Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes

ACS Synthetic Biology

Volumn 2, Issue 12, 2013, Pages 684-689

  Nomura, Yoko ^a   Zhou, Linlin ^a   Miu, Anh ^a   Yokobayashi, Yohei ^a  

^a University of California Davis   (United States)

Author keywords

aptazyme; HDV ribozyme; logic gate; riboswitch; ribozyme

Indexed keywords

GUANINE; RIBOZYME; THEOPHYLLINE; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; RIBOSWITCH;

3' UNTRANSLATED REGION; ALLOSTERISM; ARTICLE; CELL STRAIN HEK293; GENE EXPRESSION REGULATION; GENETIC TRANSFECTION; HEPATITIS DELTA VIRUS; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; MAMMAL CELL; NONHUMAN; PLASMID; PRIORITY JOURNAL; REPORTER GENE; BACILLUS SUBTILIS; CONFORMATION; GENETIC ENGINEERING; GENETICS; HEK293 CELL LINE; METABOLISM; PROCEDURES; RIBOSWITCH; SYNTHETIC BIOLOGY;

BACILLUS SUBTILIS; GENE EXPRESSION REGULATION; GENETIC ENGINEERING; GREEN FLUORESCENT PROTEINS; HEK293 CELLS; HEPATITIS DELTA VIRUS; HUMANS; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA, CATALYTIC; SYNTHETIC BIOLOGY;

EID: 84890902769     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb400037a     Document Type: Article

References (30)

1. Isaacs, F. J., Dwyer, D. J., and Collins, J. J. (2006) RNA synthetic biology Nat. Biotechnol. 24, 545-554
2. Liang, J. C., Bloom, R. J., and Smolke, C. D. (2011) Engineering biological systems with synthetic RNA molecules Mol. Cell 43, 915-926
3. Saito, H. and Inoue, T. (2009) Synthetic biology with RNA motifs Int. J. Biochem. Cell Biol. 41, 398-404
4. Weigand, J. E. and Suess, B. (2009) Aptamers and riboswitches: perspectives in biotechnology Appl. Microbiol. Biotechnol. 85, 229-236
5. Wieland, M. and Fussenegger, M. (2010) Ligand-dependent regulatory RNA parts for Synthetic Biology in eukaryotes Curr. Opin. Biotechnol. 21, 760-765
6. Ogawa, A. and Maeda, M. (2008) An artificial aptazyme-based riboswitch and its cascading system in E. coli ChemBioChem 9, 206-209
7. Wieland, M. and Hartig, J. S. (2008) Improved aptazyme design and in vivo screening enable riboswitching in bacteria Angew. Chem., Int. Ed. 47, 2604-2607
8. Wittmann, A. and Suess, B. (2011) Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast Mol. Biosyst. 7, 2419-2427
9. Win, M. N. and Smolke, C. D. (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function Proc. Natl. Acad. Sci. U.S.A. 104, 14283-14288
10. Ausländer, S., Ketzer, P., and Hartig, J. S. (2010) A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression Mol. Biosyst. 6, 807-814
11. Chen, Y. Y., Jensen, M. C., and Smolke, C. D. (2010) Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems Proc. Natl. Acad. Sci. U.S.A. 107, 8531-8536
12. Kumar, D., An, C. I., and Yokobayashi, Y. (2009) Conditional RNA interference mediated by allosteric ribozyme J. Am. Chem. Soc. 131, 13906-13907
13. Nomura, Y., Kumar, D., and Yokobayashi, Y. (2012) Synthetic mammalian riboswitches based on guanine aptazyme Chem. Commun. (Cambridge) 48, 7215-7217
14. Wieland, M., Auslander, D., and Fussenegger, M. (2012) Engineering of ribozyme-based riboswitches for mammalian cells Methods 56, 351-357
15. Webb, C. H. and Lupták, A. (2011) HDV-like self-cleaving ribozymes RNA Biol. 8, 719-727
16. Perrotta, A. T., Shih, I., and Been, M. D. (1999) Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme Science 286, 123-126
17. Rosenstein, S. P. and Been, M. D. (1990) Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions Biochemistry 29, 8011-8016
18. Wu, H. N. and Lai, M. M. (1990) RNA conformational requirements of self-cleavage of hepatitis delta virus RNA Mol. Cell. Biol. 10, 5575-5579
19. Asif-Ullah, M., Lévesque, M., Robichaud, G., and Perreault, J. P. (2007) Development of ribozyme-based gene-inactivations; the example of the hepatitis delta virus ribozyme Curr. Gene Ther. 7, 205-216
20. Kertsburg, A. and Soukup, G. A. (2002) A versatile communication module for controlling RNA folding and catalysis Nucleic Acids Res. 30, 4599-4606
21. Beaudoin, J. D. and Perreault, J. P. (2008) Potassium ions modulate a G-quadruplex-ribozyme's activity RNA 14, 1018-1025
22. Rouleau, S. G., Jodoin, R., Bisaillon, M., and Perreault, J. P. (2012) Programming a highly structured ribozyme into complex allostery using RNA oligonucleotides ACS Chem. Biol. 7, 1802-1806
23. Ruminski, D. J., Webb, C. H., Riccitelli, N. J., and Lupták, A. (2011) Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes J. Biol. Chem. 286, 41286-41295
24. Kumar, P. K. R., Suh, Y. A., Miyashiro, H., Nishikawa, F., Kawakami, J., Taira, K., and Nishikawa, S. (1992) Random mutations to evaluate the role of bases at two important single-stranded regions of genomic HDV ribozyme Nucleic Acids Res. 20, 3919-3924
25. Jenison, R. D., Gill, S. C., Pardi, A., and Polisky, B. (1994) High-resolution molecular discrimination by RNA Science 263, 1425-1429
26. Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C., and Breaker, R. R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria Cell 113, 577-586
27. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31, 3406-3415
28. Win, M. N. and Smolke, C. D. (2008) Higher-order cellular information processing with synthetic RNA devices Science 322, 456-460
29. Ketzer, P., Haas, S. F., Engelhardt, S., Hartig, J. S., and Nettelbeck, D. M. (2012) Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses Nucleic Acids Res. 40, e167
30. Webb, C. H., Riccitelli, N. J., Ruminski, D. J., and Lupták, A. (2009) Widespread occurrence of self-cleaving ribozymes Science 326, 953