Engineering a family of synthetic splicing ribozymes

Nucleic Acids Research

Volumn 38, Issue 8, 2010, Pages 2748-2755

  Che, Austin J ^a,b   Knight Jr , Thomas F ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Ginkgo Bioworks   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME;

ACCURACY; ARTICLE; BIOCHEMISTRY; CONTROLLED STUDY; ENZYME ENGINEERING; ENZYME STRUCTURE; GENE MUTATION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TETRAHYMENA; CHEMISTRY; ENZYMOLOGY; GENETIC ENGINEERING; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA SPLICING; SEQUENCE ANALYSIS; SYNTHESIS;

TETRAHYMENA;

BASE SEQUENCE; GENETIC ENGINEERING; MOLECULAR SEQUENCE DATA; MUTAGENESIS; RNA SPLICING; RNA, CATALYTIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; TETRAHYMENA;

EID: 77952527467     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq186     Document Type: Article

References (26)

1. Che, A.J. (2008) Engineering RNA logic with synthetic splicing ribozymes PhD thesis. Massachusetts Institute of Technology.
2. Schultes, E.A. and Bartel, D.P. (2000) One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science, 289, 448-452.
3. Cech, T.R. (1990) Self-splicing of group I introns. Ann. Rev. Biochem., 59, 543-568.
4. Woodson, S.A. (2005) Structure and assembly of group I introns. Curr. Opin. Struct. Biol., 15, 324-330.
5. Zhou, Y., Lu, C., Wu, Q.J., Wang, Y., Sun, Z.T., Deng, J.C. and Zhang, Y. (2008) GISSD: group I intron sequence and structure database. Nucleic Acids Res., 36, D31-D37.
6. Gorodkin, J., Heyer, L.J., Brunak, S. and Stormo, G.D. (1997) Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., 13, 583-586.
7. Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
8. Wu, M. and Tinoco, I. (1998) RNA folding causes secondary structure rearrangement. Proc. Natl Acad. Sci. USA, 95, 11555-11560.
9. Hayden, E.J., Riley, C.A., Burton, A.S. and Lehman, N. (2005) RNA-directed construction of structurally complex and active ligase ribozymes through recombination. RNA, 11, 1678-1687.
10. Riley, C.A. and Lehman, N. (2003) Generalized RNA-directed recombination of RNA. Chem. Biol., 10, 1233-1243.
11. Alexander, R.C., Baum, D.A. and Testa, S.M. (2005) 5' transcript replacement in vitro catalyzed by a group I intron-derived ribozyme. Biochem., 44, 7796-7804.
12. Baum, D.A., Sinha, J. and Testa, S.M. (2005) Molecular recognition in a trans excision-splicing ribozyme: non-Watson-Crick base pairs at the 5' splice site and omegaG at the 3' splice site can play a role in determining the binding register of reaction substrates. Biochemistry, 44, 1067-1077.
13. Fiskaa, T., Lundblad, E.W., Henriksen, J.R., Johansen, S.D. and Einvik, C. (2006) RNA reprogramming of alpha-mannosidase mRNA sequences in vitro by myxomycete group IC1 and IE ribozymes. FEBS J., 273, 2789-2800.
14. Lundblad, E.W., Haugen, P. and Johansen, S.D. (2004) Trans-splicing of a mutated glycosylasparaginase mRNA sequence by a group I ribozyme deficient in hydrolysis. Eur. J. Biochem., 271, 4932-4938.
15. Ohuchi, S.J., Ikawa, Y., Shiraishi, H. and Inoue, T. (2002) Modular engineering of a group I intron ribozyme. Nucleic Acids Res., 30, 3473-3480.
16. Couture, S., Ellington, A.D., Gerber, A.S., Cherry, J.M., Doudna, J.A., Green, R., Hanna, M., Pace, U., Rajagopal, J. and Szostak, J.W. (1990) Mutational analysis of conserved nucleotides in a self-splicing group I intron. J. Mol. Biol., 215, 345-358.
17. Oe, Y., Ikawa, Y., Shiraishi, H. and Inoue, T. (2000) Analysis of the P7 region within the catalytic core of the Tetrahymena ribozyme by employing in vitro selection. Nucleic Acids Symp. Ser., 44, 197-198.
18. Oe, Y., Ikawa, Y., Shiraishi, H. and Inoue, T. (2001) Conserved base-pairings between C266-A268 and U307-G309 in the P7 of the Tetrahymena ribozyme is nonessential for the in vitro self-splicing reaction. Biochem. Biophys. Res. Commun., 284, 948-954.
19. Ayre, B.G., Köhler, U., Turgeon, R. and Haseloff, J. (2002) Optimization of trans-splicing ribozyme efficiency and specificity by in vivo genetic selection. Nucleic Acids Res., 30, e141.
20. Köhler, U., Ayre, B.G., Goodman, H.M. and Haseloff, J. (1999) Trans-splicing ribozymes for targeted gene delivery. J. Mol. Biol., 285, 1935-1950.
21. Pan, J. and Woodson, S.A. (1998) Folding intermediates of a self-splicing RNA: mispairing of the catalytic core. J. Mol. Biol., 280, 597-609.
22. Zarrinkar, P.P. and Williamson, J.R. (1994) Kinetic intermediates in RNA folding. Science, 265, 918-924.
23. van derHorst, G., Christian, A. and Inoue, T. (1991) Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc. Natl Acad. Sci. USA, 88, 184-188.
24. Treiber, D.K., Rook, M.S., Zarrinkar, P.P. and Williamson, J.R. (1998) Kinetic intermediates trapped by native interactions in RNA folding. Science, 279, 1943-1946.
25. Beaudry, A.A. and Joyce, G.F. (1990) Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron. Biochemistry, 29, 6534-6539.
26. Williams, K.P., Imahori, H., Fujimoto, D.N. and Inoue, T. (1994) Selection of novel forms of a functional domain within the Tetrahymena ribozyme. Nucleic Acids Res., 22, 2003-2009.