and sequence specific photomodification of the single stranded and double stranded oligo- and polynucleotides, J. Mol. Recognit., 7 (1994) 177-188.
18. [18] M.J. Waring, Complex formation between ethidium bromide and nucleic acids, J. Mol. Biol., 13 (1965) 269-282.
19. [19] M.J. Waring, Structural requirements for binding of ethidium to nucleic acids, Biochim. Biophys. Acta, 114 (1966) 234-244.
20. [20] J.W. Nelson and I. Tinoco, Interaction of ethidium ion into DNA and RNA oligonucleotides, Biopolymers, 23 (1984) 213-233.
21. [21] D.C. Helfgott and N.R. Kallenback, Increased binding of ethidium bromide to polynucleotide duplexes containing mismatched bases, Nucleic Acids Res., (1979) 1011-1017.
22. [22] P.V. Searia and H. Shafer, Binding of ethidium bromide to a DNA triplex helix, J. Biol. Chem., 266 (1991) 5417-5423.
23. [23] J.L. Mergny, J.S. Sun, M. Rongee, T. Monthenay-Garestie and C. Helene, Interaction of ethidium bromide into a triple-stranded oligonucleotide, Nucleic Acids Res., 19 (1991) 1521-1526.
24. [24] J.S. Sun, R. Lavery, J. Chomilier, K. Zakrzewka, T. Monthenay-Garestier and C. Helene, Theoretical study of ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions, J. Biomol. Struct. Dyn., 9 (1991) 425-436.
25. [25] D. Sun, R.D. Sheardy and J.B. Chaires, Unusual binding of ethidium to a deoxyoligonucleotide containing a B-Z junction, Biochemistry, 30 (1991) 8722-8726.
26. [26] H. Bayley and J.V. Staros, Photoaffinity labelling and related techniques, in E.F.V. Scriven (ed.), Azides and Nitrenes. Reactivity and Utility, Academic Press, New York, 1984, pp. 433-490.
27. [27] G.B. Schuster and M.S. Platz, Photochemistry of phenyl azide, Adv. Photochem., 17 (1992) 69-143.
28. [28] N.P. Gritsan and E.A. Pritchina, Mechanism of photolysis of aromatic azides, Russ. Chem. Rev., 61 (1992) 910-939.
29. [29] T. Morita and K.L. Yielding, Induction of respiratory deficient mutants in Saccharomyces cerevisiae by mono- and diazido analog of ethidium, Mutat. Res., 56 (1977) 21-23.
30. [30] P. Wooley and S. Dorhmann, Cross-linking of double-helical nucleic acids with a photoreactive analogue of ethidium, Biochemistry, 22 (1983) 3226-3231.
31. [31] J.M. Hardwick, R.S. von Sprecken, K.L. Yielding and L.W. Yielding, Ethidium binding sites on plasmid DNA determined by photoaffinity labelling, J. Biol. Chem., 259 (1984) 11090-11097.
32. [32] R. Hayes, J.M. Schofield, R.K. Smalley and D.I.C. Scopes, Photolytic ring-expansions of 6-azidoquinolines and 6-azidodiazines: some unexpected azepine ring-opening reactions, Tetrahedron, 46 (1990) 2089-2096.
33. [33] P.E. Nielsen and O. Buchardt, Aryl azides as photoaffinity labels. A photochemical study of some 4-substituted aryl azides, Photochem. Photobiol., 35 (1982) 317-323.
34. 2O solution, Org. Magn. Reson., 14 (1980) 371-373.
35. [35] H.O. Kalinowski, S. Berger and S. Braun, Carbon-13 NMR Spectroscopy, Wiley, Chichester, 1988.
36. [36] H. Gunther, NMR Spectroscopy, Wiley, Chichester, 1980.
37. [37] S.A. Carlson and D.M. Hercules, Studies on some intermediates and products on the photoreduction of 9,10-anthraquinone, Photochem. Photobiol., 17 (1973) 123-131.
38. [38] N.P. Gritsan and N.M. Bazhin, Mechanism of photolysis of 2-amino-1,4-naphthoquinone derivatives, Izv. Akad. Nauk SSSR, Ser. Khim., 1 (1981) 280-285.
39. [39] M.J.S. Dewar, E.G. Zoebich, E.F. Healy and J.J.P. Stewart, AM1: a new general purpose quantum mechanical molecular model, J. Am. Chem. Soc., 107 (1985) 3902-3909.
40. [40] A.A. Bliznyuk and A.A. Voityuk, Complex of programs for calculations of electronic structure, physico-chemical properties and reactivity of molecular systems by semi-empirical method MNDO, MNDOC and AM1, Zh. Strukt. Khim., 27 (4) (1986) 190-192.
41. [41] A.A. Voityuk and A.A. Bliznyuk, Quantum chemical study of mechanisms of amides hydrolysis in gas phase and aqueous solution, Izv. Akad. Nauk SSSR. Ser. Khim., 8 (1989) 1785-1792.
42. [42] J. Del Bene and H.H. Jaffe, Use of CNDO method in Spectroscopy. I. Benzene, pyridine, and the diazines, J. Chem. Phys., 48 (1968) 1807-1813.
43. [43] A.R. Katriszky (ed.), Comprehensive Heterocyclic Chemistry, Vol. 2, Pergamon, Oxford, 1984, p. 26.
44. [44] M.S. Platz, Physical and spectroscopic methods, in E.F.V. Scriven (ed.), Azides and Nitrenes. Reactivity and Utility, Academic Press, New York, 1984, pp. 359-393.
45. [45] P.A.S. Smith, Aryl and heteroaryl azides and nitrenes, in E.F.V. Scriven (ed.), Azides and Nitrenes. Reactivity and Utility, Academic Press, New York, 1984, pp. 95-204.
46. [46] E. Wasserman, Electron spin resonance of nitrenes, Prog. Phys. Org. Chem., 8 (1971) 319-336.
47. [47] E. Leyva, M.S. Platz, G. Persy and J. Wirz, Photochemistry of phenyl azide: the role singlet and triplet phenylnitrene as transient intermediates, J. Am. Chem. Soc., 108 (1986) 3783-3790.
48. [48] Y.-Z. Li, J.P. Kirby, M.W. George, M. Poliakoff and G.B. Schuster, 1,2-didehydroazepines from the photolysis of substituted aryl azides: analysis of their chemical and physical properties by time-resolved spectroscopic methods, J. Am. Chem. Soc., 110 (1988) 8092-8098.
49. [49] A.K. Schrock and G.B. Schuster, Photochemistry of naphthyl and pyrenyl azides: chemical properties of the transient intermediates by laser spectroscopy, J. Am. Chem. Soc., 106 (1984) 5234-5240.
50. [50] N.P. Gritsan and E.A. Pritchina, Mechanism of photochemical transformation of aromatic azides, Journal of Information Recording Materials, 17 (1989) 391-404.
51. [51] S.-J. Kim, T.P. Hamilton and H.F. Schaefer, Phenylnitrene: energetics, vibrational frequencies, and molecular structure, J. Am. Chem. Soc., 114 (1992) 5349-5355.
52. [52] D.A. Hrovat, E.E. Waali and W.T. Borden, Ab initio calculations of the singlet-triplet energy difference in phenylnitrene, J. Am. Chem. Soc., 114 (1992) 8698-8699.
53. [53] S.C. Hixon, W.E. White, Jr. and K.L. Yielding, Selective covalent binding analog to mitochondrial DNA with production of petite mutants in yeast by photoaffinity labelling, J. Mol. Biol., 92 (1975) 319-329.
54. [54] D.E. Graves, L.A.W. Yielding, C.L. Watkins and K.L. Yielding, Synthesis, separation and characterization of the mono-and diazide analogs of ethidium bromide, Biochim. Biophys. Acta, 479 (1977) 98-104.
55. [55] V.A. Smirnov, S.B. Brichkin, M.V. Alfimov, L.I. Tyltina and L.F. Avramenko, Photolysis of azides. Photodissociation of para-azido-malachite green, Khim. Vys. Energ., 13 (1979) 156-160.
56. [56] V.Ya. Pochinok, V.V. Smimov, S.B. Brichkin, L.F. Avramenko, L.I. Tyltina, T.F. Grigorenko, I.A. Ol'shevskaya and V.I. Skopenko, Photochemistry of azide derivatives of dyes in solution, Ukr. Khim. ZA., 50 (1984) 296-301.
57. [57] K.A. Schnapp, R. Roe, E. Leyva, N. Soudararajan and M. Platz, Exploratory photochemistry of fluorinated aryl azides. Implications for the design of photoaffinity labeling reagents, Bioconjugate Chem., 4 (1993) 172-177.
58. [58] K.A. Schnapp and M. Platz, A laser flash photolysis study of di-, triand tetrafluorinated phenylnitrenes; implications for photoaffinity labeling, Bioconjugate Chem., 4 (1993) 178-184.