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Volumn 388, Issue 8, 2007, Pages 779-786

Engineering high-speed allosteric hammerhead ribozymes

Author keywords

Aptamer; Riboswitch; RNA folding; RNA switch; Self cleavage; Theophylline

Indexed keywords

ENZYME VARIANT; HAMMERHEAD RIBOZYME; MAGNESIUM; RNA; THEOPHYLLINE;

EID: 34547519117     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2007.105     Document Type: Article
Times cited : (51)

References (45)
  • 1
    • 33750999084 scopus 로고    scopus 로고
    • Controlling the rate of organic reactions: Rational design of allosteric Diels-Alderase ribozymes
    • Amontov, S. and Jaschke, A. (2006). Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes. Nucleic Acids Res. 34, 5032-5038.
    • (2006) Nucleic Acids Res , vol.34 , pp. 5032-5038
    • Amontov, S.1    Jaschke, A.2
  • 2
    • 21444457242 scopus 로고    scopus 로고
    • Programmable ligand-controlled riboregulators of eukaryotic gene expression
    • Bayer, T.S. and Smolke, C.D. (2005). Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23, 337-343.
    • (2005) Nat. Biotechnol , vol.23 , pp. 337-343
    • Bayer, T.S.1    Smolke, C.D.2
  • 3
    • 0036469778 scopus 로고    scopus 로고
    • Engineered allosteric ribozymes as biosensor components
    • Breaker, R.R. (2002). Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13, 31-39.
    • (2002) Curr. Opin. Biotechnol , vol.13 , pp. 31-39
    • Breaker, R.R.1
  • 4
    • 11144330098 scopus 로고    scopus 로고
    • Natural and engineered nucleic acids as tools to explore biology
    • Breaker, R.R. (2004). Natural and engineered nucleic acids as tools to explore biology. Nature 432, 838-845.
    • (2004) Nature , vol.432 , pp. 838-845
    • Breaker, R.R.1
  • 6
    • 0037863216 scopus 로고    scopus 로고
    • In vivo evolution of an RNA-based transcriptional activator
    • Buskirk, A.R., Kehayova, P.D., Landrigan, A., and Liu, D.R. (2003). In vivo evolution of an RNA-based transcriptional activator. Chem. Biol. 10, 533-540.
    • (2003) Chem. Biol , vol.10 , pp. 533-540
    • Buskirk, A.R.1    Kehayova, P.D.2    Landrigan, A.3    Liu, D.R.4
  • 8
    • 0142105383 scopus 로고    scopus 로고
    • Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity
    • De la Pena, M., Gago, S., and Flores, R. (2003). Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J. 22, 5561-5570.
    • (2003) EMBO J , vol.22 , pp. 5561-5570
    • De la Pena, M.1    Gago, S.2    Flores, R.3
  • 9
    • 6044261460 scopus 로고    scopus 로고
    • Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation
    • Desai, S.K. and Gallivan, J.P. (2004). Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc. 126, 13247-13254.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 13247-13254
    • Desai, S.K.1    Gallivan, J.P.2
  • 10
    • 0023663396 scopus 로고
    • Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
    • Forster, A.C. and Symons, R.H. (1987). Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 49, 211-220.
    • (1987) Cell , vol.49 , pp. 211-220
    • Forster, A.C.1    Symons, R.H.2
  • 11
    • 33847375887 scopus 로고    scopus 로고
    • Computational selection of nucleic acid biosensors via slip structure model
    • Hall, B., Hesselberth, J.R., and Ellington, A.D. (2007). Computational selection of nucleic acid biosensors via slip structure model. Biosens. Bioelectron. 22, 1939-1947.
    • (2007) Biosens. Bioelectron , vol.22 , pp. 1939-1947
    • Hall, B.1    Hesselberth, J.R.2    Ellington, A.D.3
  • 12
    • 0036903567 scopus 로고    scopus 로고
    • Folding and activity of the hammerhead ribozyme
    • Hammann, C. and Lilly, D.M. (2002). Folding and activity of the hammerhead ribozyme. ChemBioChem 3, 691-700.
    • (2002) ChemBioChem , vol.3 , pp. 691-700
    • Hammann, C.1    Lilly, D.M.2
  • 13
    • 0029163563 scopus 로고
    • RNA chaperones and the RNA Folding problem
    • Herschlag, D. (1995). RNA chaperones and the RNA Folding problem. J. Biol. Chem. 270, 20871-20874.
    • (1995) J. Biol. Chem , vol.270 , pp. 20871-20874
    • Herschlag, D.1
  • 14
    • 0028224199 scopus 로고
    • High-resolution molecular discrimination by RNA
    • Jenison, R.D., Gill, S.C., Pardi, A., and Polisky, B. (1994). High-resolution molecular discrimination by RNA. Science 263, 1425-1429.
    • (1994) Science , vol.263 , pp. 1425-1429
    • Jenison, R.D.1    Gill, S.C.2    Pardi, A.3    Polisky, B.4
  • 15
    • 0036849338 scopus 로고    scopus 로고
    • A versatile communication module for controlling RNA folding and catalysis
    • Kertsburg, A. and Soukup, G.A. (2002). A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res. 30, 4599-4606.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4599-4606
    • Kertsburg, A.1    Soukup, G.A.2
  • 16
    • 0043009734 scopus 로고    scopus 로고
    • Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
    • Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S.D. (2003). Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10, 708-712.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 708-712
    • Khvorova, A.1    Lescoute, A.2    Westhof, E.3    Jayasena, S.D.4
  • 17
    • 34547516089 scopus 로고    scopus 로고
    • Rational design of an allosteric effector on a designed ribozyme
    • Kuramitsu, S., Ikawa, Y., and Inoue, T. (2005). Rational design of an allosteric effector on a designed ribozyme. Nucleic Acids Symp. Ser. 49, 349-350.
    • (2005) Nucleic Acids Symp. Ser , vol.49 , pp. 349-350
    • Kuramitsu, S.1    Ikawa, Y.2    Inoue, T.3
  • 18
    • 33750220929 scopus 로고    scopus 로고
    • Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection
    • Link, K.H., Guo, L., and Breaker, R.R. (2006). Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection. Nucleic Acids Res. 34, 4968-4975.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4968-4975
    • Link, K.H.1    Guo, L.2    Breaker, R.R.3
  • 19
    • 0028339955 scopus 로고
    • Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem-I deletions
    • Long, D.M. and Uhlenbeck, O.C. (1994). Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem-I deletions. Proc. Natl. Acad. Sci. USA 91, 6977-6981.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 6977-6981
    • Long, D.M.1    Uhlenbeck, O.C.2
  • 20
    • 21244459458 scopus 로고    scopus 로고
    • Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast
    • Mahen, E.M., Harger, J.W., Calderon, E.M., and Fedor, M.J. (2005). Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. Mol. Cell 19, 27-37.
    • (2005) Mol. Cell , vol.19 , pp. 27-37
    • Mahen, E.M.1    Harger, J.W.2    Calderon, E.M.3    Fedor, M.J.4
  • 21
    • 33746228126 scopus 로고    scopus 로고
    • Tertiary contacts distant from the active site prime a ribozyme for catalysis
    • Martick, M. and Scott, W.G. (2006). Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309-320.
    • (2006) Cell , vol.126 , pp. 309-320
    • Martick, M.1    Scott, W.G.2
  • 22
    • 34047153339 scopus 로고    scopus 로고
    • RNA chaperone activity and RNA-binding properties of the E. coli protein StpA
    • Mayer, O., Rajkowitsch, L., Lorenz, C., Konrat, R., and Schroeder, R. (2007). RNA chaperone activity and RNA-binding properties of the E. coli protein StpA. Nucleic Acids Res. 35, 1257-1269.
    • (2007) Nucleic Acids Res , vol.35 , pp. 1257-1269
    • Mayer, O.1    Rajkowitsch, L.2    Lorenz, C.3    Konrat, R.4    Schroeder, R.5
  • 23
    • 27944493648 scopus 로고    scopus 로고
    • Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
    • Penchovsky, R. and Breaker, R. R. (2005). Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat. Biotechnol. 23, 1424-1433.
    • (2005) Nat. Biotechnol , vol.23 , pp. 1424-1433
    • Penchovsky, R.1    Breaker, R.R.2
  • 26
    • 0034655587 scopus 로고    scopus 로고
    • Design and optimization of effector-activated ribozyme ligases
    • Robertson, M.P. and Ellington, A.D. (2000). Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res. 28, 1751-1759.
    • (2000) Nucleic Acids Res , vol.28 , pp. 1751-1759
    • Robertson, M.P.1    Ellington, A.D.2
  • 28
    • 0037377340 scopus 로고    scopus 로고
    • Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA
    • Silverman, S.K. (2003). Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9, 377-383.
    • (2003) RNA , vol.9 , pp. 377-383
    • Silverman, S.K.1
  • 29
    • 0033616774 scopus 로고    scopus 로고
    • Engineering precision RNA molecular switches
    • Soukup, G.A. and Breaker, R.R. (1999a). Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA 96, 3584-3589.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 3584-3589
    • Soukup, G.A.1    Breaker, R.R.2
  • 30
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • Soukup, G.A. and Breaker, R.R. (1999b). Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5, 1308-1325.
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 32
    • 0034640131 scopus 로고    scopus 로고
    • Altering molecular recognition of RNA aptamers by allosteric selection
    • Soukup, G.A., Emilsson, G.A.M., and Breaker, R.R. (2000). Altering molecular recognition of RNA aptamers by allosteric selection. J. Mol. Biol. 298, 623-632.
    • (2000) J. Mol. Biol , vol.298 , pp. 623-632
    • Soukup, G.A.1    Emilsson, G.A.M.2    Breaker, R.R.3
  • 33
    • 0035001974 scopus 로고    scopus 로고
    • Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes
    • Soukup, G.A., DeRose, E.C., Koizumi, M., and Breaker, R.R. (2001). Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 7, 524-536.
    • (2001) RNA , vol.7 , pp. 524-536
    • Soukup, G.A.1    DeRose, E.C.2    Koizumi, M.3    Breaker, R.R.4
  • 34
    • 2542601538 scopus 로고    scopus 로고
    • A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo
    • Suess, B., Fink, B., Berens, C., Stentz, R., and Hillen, W. (2004). A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res. 32, 1610-1614.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1610-1614
    • Suess, B.1    Fink, B.2    Berens, C.3    Stentz, R.4    Hillen, W.5
  • 35
    • 0037062920 scopus 로고    scopus 로고
    • Emerging clinical applications of RNA
    • Sullenger, B.A. and Gilboa, E. (2002). Emerging clinical applications of RNA. Nature 418, 252-258.
    • (2002) Nature , vol.418 , pp. 252-258
    • Sullenger, B.A.1    Gilboa, E.2
  • 36
    • 0031171217 scopus 로고    scopus 로고
    • Rational design of allosteric ribozymes
    • Tang, J. and Breaker, R.R. (1997). Rational design of allosteric ribozymes. Chem. Biol. 4, 453-459.
    • (1997) Chem. Biol , vol.4 , pp. 453-459
    • Tang, J.1    Breaker, R.R.2
  • 38
    • 0344874278 scopus 로고    scopus 로고
    • Less isn't always more
    • Uhlenbeck, O.C. (2003). Less isn't always more. RNA 9, 1415-1417.
    • (2003) RNA , vol.9 , pp. 1415-1417
    • Uhlenbeck, O.C.1
  • 39
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • Wickiser, J.K., Cheah, M.T., Breaker, R.R., and Crothers, D.M. (2005b). The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44, 13404-13414.
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 40
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • Wickiser, J.K., Winkler, W.C., Breaker, R.R., and Crothers, D.M. (2005a). The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18, 49-60.
    • (2005) Mol. Cell , vol.18 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 41
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., and Breaker, R.R. (2004). Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281-286.
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Roth, A.3    Collins, J.A.4    Breaker, R.R.5
  • 42
    • 0034043484 scopus 로고    scopus 로고
    • Recent insights on RNA folding mechanisms from catalytic RNA
    • Woodson, S.A. (2000). Recent insights on RNA folding mechanisms from catalytic RNA. Cell. Mol. Life Sci. 57, 796-808.
    • (2000) Cell. Mol. Life Sci , vol.57 , pp. 796-808
    • Woodson, S.A.1
  • 43
    • 33646192489 scopus 로고    scopus 로고
    • Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries
    • Yen, L., Magnier, M., Weissleder, R., Stockwell, B.R., and Mulligan, R.C. (2006). Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries. RNA 12, 797-806.
    • (2006) RNA , vol.12 , pp. 797-806
    • Yen, L.1    Magnier, M.2    Weissleder, R.3    Stockwell, B.R.4    Mulligan, R.C.5
  • 44
  • 45
    • 13844315455 scopus 로고    scopus 로고
    • Engineered allosteric ribozymes that respond to specific divalent metal ions
    • Zivarts, M., Liu, Y., and Breaker, R.R. (2005). Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res. 33, 622-631.
    • (2005) Nucleic Acids Res , vol.33 , pp. 622-631
    • Zivarts, M.1    Liu, Y.2    Breaker, R.R.3


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