Biofunction-assisted sensors based on a new method for converting aptazyme activity into reporter protein expression with high efficiency in wheat germ extract

ChemBioChem

Volumn 10, Issue 15, 2009, Pages 2465-2468

  Ogawa, Atsushi ^a  

^a EHIME UNIVERSITY   (Japan)

Author keywords

Aptazymes; Biosensors; Cell free translation; Ribozymes; Wheat germ extract

Indexed keywords

APTAMER; INITIATION FACTOR; LUCIFERASE; MESSENGER RNA; RIBOZYME; THEOPHYLLINE;

5' UNTRANSLATED REGION; ARTICLE; BIOSENSOR; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME MECHANISM; EUKARYOTE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA CLEAVAGE; RNA TRANSLATION; SENSITIVITY ANALYSIS; WHEAT GERM;

APTAMERS, NUCLEOTIDE; BIOSENSING TECHNIQUES; CELL-FREE SYSTEM; LUCIFERASES; PLANT EXTRACTS; PROTEIN BIOSYNTHESIS; RNA, CATALYTIC; RNA, MESSENGER; THEOPHYLLINE; TRITICUM;

EUKARYOTA; TRITICUM AESTIVUM;

EID: 70350542595     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200900497     Document Type: Article

References (39)

1. R. R. Breaker, Curr. Opin. Biotechnol. 2002, 13, 31-39.
2. A. Roth, R. R. Breaker, Methods Mol. Biol. 2004, 252, 145-164.
3. a) J. Liu, Z. Cao, Y. Lu, Chem. Rev. 2009, 109, 1948-1998;
4. b) I. Willner, M. Zayats, Angew. Chem. 2007, 119, 6528-6538;
5. Angew. Chem. Int. Ed. 2007, 46, 6408-6418;
6. c) N. K. Navani, Y. Li, Curr. Opin. Chem. Biol. 2006, 10, 272-281;
7. d) N. Muranaka, V. Sharma, Y. Nomura, Y. Yokobayashi, Anal. Lett. 2009, 42, 108-122.
8. a) S. Seetharaman, M. Zivarts, N. Sudarsan and R. R. Breaker, Nat. Biotechnol. 2001, 19, 336-341;
9. b) C. Frauendorf and A. Jaschke, Bioorg. Med. Chem. 2001, 9, 2521-2524;
10. c) P. T. Sekella, D. Rueda, N. G. Walter, RNA 2002, 8, 1242-1252;
11. d) J. Liu, Y. Lu, Anal. Chem. 2004, 76, 1627-1632;
12. e) S. Cho, J.-E. Kim, B.-R. Lee, J.-H. Kim, B.-G. Kim, Nucleic Acids Res. 2005, 33, e177;
13. f) S. M. Knudsen, J. Lee, A. D. Ellington, C. A. Savran, J. Am. Chem. Soc. 2006, 128, 15936-15937;
14. g) A. Ogawa, M. Maeda, Bioorg. Med. Chem. Lett. 2008, 18, 6517-6520;
15. h) C. de Silva, N. G. Walter, RNA 2009, 15, 76-84;
16. i) A. Ogawa, M. Maeda, Chem. Lett. 2009, 38, 848-849;
17. j) A. Ogawa, M. Maeda, Chem. Commun. 2009, 4666-4668.
18. a) K. M. Thompson, H. A. Syrett, S. M. Knudsen, A. D. Ellington, BMC Biotechnol. 2002, 2, 21;
19. b) L. Yen, J. Svendsen, J.-S. Lee, J. T. Gray, M. Magnier, T. Baba, R. J. D'Amato, R. C. Mulligan, Nature 2004, 431, 471-476;
20. c) A. Ogawa, M. Maeda, Bioorg. Med. Chem. Lett. 2007, 17, 3156-3160;
21. d) M. N. Win, C. D. Smolke, Proc. Natl. Acad. Sci. USA 2007, 104, 14283-14288;
22. e) A. Ogawa, M. Maeda, ChemBioChem 2008, 9, 206-209;
23. f) M. Wieland, J. S. Hartig, Angew. Chem. 2008, 120, 2643-2646;
24. Angew. Chem. Int. Ed. 2008, 47, 2604-2607;
25. g) A. Ogawa, M. Maeda, ChemBio-Chem 2008, 9, 2204-2208;
26. h) M. Wieland, A. Benz, B. Klauser, J. S. Hartig, Angew. Chem. 2009, 121, 2753-2756;
27. Angew. Chem. Int. Ed. 2009, 48, 2715-2718.
28. K. Madin, T. Sawasaki, T. Ogasawara, Y. Endo, Proc. Natl. Acad. Sci. USA 2000, 97, 559-564.
29. 5′-Cap-free mRNA with 5′-GAA is translated as efficiently as 5′-capped mRNA according to the following literature: a) T. Sawasaki, T. Ogasawara, R. Morishita, Y. Endo, Proc. Natl. Acad. Sci. USA 2002, 99, 14652-14657;
30. b) N. Kamura, T. Sawasaki, Y. Kasahara, K. Takai, Y. Endo, Bioorg. Med. Chem. Lett. 2005, 15, 5402-5406.
31. G. A. Soukup, G. A. M. Emilsson, R. R. Breaker, J. Mol. Biol. 2000, 298, 623-632.
32. Because the theophylline-dependent aptazyme originally has mSTART and mSTOP, mSTART was mutated from AUG to AAG to construct a mSTART-free aptazyme. Incidentally, AUG (mSTART) resides in a core of hammer-head ribozyme. Therefore, all aptazymes based on hammer-head ribozyme have mSTART.
33. This slight suppression effect is probably due to the greater elongation of the 5′-terminal duplex as compared to mRNA 4 upon duplex formation rather than the 5′-side of E01 forming a duplex (see Figure S1).
34. It should be noted that this mSTART resides in a weak context, so that the mimic gene effect is somewhat small. See the following reference regarding translation of an upstream open reading frame in a weak context using wheat germ extract: O. David-Assael, H. Saul, K. Mizrahi, E. Leviad, T. Mizrachy-Dagri, E. Brook, I. Berezin, O. Shaul, Plant Sci. 2007, 172, 354-362.
35. I verified that theophylline did not significantly affect the translation efficiency using nonfused mRNA 1.
36. [5c]
37. G. A. Soukup, E. C. DeRose, M. Koizumi, R. R. Breaker, RNA 2001, 7, 524-536.
38. [9]
39. In the present method, aptazyme reactions and translation are performed separately (like mRNA splicing and translation occurring in different places in eukaryotic cells). Thus, aptazyme reactions can be carried out under optimized conditions. This is one of the reasons for the high translation efficiency in the ON state. In contrast, in the previous method, although these processes occur simultaneously, separation of the aptazyme reaction from translation does not appear to significantly affect the ON/OFF translation efficiencies. This, therefore, does not explain the higher sensitivity of this new method.