Fluorescent sensors for specific RNA: A general paradigm using chemistry and combinatorial biology

Journal of the American Chemical Society

Volumn 129, Issue 15, 2007, Pages 4785-4794

  Sparano, Brian A ^a   Koide, Kazunori ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANILINE; BIOSENSORS; CONFORMATIONS; ELECTRON TRANSITIONS; FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; LIGANDS;

FLUORESCENT INTENSITIES; FLUORESCENT SENSORS; PHOTOINDUCED ELECTRON TRANSFER; QUENCHERS;

RNA;

ANILINE DERIVATIVE; DICHLOROFLUORESCEIN; RNA;

ARTICLE; COMBINATORIAL CHEMISTRY; ELECTRON TRANSPORT; FLUORESCENCE; LIGAND BINDING; RNA CONFORMATION; RNA STRUCTURE;

CYCLODEXTRINS; DATABASES, GENETIC; ELECTRONS; FLUORESCEINS; GENE EXPRESSION; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR STRUCTURE; PHOTOCHEMISTRY; RNA;

EID: 34247523672     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja070111z     Document Type: Article

References (66)

1. Chudakov, D. M.; Lukyanov, S.; Lukyanov, K. A. Trends Biolechnol. 2005, 23, 605-613.
2. Giepmans, B. N. G.; Adams, S. R.; Ellisman, M. H.; Tsien, R. Y. Science 2006, 312, 217-224.
3. Griffin, B. A.; Adams, S. R.; Tsien, R. Y. Science 1998, 281, 269-272.
4. Li, X.; Zhao, X.; Fang, Y.; Jiang, X.; Duong, T.; Fan, C.; Huang, C.-C.; Kain, S. R. J. Biol. Chem. 1998, 273, 34970-34975.
5. Gygi, S. P.; Rochon, Y.; Franza, B. R.; Aebersold, R. Mol. Cell. Biol. 1999, 19, 1720-1730.
6. Raj, A.; Peskin, C. S.; Tranchina, D.; Vargas, D. Y.; Tyagi, S. PLoS Biol. 2006, 4, e309.
7. Rodriguez-Inigo, E.; Casqueiro, M.; Navas, S.; Bartolome, J.; Pardo, M.; Carreno, V. J. Med. Virol. 2000, 60, 269-274.
8. Knuchel, M. C.; Graf, B.; Schlaepfer, E.; Kuster, H.; Fischer, M.; Weber, R.; Cone, R. W. J. Histochem. Cytochem. 2000, 48, 285-294.
9. Namba, T.; Oida, H.; Sugimoto, Y.; Kakizuka, A.; Negishi, M.; Ichikawa, A.; Narumiya, S. J. Biol. Chem. 1994, 269, 9986-9992.
10. Ekong, R.; Wolfe, J. Curr. Opin. Biotechnol. 1998, 9, 19-24.
11. Dirks, R.; Daniel, K.; Raap, A. J. Cell Sci. 1995, 108, 2565-2572.
12. Kohler, S. Exp. Parasitol. 1999, 92, 249-262.
13. Tyagi, S.; Kramer, F. R. Nat. Biotechnol. 1996, 14, 303-308.
14. Tan, W.; Wang, K.; Drake, T. J. Curr. Opin. Chem. Biol. 2004, 8, 547-553.
15. Bratu, D. P.; Cha, B.-J.; Mhlanga, M. M.; Kramer, F. R.; Tyagi, S. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13308-13313.
16. Santangelo, P. J.; Nitin, N.; Bao, G. J. Biomed. Opt. 2005, 10, 044025.
17. Vargas, D. Y.; Raj, A.; Marras, S. A. E.; Kramer, F. R.; Tyagi, S. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17008-17013.
18. Browne, K. A. J. Am. Chem. Soc. 2005, 127, 1989-1994.
19. Dirks, R. W.; Molenaar, C.; Tanke, H. J. Methods 2003, 29, 51-57.
20. Bertrand, E.; Chartrand, P.; Schaefer, M.; Shenoy, S. M.; Singer, R. H.; Long, R. M. Mol. Cell 1998, 2, 437-445.
21. Fusco, D.; Accornero, N.; Lavoie, B.; Shenoy, S. M.; Blanchard, J. M.; Singer, R. H.; Bertrand, E. Curr. Biol. 2003, 13, 161-167.
22. Le, T. T.; Harlepp, S.; Guet, C. C.; Dittmar, K.; Emonet, T.; Pan, T.; Cluzel, P. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 9160-9164.
23. Beach, D. L.; Salmon, E. D.; Bloom, K. Curr. Biol. 1999, 9, 569-578.
24. Kloc, M.; Zearfoss, N. R.; Etkin, L. D. Cell 2002, 108, 533-44.
25. Singer, R. H. Curr. Biol. 2003, 13, R673-R675.
26. Forrest, K. M.; Gavis, E. R. Curr. Biol 2003, 13, 1159-1168.
27. Shav-Tal, Y.; Darzacq, X.; Shenoy, S. M.; Fusco, D.; Janicki, S. M.; Spector, D. L.; Singer, R. H. Science 2004, 304, 1797-1800.
28. Janicki, S. M.; Tsukamoto, T.; Salghetti, S. E.; Tansey, W. P.; Sachidanandam, R.; Prasanth, K. V.; Ried, T.; Shav-Tal, Y.; Bertrand, E.; Singer, R. H. Cell 2004, 116, 683-698.
29. Golding, I.; Paulsson, J.; Zawilski, S. M.; Cox, E. C. Cell 2005, 123, 1025-1036.
30. Abe, H.; Kool, E. T. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 263-268.
31. Sando, S.; Kool, E. T. J. Am. Chem. Soc. 2002, 124, 9686-9687.
32. Tanaka, K.; Miura, T.; Umezawa, N.; Urano, Y.; Kikuchi, K.; Higuchi, T.; Nagano, T. J. Am. Chem. Soc. 2001, 123, 2530-2536.
33. Onoda, M.; Uchiyama, S.; Santa, T.; Imai, K. Anal. Chem. 2002, 74, 4089-4096.
34. Hirano, T.; Kikuchi, K.; Urano, Y.; Nagano, T. J. Am. Chem. Soc. 2002, 124, 6555-6562.
35. Shults, M. D.; Pearce, D. A.; Imperiali, B. J. Am. Chem. Soc. 2003, 125, 10591-10597.
36. Pearce, D. A.; Jotterand, N.; Carrico, I. S.; Imperiali, B. J. Am. Chem. Soc. 2001, 123, 5160-5161.
37. Walkup, G. K.; Burdette, S. C.; Lippard, S. J.; Tsien, R. Y. J. Am. Chem. Soc. 2000, 122, 5644-5645.
38. Zeng, L.; Miller, E. W.; Pralle, A.; Isacoff, E. Y.; Chang, C. J. J. Am. Chem. Soc. 2006, 128, 10-11.
39. Farruggia, G.; Iotti, S.; Prodi, L.; Montalti, M.; Zaccheroni, N.; Savage, P. B.; Trapani, V.; Sale, P.; Wolf, F. I. J. Am. Chem. Soc. 2006, 128, 344-350.
40. Lakowicz, J. R. Principles of fluorescence spectroscopy, 2nd ed.; Kluwer Academic/Plenum Publishers: New York, 1999.
41. Rehm, D.; Weller, A. Isr. J. Chem. 1970, 8, 259-271.
42. Munkholm, C.; Parkinson, D.-R.; Walt, D. R. J. Am. Chem. Soc. 1990, 112, 2608-2612.
43. Ueno, T.; Urano, Y.; Setsukinai, K.; Takakusa, H.; Kojima, H.; Kikuchi, K.; Ohkubo, K.; Fukuzumi, S.; Nagano, T. J. Am. Chem. Soc. 2004, 126, 14079-14085.
44. Torrado, A.; Imperiali, B. J. Org. Chem. 1996, 61, 8940-8948.
45. Sparano, B. A.; Shahi, S. P.; Koide, K. Org. Lett. 2004, 6, 1947-1949.
46. For the preliminary results of this work, see: Sparano, B. A.; Koide, K. J. Am. Chem. Soc. 2005, 127, 14954-14955.
47. McHedlov-Petrossyan, N. O.; Rubtsov, M. I.; Kukatskaya, L. L. Dyes Pigm. 1992, 18, 179-198.
48. Martin, M. M.; Lindqvist, L. J. Lumin. 1975, 10, 381-390.
49. Burdette, S. C.; Walkup, G. K.; Spingler, B.; Tsien, R. Y.; Lippard, S. J. J. Am. Chem. Soc. 2001, 123, 7831-7841.
50. Meadow, J. R.; Reid, E. E. J. Am. Chem. Soc. 1954, 76, 3479-3481.
51. 2O for two-dimensional NMR studies. The quantum yield relationships in DMSO show the same trends as in pH 7 phosphate buffer.
52. Rekharsky, M. V.; Goldberg, R. N.; Schwarz, F. P.; Tewari, Y. B.; Ross, P. D.; Yamashoji, Y.; Inoue, Y. J. Am. Chem. Soc. 1995, 117, 8830-8840.
53. Rekharsky, M. V.; Inoue, Y. Chem. Rev. 1998, 98, 1875-1918.
54. The concentration of β-cyclodextrin could not be increased further because of its low solubility.
55. Ellington, A. D.; Szostak, J. W. Nature 1990, 346, 818-822.
56. Robertson, D. L.; Joyce, G. F. Nature 1990, 344, 467-468.
57. Tuerk, C.; Gold, L. Science 1990, 249, 505-510.
58. Battel, D. P.; Szostak, J. W. Science 1993, 261, 1411-1418.
59. Holeman, L. A.; Robinson, S. L.; Szostak, J. W.; Wilson, C. Folding Des. 1998, 3, 423-431.
60. Sassanfar, M.; Szostak, J. W. Nature 1993, 364, 550-553.
61. Wilson, C.; Szostak, J. W. Nature 1995, 374, 777-782.
62. Zuker, M. Nucleic Acids Res. 2003, 31, 3406-3415.
63. Breaker, R. R.; Joyce, G. F. Trends Biotechnol. 1994, 12, 268-275.
64. Although not statistically significant, the choice to test only three aptamers was purely an economic one: the expensive process of producing sufficient RNA for evaluating fluorescent enhancement ability restricted us to testing only those aptamers that were well represented in the sequenced hits and lowing the maximum concentration from 100 μM to 50 μM.
65. For an account, see: Koide, K. Am. Biotechnol. Lab. 2006, 24, 8-10.
66. The choice of 100 μM was a practical one, with the yield of each large scale in-vitro transcription reaction yielding only 10-15 nanomoles of RNA.