A light-modulated sequence-specific DNA-binding peptide

Angewandte Chemie - International Edition

Volumn 39, Issue 17, 2000, Pages 3104-3107

  Caamaño, Ana M ^a   Vázquez, M Eugenio ^a   Martínez Costas, José ^a   Castedo, Luis ^a   Mascareñas, José L ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

Azo compounds; Circular dichroism; DNA recognition; Peptides

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; AUTORADIOGRAPHY; BINDING AFFINITY; BINDING SITE; CIS TRANS ISOMERISM; CONFORMATIONAL TRANSITION; CONSENSUS SEQUENCE; DNA BINDING; DNA SEQUENCE; GENE EXPRESSION; PROMOTER REGION; PROTEIN DNA INTERACTION;

EID: 0039599107     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/1521-3773(20000901)39:17<3104::AID-ANIE3104>3.0.CO;2-0     Document Type: Article

References (41)

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15. This conformational switching can be induced by a variety of signals, including ligands, such as hormones: G. Klock, U. Strahle, G. Schutz, Nature 1987, 329, 734-736; metal ions: D. R. Winge, L. T. Jensen, C. Srinivasan, Curr. Biol. 1998, 2, 216-221: heat: Ref. [2d] Chap. 4; or even redox changes: C. Abate, L. Patel, F. J. Rauscher, T. Curran, Science 1990, 249, 1157-1161.
16. One of the main goals of current molecular medicine is to find ways to turn particular genes on or off, at will. Several strategies based on small molecules have been developed. For reviews, see: a) T. Clakson, Curr. Opin. Chem. Biol. 1997, 1, 210-211; b) C. Denison, T. Kodadek, Chem. Biol. 1998, 5, R129-R145; c) D. M. Harvey, C. T. Caskey, Curr. Opin. Chem. Biol. 1998, 2, 512-518.
17. One of the main goals of current molecular medicine is to find ways to turn particular genes on or off, at will. Several strategies based on small molecules have been developed. For reviews, see: a) T. Clakson, Curr. Opin. Chem. Biol. 1997, 1, 210-211; b) C. Denison, T. Kodadek, Chem. Biol. 1998, 5, R129-R145; c) D. M. Harvey, C. T. Caskey, Curr. Opin. Chem. Biol. 1998, 2, 512-518.
18. One of the main goals of current molecular medicine is to find ways to turn particular genes on or off, at will. Several strategies based on small molecules have been developed. For reviews, see: a) T. Clakson, Curr. Opin. Chem. Biol. 1997, 1, 210-211; b) C. Denison, T. Kodadek, Chem. Biol. 1998, 5, R129-R145; c) D. M. Harvey, C. T. Caskey, Curr. Opin. Chem. Biol. 1998, 2, 512-518.
19. It has been reported that certain distilbazolium compounds behave as photoisomerizable DNA ligands, but their affinities and specifities are rather low: B. Juskowiak, M. Ohba, M. Sato, S. Takenaga, M. Takagi, H. Kondo, Bull. Chem. Soc. Jpn. 1999, 72, 265-277.
20. a) R. V. Talanian, C. J. McKnight, P. S. Kim, Science 1990, 249, 769-771;
21. b) R. V. Talanian, C. J. McKnight, R. Rutkowski, P. S. Kim, Biochemistry 1992, 31, 6871-6875.
22. The shape and size of the dimerizing link can considerably affect the DNA-binding characteristics of the bZIP mimetics: a) B. Cuenoud, A. Shepartz, Science 1993, 259, 510-513; b) B. Cuenoud, A. Shepartz, Proc. Natl. Acad. Sci. USA 1993, 90, 1154-1159; c) T. Morii, M. Shimomura, M. Morimoto, I. Saito, J. Am. Chem. Soc. 1993, 115, 1150-1151; d) M. Okagami, M. Ueno, K. Makino, M. Shimomura, T. Morii, Y. Sugiura, Biorg. Med Chem. 1995, 3, 777-784; e) T. Morii, Y. Saimei, M. Okagami, K. Makino, Y. Sugiura, J. Am. Chem. Soc. 1997, 119, 3649-3655; f) Y. Aizawa, Y. Sugiura, T. Morii, Biochemistry 1999, 38, 1626-1632.
23. The shape and size of the dimerizing link can considerably affect the DNA-binding characteristics of the bZIP mimetics: a) B. Cuenoud, A. Shepartz, Science 1993, 259, 510-513; b) B. Cuenoud, A. Shepartz, Proc. Natl. Acad. Sci. USA 1993, 90, 1154-1159; c) T. Morii, M. Shimomura, M. Morimoto, I. Saito, J. Am. Chem. Soc. 1993, 115, 1150-1151; d) M. Okagami, M. Ueno, K. Makino, M. Shimomura, T. Morii, Y. Sugiura, Biorg. Med Chem. 1995, 3, 777-784; e) T. Morii, Y. Saimei, M. Okagami, K. Makino, Y. Sugiura, J. Am. Chem. Soc. 1997, 119, 3649-3655; f) Y. Aizawa, Y. Sugiura, T. Morii, Biochemistry 1999, 38, 1626-1632.
24. The shape and size of the dimerizing link can considerably affect the DNA-binding characteristics of the bZIP mimetics: a) B. Cuenoud, A. Shepartz, Science 1993, 259, 510-513; b) B. Cuenoud, A. Shepartz, Proc. Natl. Acad. Sci. USA 1993, 90, 1154-1159; c) T. Morii, M. Shimomura, M. Morimoto, I. Saito, J. Am. Chem. Soc. 1993, 115, 1150-1151; d) M. Okagami, M. Ueno, K. Makino, M. Shimomura, T. Morii, Y. Sugiura, Biorg. Med Chem. 1995, 3, 777-784; e) T. Morii, Y. Saimei, M. Okagami, K. Makino, Y. Sugiura, J. Am. Chem. Soc. 1997, 119, 3649-3655; f) Y. Aizawa, Y. Sugiura, T. Morii, Biochemistry 1999, 38, 1626-1632.
25. The shape and size of the dimerizing link can considerably affect the DNA-binding characteristics of the bZIP mimetics: a) B. Cuenoud, A. Shepartz, Science 1993, 259, 510-513; b) B. Cuenoud, A. Shepartz, Proc. Natl. Acad. Sci. USA 1993, 90, 1154-1159; c) T. Morii, M. Shimomura, M. Morimoto, I. Saito, J. Am. Chem. Soc. 1993, 115, 1150-1151; d) M. Okagami, M. Ueno, K. Makino, M. Shimomura, T. Morii, Y. Sugiura, Biorg. Med Chem. 1995, 3, 777-784; e) T. Morii, Y. Saimei, M. Okagami, K. Makino, Y. Sugiura, J. Am. Chem. Soc. 1997, 119, 3649-3655; f) Y. Aizawa, Y. Sugiura, T. Morii, Biochemistry 1999, 38, 1626-1632.
26. The shape and size of the dimerizing link can considerably affect the DNA-binding characteristics of the bZIP mimetics: a) B. Cuenoud, A. Shepartz, Science 1993, 259, 510-513; b) B. Cuenoud, A. Shepartz, Proc. Natl. Acad. Sci. USA 1993, 90, 1154-1159; c) T. Morii, M. Shimomura, M. Morimoto, I. Saito, J. Am. Chem. Soc. 1993, 115, 1150-1151; d) M. Okagami, M. Ueno, K. Makino, M. Shimomura, T. Morii, Y. Sugiura, Biorg. Med Chem. 1995, 3, 777-784; e) T. Morii, Y. Saimei, M. Okagami, K. Makino, Y. Sugiura, J. Am. Chem. Soc. 1997, 119, 3649-3655; f) Y. Aizawa, Y. Sugiura, T. Morii, Biochemistry 1999, 38, 1626-1632.
27. The shape and size of the dimerizing link can considerably affect the DNA-binding characteristics of the bZIP mimetics: a) B. Cuenoud, A. Shepartz, Science 1993, 259, 510-513; b) B. Cuenoud, A. Shepartz, Proc. Natl. Acad. Sci. USA 1993, 90, 1154-1159; c) T. Morii, M. Shimomura, M. Morimoto, I. Saito, J. Am. Chem. Soc. 1993, 115, 1150-1151; d) M. Okagami, M. Ueno, K. Makino, M. Shimomura, T. Morii, Y. Sugiura, Biorg. Med Chem. 1995, 3, 777-784; e) T. Morii, Y. Saimei, M. Okagami, K. Makino, Y. Sugiura, J. Am. Chem. Soc. 1997, 119, 3649-3655; f) Y. Aizawa, Y. Sugiura, T. Morii, Biochemistry 1999, 38, 1626-1632.
28. The cis/trans photoisomerization of azobenzene derivatives is well documented: a) "Biological Applications of Photochemical Switches": 1. Willner, B. Willner in Bioorganic Photochemistry, Vol. 2 (Ed.: H. Morrison), Wiley, New York, 1993, pp. 1-110; b) I. Willner, S. Rubin, Angew. Chem. 1996, 108, 419-439; Angew. Chem. Int. Ed. Engl. 1996, 35, 367-385; c) H. Rau in Photochemistry and Photophysics, Vol II (Ed.: J. F. Rebek), CRC, Boca Raton, FL, 1990, pp. 119-141.
29. The cis/trans photoisomerization of azobenzene derivatives is well documented: a) "Biological Applications of Photochemical Switches": 1. Willner, B. Willner in Bioorganic Photochemistry, Vol. 2 (Ed.: H. Morrison), Wiley, New York, 1993, pp. 1-110; b) I. Willner, S. Rubin, Angew. Chem. 1996, 108, 419-439; Angew. Chem. Int. Ed. Engl. 1996, 35, 367-385; c) H. Rau in Photochemistry and Photophysics, Vol II (Ed.: J. F. Rebek), CRC, Boca Raton, FL, 1990, pp. 119-141.
30. The cis/trans photoisomerization of azobenzene derivatives is well documented: a) "Biological Applications of Photochemical Switches": 1. Willner, B. Willner in Bioorganic Photochemistry, Vol. 2 (Ed.: H. Morrison), Wiley, New York, 1993, pp. 1-110; b) I. Willner, S. Rubin, Angew. Chem. 1996, 108, 419-439; Angew. Chem. Int. Ed. Engl. 1996, 35, 367-385; c) H. Rau in Photochemistry and Photophysics, Vol II (Ed.: J. F. Rebek), CRC, Boca Raton, FL, 1990, pp. 119-141.
31. The cis/trans photoisomerization of azobenzene derivatives is well documented: a) "Biological Applications of Photochemical Switches": 1. Willner, B. Willner in Bioorganic Photochemistry, Vol. 2 (Ed.: H. Morrison), Wiley, New York, 1993, pp. 1-110; b) I. Willner, S. Rubin, Angew. Chem. 1996, 108, 419-439; Angew. Chem. Int. Ed. Engl. 1996, 35, 367-385; c) H. Rau in Photochemistry and Photophysics, Vol II (Ed.: J. F. Rebek), CRC, Boca Raton, FL, 1990, pp. 119-141.
32. Qualitative modeling was carried out by reference to X-ray structural data for GCN4 hound to the ATF/CREB site: P. König, T. J. Richmond, J. Mol. Biol. 1993, 233, 139-154. See Supporting Information for more details.
33. 1] found: 6110.2; calculated: 6110.3.
34. Irradiation at 365 nm was performed with a 8 W UV lamp, at a concentration of 2 μM.
35. The isomer ratio was calculated by integration of the HPLC peaks corrected by the extinction coefficients. Remarkably, the equilibrium cis:trans ratio is slightly higher than for the azobenzene precursor 2 (90:10).
36. Irradiation was performed in a spectrofluorometer (Fluromer-2; light source: 150 W xenon lamp; 5 nm path). At a concentration of 2 μM, isomer trans-3 was obtained after 15 min.
37. In the absence of visible light, the isomerization of cis-3 to trans-3 at 35 C had a half-life of approximately 65 h.
38. It should be borne in mind that cis-3 is contaminated by 5% of the trans isomer.
39. An azobenzene-peptide hybrid related to 3 but lacking the two glycines at the C terminus is unable to bind to the CREB site in either the cis or trans form (results not shown).
40. 32P end-labelled CREB18-half2 as the DNA probe.
41. The UV spectrum of the peptide - DNA complex after 4 h irradiation with visible light is identical to that obtained before irradiation, suggesting that the cis-azobenzene unit was unable to switch to the trans form (see the Supporting Information).