-
1
-
-
33746228126
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
10
-
-
4444297561
-
Fast cleavage kinetics of a natural hammerhead ribozyme
-
Canny, M. D., Jucker, F. M., Kellogg, E., Khvorova, A., Jayasena, S. D., and Pardi, A. (2004) Fast cleavage kinetics of a natural hammerhead ribozyme J. Am. Chem. Soc. 126, 10848-10849
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 10848-10849
-
-
Canny, M.D.1
Jucker, F.M.2
Kellogg, E.3
Khvorova, A.4
Jayasena, S.D.5
Pardi, A.6
-
11
-
-
0030013338
-
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
-
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
-
13
-
-
0023785594
-
RNA structure prediction
-
Turner, D. H., Sugimoto, N., and Freier, S. M. (1988) RNA structure prediction Annu. Rev. Biophys. Chem. 17, 167-192
-
(1988)
Annu. Rev. Biophys. Chem.
, vol.17
, pp. 167-192
-
-
Turner, D.H.1
Sugimoto, N.2
Freier, S.M.3
-
14
-
-
75549088409
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
0033574151
-
RNA folding and misfolding of the hammerhead ribozyme
-
Bassi, G. S., Mollegaard, N. E., Murchie, A. I., and Lilley, D. M. (1999) RNA folding and misfolding of the hammerhead ribozyme Biochemistry 38, 3345-3354
-
(1999)
Biochemistry
, vol.38
, pp. 3345-3354
-
-
Bassi, G.S.1
Mollegaard, N.E.2
Murchie, A.I.3
Lilley, D.M.4
-
28
-
-
63649098099
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
36
-
-
21044455455
-
Folding and catalysis of the hairpin ribozyme
-
Wilson, T. J., Nahas, M., Ha, T., and Lilley, D. M. (2005) Folding and catalysis of the hairpin ribozyme Biochem. Soc. Trans. 33, 461-465
-
(2005)
Biochem. Soc. Trans.
, vol.33
, pp. 461-465
-
-
Wilson, T.J.1
Nahas, M.2
Ha, T.3
Lilley, D.M.4
-
37
-
-
0033600553
-
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
|