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Volumn 49, Issue 21, 2010, Pages 4494-4500

Enhanced product stability in the hammerhead ribozyme

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC CORE; CLEAVAGE RATES; PRODUCT COMPLEX; PRODUCT STABILITY; RATE OF DISSOCIATION; RIBOZYMES; TERTIARY INTERACTIONS; TRANSITION STATE; X-RAY STRUCTURE;

EID: 77952825871     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi902025m     Document Type: Article
Times cited : (8)

References (37)
  • 1
    • 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
  • 2
    • 54749153656 scopus 로고    scopus 로고
    • Capturing hammerhead ribozyme structures in action by modulating general base catalysis
    • Chi, Y. I., Martick, M., Lares, M., Kim, R., Scott, W. G., and Kim, S. H. (2008) Capturing hammerhead ribozyme structures in action by modulating general base catalysis PLoS Biol. 6, 2060-2068
    • (2008) PLoS Biol. , vol.6 , pp. 2060-2068
    • Chi, Y.I.1    Martick, M.2    Lares, M.3    Kim, R.4    Scott, W.G.5    Kim, S.H.6
  • 3
    • 67349123194 scopus 로고    scopus 로고
    • Comparative enzymology and structural biology of RNA self-cleavage
    • Fedor, M. J. (2009) Comparative enzymology and structural biology of RNA self-cleavage Annu. Rev. Biophys. 38, 271-299
    • (2009) Annu. Rev. Biophys. , vol.38 , pp. 271-299
    • Fedor, M.J.1
  • 4
    • 0030476765 scopus 로고    scopus 로고
    • Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
    • Scott, W. G., Murray, J. B., Arnold, J. R., Stoddard, B. L., and Klug, A. (1996) Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme Science 274, 2065-2069
    • (1996) Science , vol.274 , pp. 2065-2069
    • Scott, W.G.1    Murray, J.B.2    Arnold, J.R.3    Stoddard, B.L.4    Klug, A.5
  • 5
    • 0028063567 scopus 로고
    • Three-dimensional structure of a hammerhead ribozyme
    • Pley, H. W., Flaherty, K. M., and McKay, D. B. (1994) Three-dimensional structure of a hammerhead ribozyme Nature 372, 68-74
    • (1994) Nature , vol.372 , pp. 68-74
    • Pley, H.W.1    Flaherty, K.M.2    McKay, D.B.3
  • 6
    • 38049029204 scopus 로고    scopus 로고
    • Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis
    • Nelson, J. A. and Uhlenbeck, O. C. (2008) Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis RNA 14, 43-54
    • (2008) RNA , vol.14 , pp. 43-54
    • Nelson, J.A.1    Uhlenbeck, O.C.2
  • 7
    • 46849108485 scopus 로고    scopus 로고
    • Catalytic diversity of extended hammerhead ribozymes
    • Shepotinovskaya, I. V. and Uhlenbeck, O. C. (2008) Catalytic diversity of extended hammerhead ribozymes Biochemistry 47, 7034-7042
    • (2008) Biochemistry , vol.47 , pp. 7034-7042
    • Shepotinovskaya, I.V.1    Uhlenbeck, O.C.2
  • 8
    • 27644432146 scopus 로고    scopus 로고
    • Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants
    • Nelson, J. A., Shepotinovskaya, I., and Uhlenbeck, O. C. (2005) Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants Biochemistry 44, 14577-14585
    • (2005) Biochemistry , vol.44 , pp. 14577-14585
    • Nelson, J.A.1    Shepotinovskaya, I.2    Uhlenbeck, O.C.3
  • 9
    • 0028288686 scopus 로고
    • A kinetic and thermodynamic framework for the hammerhead ribozyme reaction
    • Hertel, K. J., Herschlag, D., and Uhlenbeck, O. C. (1994) A kinetic and thermodynamic framework for the hammerhead ribozyme reaction Biochemistry 33, 3374-3385
    • (1994) Biochemistry , vol.33 , pp. 3374-3385
    • Hertel, K.J.1    Herschlag, D.2    Uhlenbeck, O.C.3
  • 11
    • 0030013338 scopus 로고    scopus 로고
    • Specificity of hammerhead ribozyme cleavage
    • Hertel, K. J., Herschlag, D., and Uhlenbeck, O. C. (1996) Specificity of hammerhead ribozyme cleavage EMBO J. 15, 3751-3757
    • (1996) EMBO J. , vol.15 , pp. 3751-3757
    • Hertel, K.J.1    Herschlag, D.2    Uhlenbeck, O.C.3
  • 12
    • 0032374090 scopus 로고    scopus 로고
    • Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme
    • Hertel, K. J., Stage-Zimmermann, T. K., Ammons, G., and Uhlenbeck, O. C. (1998) Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme Biochemistry 37, 16983-16988
    • (1998) Biochemistry , vol.37 , pp. 16983-16988
    • Hertel, K.J.1    Stage-Zimmermann, T.K.2    Ammons, G.3    Uhlenbeck, O.C.4
  • 14
    • 75549088409 scopus 로고    scopus 로고
    • NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
    • Turner, D. H. and Mathews, D. H. (2010) NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure Nucleic Acids Res. 38, D280-D282
    • (2010) Nucleic Acids Res. , vol.38
    • Turner, D.H.1    Mathews, D.H.2
  • 15
    • 0030752599 scopus 로고    scopus 로고
    • Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state
    • Baidya, N., Ammons, G. E., Matulic-Adamic, J., Karpeisky, A. M., Beigelman, L., and Uhlenbeck, O. C. (1997) Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state RNA 3, 1135-1142
    • (1997) RNA , vol.3 , pp. 1135-1142
    • Baidya, N.1    Ammons, G.E.2    Matulic-Adamic, J.3    Karpeisky, A.M.4    Beigelman, L.5    Uhlenbeck, O.C.6
  • 16
    • 26844503355 scopus 로고    scopus 로고
    • Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme
    • Kim, N. K., Murali, A., and DeRose, V. J. (2005) Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme J. Am. Chem. Soc. 127, 14134-14135
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 14134-14135
    • Kim, N.K.1    Murali, A.2    Derose, V.J.3
  • 17
    • 1942533453 scopus 로고    scopus 로고
    • Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
    • Penedo, J. C., Wilson, T. J., Jayasena, S. D., Khvorova, A., and Lilley, D. M. (2004) Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements RNA 10, 880-888
    • (2004) RNA , vol.10 , pp. 880-888
    • Penedo, J.C.1    Wilson, T.J.2    Jayasena, S.D.3    Khvorova, A.4    Lilley, D.M.5
  • 18
    • 52949104434 scopus 로고    scopus 로고
    • Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme
    • Boots, J. L., Canny, M. D., Azimi, E., and Pardi, A. (2008) Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme RNA 14, 2212-2222
    • (2008) RNA , vol.14 , pp. 2212-2222
    • Boots, J.L.1    Canny, M.D.2    Azimi, E.3    Pardi, A.4
  • 19
    • 33749267488 scopus 로고    scopus 로고
    • Extraordinary rates of transition metal ion-mediated ribozyme catalysis
    • Roychowdhury-Saha, M. and Burke, D. H. (2006) Extraordinary rates of transition metal ion-mediated ribozyme catalysis RNA 12, 1846-1852
    • (2006) RNA , vol.12 , pp. 1846-1852
    • Roychowdhury-Saha, M.1    Burke, D.H.2
  • 20
    • 33947645368 scopus 로고    scopus 로고
    • Efficient ligation of the Schistosoma hammerhead ribozyme
    • Canny, M. D., Jucker, F. M., and Pardi, A. (2007) Efficient ligation of the Schistosoma hammerhead ribozyme Biochemistry 46, 3826-3834
    • (2007) Biochemistry , vol.46 , pp. 3826-3834
    • Canny, M.D.1    Jucker, F.M.2    Pardi, A.3
  • 21
    • 12844269766 scopus 로고    scopus 로고
    • Characterization of a native hammerhead ribozyme derived from schistosomes
    • Osborne, E. M., Schaak, J. E., and Derose, V. J. (2005) Characterization of a native hammerhead ribozyme derived from schistosomes RNA 11, 187-196
    • (2005) RNA , vol.11 , pp. 187-196
    • Osborne, E.M.1    Schaak, J.E.2    Derose, V.J.3
  • 22
    • 33749032381 scopus 로고    scopus 로고
    • 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
    • 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures Proc. Natl. Acad. Sci. U.S.A. 103, 14003-14008
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 14003-14008
    • Grilley, D.1    Soto, A.M.2    Draper, D.E.3
  • 23
    • 4544250970 scopus 로고    scopus 로고
    • Analysis on a cooperative pathway involving multiple cations in hammerhead reactions
    • Takagi, Y., Inoue, A., and Taira, K. (2004) Analysis on a cooperative pathway involving multiple cations in hammerhead reactions J. Am. Chem. Soc. 126, 12856-12864
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 12856-12864
    • Takagi, Y.1    Inoue, A.2    Taira, K.3
  • 24
    • 0035001461 scopus 로고    scopus 로고
    • Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations
    • O'Rear, J. L., Wang, S., Feig, A. L., Beigelman, L., Uhlenbeck, O. C., and Herschlag, D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations RNA 7, 537-545
    • (2001) RNA , vol.7 , pp. 537-545
    • O'Rear, J.L.1    Wang, S.2    Feig, A.L.3    Beigelman, L.4    Uhlenbeck, O.C.5    Herschlag, D.6
  • 25
    • 0035020626 scopus 로고    scopus 로고
    • The hammerhead cleavage reaction in monovalent cations
    • Curtis, E. A. and Bartel, D. P. (2001) The hammerhead cleavage reaction in monovalent cations RNA 7, 546-552
    • (2001) RNA , vol.7 , pp. 546-552
    • Curtis, E.A.1    Bartel, D.P.2
  • 26
    • 0032192761 scopus 로고    scopus 로고
    • The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
    • Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone Chem. Biol. 5, 587-595
    • (1998) Chem. Biol. , vol.5 , pp. 587-595
    • Murray, J.B.1    Seyhan, A.A.2    Walter, N.G.3    Burke, J.M.4    Scott, W.G.5
  • 27
  • 28
    • 63649098099 scopus 로고    scopus 로고
    • Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation
    • Lee, T. S., Giambasu, G. M., Sosa, C. P., Martick, M., Scott, W. G., and York, D. M. (2009) Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation J. Mol. Biol. 388, 195-206
    • (2009) J. Mol. Biol. , vol.388 , pp. 195-206
    • Lee, T.S.1    Giambasu, G.M.2    Sosa, C.P.3    Martick, M.4    Scott, W.G.5    York, D.M.6
  • 29
    • 34250367504 scopus 로고    scopus 로고
    • Functional analysis of hairpin ribozyme active site architecture
    • Cottrell, J. W., Kuzmin, Y. I., and Fedor, M. J. (2007) Functional analysis of hairpin ribozyme active site architecture J. Biol. Chem. 282, 13498-13507
    • (2007) J. Biol. Chem. , vol.282 , pp. 13498-13507
    • Cottrell, J.W.1    Kuzmin, Y.I.2    Fedor, M.J.3
  • 30
    • 4544271717 scopus 로고    scopus 로고
    • Analysis of the conserved P9-G10.1 metal-binding motif in hammerhead ribozymes with an extra nucleotide inserted between A9 and G10.1 residues
    • Warashina, M., Kuwabara, T., Nakamatsu, Y., Takagi, Y., Kato, Y., and Taira, K. (2004) Analysis of the conserved P9-G10.1 metal-binding motif in hammerhead ribozymes with an extra nucleotide inserted between A9 and G10.1 residues J. Am. Chem. Soc. 126, 12291-12297
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 12291-12297
    • Warashina, M.1    Kuwabara, T.2    Nakamatsu, Y.3    Takagi, Y.4    Kato, Y.5    Taira, K.6
  • 31
    • 0035860684 scopus 로고    scopus 로고
    • An extra nucleotide in the consensus catalytic core of a viroid hammerhead ribozyme: Implications for the design of more efficient ribozymes
    • De la Pena, M. and Flores, R. (2001) An extra nucleotide in the consensus catalytic core of a viroid hammerhead ribozyme: Implications for the design of more efficient ribozymes J. Biol. Chem. 276, 34586-34593
    • (2001) J. Biol. Chem. , vol.276 , pp. 34586-34593
    • De La Pena, M.1    Flores, R.2
  • 32
    • 0034708334 scopus 로고    scopus 로고
    • Structure and function of the hairpin ribozyme
    • Fedor, M. J. (2000) Structure and function of the hairpin ribozyme J. Mol. Biol. 297, 269-291
    • (2000) J. Mol. Biol. , vol.297 , pp. 269-291
    • Fedor, M.J.1
  • 33
    • 0022479968 scopus 로고
    • Nucleotide sequence of satellite tobacco ringspot virus RNA and its relationship to multimeric forms
    • DOI 10.1016/0042-6822(86)90041-3
    • Buzayan, J. M., Gerlach, W. L., Bruening, G., Keese, P., and Gould, A. R. (1986) Nucleotide sequence of satellite tobacco ringspot virus RNA and its relationship to multimeric forms Virology 151, 186-199 (Pubitemid 16073434)
    • (1986) Virology , vol.151 , Issue.2 , pp. 186-199
    • Buzayan, J.M.1    Gerlach, W.L.2    Bruening, G.3
  • 34
    • 0033065715 scopus 로고    scopus 로고
    • The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form
    • Thomson, J. B. and Lilley, D. M. (1999) The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form RNA 5, 180-187
    • (1999) RNA , vol.5 , pp. 180-187
    • Thomson, J.B.1    Lilley, D.M.2
  • 35
    • 0032522574 scopus 로고    scopus 로고
    • Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
    • Walter, N. G., Hampel, K. J., Brown, K. M., and Burke, J. M. (1998) Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer EMBO J. 17, 2378-2391
    • (1998) EMBO J. , vol.17 , pp. 2378-2391
    • Walter, N.G.1    Hampel, K.J.2    Brown, K.M.3    Burke, J.M.4
  • 37
    • 0033600553 scopus 로고    scopus 로고
    • Tertiary structure stabilization promotes hairpin ribozyme ligation
    • Fedor, M. J. (1999) Tertiary structure stabilization promotes hairpin ribozyme ligation Biochemistry 38, 11040-11050
    • (1999) Biochemistry , vol.38 , pp. 11040-11050
    • Fedor, M.J.1


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