-
1
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
Ferre-D’Amare, A.R., Zhou, K. & Doudna, J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998).
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferre-D’amare, A.R.1
Zhou, K.2
Doudna, J.A.3
-
2
-
-
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. & Scott, W.G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5, 587-595 (1998).
-
(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
-
3
-
-
0033215448
-
Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
-
Perrotta, A.T., Shih, I. & Been, M.D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science 286, 123-126 (1999).
-
(1999)
Science
, vol.286
, pp. 123-126
-
-
Perrotta, A.T.1
Shih, I.2
Been, M.D.3
-
4
-
-
0035852640
-
Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage
-
Shih, I.H. & Been, M.D. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc. Natl. Acad. Sci. USA 98, 1489-1494 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 1489-1494
-
-
Shih, I.H.1
Been, M.D.2
-
5
-
-
0034712097
-
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
-
Nakano, S., Chadalavada, D.M. & Bevilacqua, P.C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 287, 1493-1497 (2000).
-
(2000)
Science
, vol.287
, pp. 1493-1497
-
-
Nakano, S.1
Chadalavada, D.M.2
Bevilacqua, P.C.3
-
6
-
-
0035890245
-
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
-
Pinard, R. et al. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 20, 6434-6442 (2001).
-
(2001)
EMBO J
, vol.20
, pp. 6434-6442
-
-
Pinard, R.1
-
7
-
-
0036237379
-
Rescue of an abasic hairpin ribozyme by cationic nucleobases: Evidence for a novel mechanism of RNA catalysis
-
Lebruska, L.L., Kuzmine, I.I. & Fedor, M.J. Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis. Chem. Biol. 9, 465-473 (2002).
-
(2002)
Chem. Biol.
, vol.9
, pp. 465-473
-
-
Lebruska, L.L.1
Kuzmine, I.I.2
Fedor, M.J.3
-
8
-
-
0037111875
-
Transition state stabilization by a catalytic RNA
-
Rupert, P.B., Massey, A.P., Sigurdsson, S.T. & Ferre-D’Amare, A.R. Transition state stabilization by a catalytic RNA. Science 298, 1421-1424 (2002).
-
(2002)
Science
, vol.298
, pp. 1421-1424
-
-
Rupert, P.B.1
Massey, A.P.2
Sigurdsson, S.T.3
Ferre-D’amare, A.R.4
-
9
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
-
Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289, 905-920 (2000).
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
10
-
-
2542470615
-
The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release
-
Youngman, E.M., Brunelle, J.L., Kochaniak, A.B. & Green, R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117, 589-599 (2004).
-
(2004)
Cell
, vol.117
, pp. 589-599
-
-
Youngman, E.M.1
Brunelle, J.L.2
Kochaniak, A.B.3
Green, R.4
-
11
-
-
0035997396
-
Catalytic strategies of the hepatitis delta virus ribozymes
-
Shih, I.H. & Been, M.D. Catalytic strategies of the hepatitis delta virus ribozymes. Annu. Rev. Biochem. 71, 887-917 (2002).
-
(2002)
Annu. Rev. Biochem.
, vol.71
, pp. 887-917
-
-
Shih, I.H.1
Been, M.D.2
-
13
-
-
0037133526
-
a perturbation in genomic hepatitis delta virus ribozyme catalysis evidenced by nucleotide analogue interference mapping
-
a perturbation in genomic hepatitis delta virus ribozyme catalysis evidenced by nucleotide analogue interference mapping. Biochemistry 41, 3667-3675 (2002).
-
(2002)
Biochemistry
, vol.41
, pp. 3667-3675
-
-
Oyelere, A.K.1
Kardon, J.R.2
Strobel, S.A.3
-
14
-
-
2442641641
-
A conformational switch controls hepatitis delta virus ribozyme catalysis
-
Ke, A., Zhou, K., Ding, F., Cate, J.H. & Doudna, J.A. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429, 201-205 (2004).
-
(2004)
Nature
, vol.429
, pp. 201-205
-
-
Ke, A.1
Zhou, K.2
Ding, F.3
Cate, J.H.4
Doudna, J.A.5
-
15
-
-
0037154091
-
Reaction pathway of the trans-acting hepatitis delta virus ribozyme: A conformational change accompanies catalysis
-
Pereira, M.J., Harris, D.A., Rueda, D. & Walter, N.G. Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis. Biochemistry 41, 730-740 (2002).
-
(2002)
Biochemistry
, vol.41
, pp. 730-740
-
-
Pereira, M.J.1
Harris, D.A.2
Rueda, D.3
Walter, N.G.4
-
16
-
-
0037044320
-
Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis
-
Harris, D.A., Rueda, D. & Walter, N.G. Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis. Biochemistry 41, 12051-12061 (2002).
-
(2002)
Biochemistry
, vol.41
, pp. 12051-12061
-
-
Harris, D.A.1
Rueda, D.2
Walter, N.G.3
-
17
-
-
3042667859
-
Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozymeand its substrate
-
Ouellet, J. & Perreault, J.P. Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozymeand its substrate. RNA 10, 1059-1072 (2004).
-
(2004)
RNA
, vol.10
, pp. 1059-1072
-
-
Ouellet, J.1
Perreault, J.P.2
-
18
-
-
0037418547
-
Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of the hairpin ribozyme
-
Bevilacqua, P.C. Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of the hairpin ribozyme. Biochemistry 42, 2259-2265(2003).
-
(2003)
Biochemistry
, vol.42
, pp. 2259-2265
-
-
Bevilacqua, P.C.1
-
19
-
-
0027949817
-
Value of general acid-base catalysis to ribonuclease-A
-
Thompson, J.E. & Raines, R.T. Value of general acid-base catalysis to ribonuclease-A. J. Am. Chem. Soc. 116, 5467-5468 (1994).
-
(1994)
J. Am. Chem. Soc
, vol.116
, pp. 5467-5468
-
-
Thompson, J.E.1
Raines, R.T.2
-
20
-
-
0029818948
-
Mechanistic consequences of mutation of active site carboxylates in a retaining β-1,4-glycanase from
-
MacLeod, A.M., Tull, D., Rupitz, K., Warren, R.A. & Withers, S.G. Mechanistic consequences of mutation of active site carboxylates in a retaining β-1,4-glycanase from Cellulomonas fimi. Biochemistry 35, 13165-13172 (1996).
-
(1996)
Cellulomonas Fimi. Biochemistry
, vol.35
, pp. 13165-13172
-
-
Macleod, A.M.1
Tull, D.2
Rupitz, K.3
Warren, R.A.4
Withers, S.G.5
-
21
-
-
0034635121
-
Effects on general acid catalysis from mutations of the invariant tryptophan and arginine residues in the protein tyrosine phosphatase from Yersinia
-
Hoff, R.H., Hengge, A.C., Wu, L., Keng, Y.F. & Zhang, Z.Y. Effects on general acid catalysis from mutations of the invariant tryptophan and arginine residues in the protein tyrosine phosphatase from Yersinia. Biochemistry 39, 46-54 (2000).
-
(2000)
Biochemistry
, vol.39
, pp. 46-54
-
-
Hoff, R.H.1
Hengge, A.C.2
Wu, L.3
Keng, Y.F.4
Zhang, Z.Y.5
-
22
-
-
0034142032
-
The role of the cleavage site 2′-hydroxyl in the Tetrahymena group I ribozyme reaction
-
Yoshida, A., Shan, S., Herschlag, D. & Piccirilli, J.A. The role of the cleavage site 2′-hydroxyl in the Tetrahymena group I ribozyme reaction. Chem. Biol. 7, 85-96 (2000).
-
(2000)
Chem. Biol.
, vol.7
, pp. 85-96
-
-
Yoshida, A.1
Shan, S.2
Herschlag, D.3
Piccirilli, J.A.4
-
23
-
-
0037425552
-
A novel calcium-dependent bacterial phosphatidylinositol-specific phospholipase C displaying unprecedented magnitudes of thio effect, inverse thio effect, and stereoselectivity
-
Zhao, L., Liu, Y., Bruzik, K.S. & Tsai, M.D. A novel calcium-dependent bacterial phosphatidylinositol-specific phospholipase C displaying unprecedented magnitudes of thio effect, inverse thio effect, and stereoselectivity. J. Am. Chem. Soc. 125, 22-23 (2003).
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 22-23
-
-
Zhao, L.1
Liu, Y.2
Bruzik, K.S.3
Tsai, M.D.4
-
24
-
-
0033634688
-
Catalytic mechanism of DNA topoisomerase IB
-
Krogh, B.O. & Shuman, S. Catalytic mechanism of DNA topoisomerase IB. Mol. Cell 5, 1035-1041 (2000).
-
(2000)
Mol. Cell
, vol.5
, pp. 1035-1041
-
-
Krogh, B.O.1
Shuman, S.2
-
25
-
-
0031006592
-
Application of a 5′-bridging phosphorothioate to probe divalent metal and hammerhead ribozyme mediated RNA cleavage
-
Kuimelis, R.G. & McLaughlin, L.W. Application of a 5′-bridging phosphorothioate to probe divalent metal and hammerhead ribozyme mediated RNA cleavage. Bioorg. Med. Chem. 5, 1051-1061 (1997).
-
(1997)
Bioorg. Med. Chem.
, vol.5
, pp. 1051-1061
-
-
Kuimelis, R.G.1
McLaughlin, L.W.2
-
26
-
-
0031461748
-
Explanation by the double-metal-ionmechanism of catalysis for the differential metal ion effects on the cleavage rates of 5′-oxyand 5′-thio substrates by a hammerhead ribozyme
-
Zhou, D.M., Zhang, L.H. & Taira, K. Explanation by the double-metal-ionmechanism of catalysis for the differential metal ion effects on the cleavage rates of 5′-oxyand 5′-thio substrates by a hammerhead ribozyme. Proc. Natl. Acad. Sci. USA 94, 14343-14348 (1997).
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 14343-14348
-
-
Zhou, D.M.1
Zhang, L.H.2
Taira, K.3
-
27
-
-
1942520502
-
Carboxyl-group participation in phosphorothioate hydrolysis: Hydrolysis of s-(2-carboxyphenyl) phosphorothioate
-
Fife, T.H. & Milstien, S. Carboxyl-group participation in phosphorothioate hydrolysis: hydrolysis of s-(2-carboxyphenyl) phosphorothioate. J. Org. Chem. 34, 4007-4012 (1969).
-
(1969)
J. Org. Chem.
, vol.34
, pp. 4007-4012
-
-
Fife, T.H.1
Milstien, S.2
-
28
-
-
0032125579
-
Caged RNA: Photo-control of a ribozyme reaction
-
Chaulk, S.G. & MacMillan, A.M. Caged RNA: photo-control of a ribozyme reaction. Nucleic Acids Res. 26, 3173-3178 (1998).
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 3173-3178
-
-
Chaulk, S.G.1
Macmillan, A.M.2
-
29
-
-
0040778233
-
Kinetic scheme for intermolecular RNA cleavage by a ribozyme derived from hepatitis delta virus RNA
-
Shih, I. & Been, M.D. Kinetic scheme for intermolecular RNA cleavage by a ribozyme derived from hepatitis delta virus RNA. Biochemistry 39, 9055-9066 (2000).
-
(2000)
Biochemistry
, vol.39
, pp. 9055-9066
-
-
Shih, I.1
Been, M.D.2
-
30
-
-
0347763707
-
Catalytic roles for proton transfer and protonation in ribozymes
-
Bevilacqua, P.C., Brown, T.S., Nakano, S. & Yajima, R. Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers 73, 90-109 (2004).
-
(2004)
Biopolymers
, vol.73
, pp. 90-109
-
-
Bevilacqua, P.C.1
Brown, T.S.2
Nakano, S.3
Yajima, R.4
-
31
-
-
0035085466
-
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent inter actions
-
Juneau, K., Podell, E., Harrington, D.J. & Cech, T.R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent inter actions. Structure 9, 221-231 (2001).
-
(2001)
Structure
, vol.9
, pp. 221-231
-
-
Juneau, K.1
Podell, E.2
Harrington, D.J.3
Cech, T.R.4
-
32
-
-
0033536648
-
Synthesis of the analogue nucleoside 3-deaza-2′-deoxycytidine and its template activity with DNA polymerase
-
Searls, T. & McLaughlin, L.W. Synthesis of the analogue nucleoside 3-deaza-2′-deoxycytidine and its template activity with DNA polymerase. Tetrahedron 55, 11985-11996 (1999).
-
(1999)
Tetrahedron
, vol.55
, pp. 11985-11996
-
-
Searls, T.1
McLaughlin, L.W.2
-
33
-
-
84987344598
-
Improved synthesis of 3-deazacytosine, 3-deazauracil, 3-deazacytidine, and 3-deazauridine
-
Cook, P.D., Day, R.T. & Robins, R.K. Improved synthesis of 3-deazacytosine, 3-deazauracil, 3-deazacytidine, and 3-deazauridine. J. Heterocyclic Chem. 14, 1295-1298 (1977).
-
(1977)
J. Heterocyclic Chem
, vol.14
, pp. 1295-1298
-
-
Cook, P.D.1
Day, R.T.2
Robins, R.K.3
-
34
-
-
84984767786
-
Use of analogue nucleosides to probe function in the hammerhead ribozyme
-
(eds. Krupp, G. & Gaur, R.K., Eaton Publishing, Natick, Massachusetts
-
Bevers, S. & Mclaughlin, L.W. Use of analogue nucleosides to probe function in the hammerhead ribozyme. in Ribozyme:Biochemistry and Biotechnology (eds. Krupp, G. & Gaur, R.K.) 171-190 (Eaton Publishing, Natick, Massachusetts, 2000).
-
(2000)
Ribozyme:Biochemistry and Biotechnology
, pp. 171-190
-
-
Bevers, S.1
McLaughlin, L.W.2
-
35
-
-
0026680843
-
Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites
-
Moore, M.J. & Sharp, P.A. Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science 256, 992-997 (1992).
-
(1992)
Science
, vol.256
, pp. 992-997
-
-
Moore, M.J.1
Sharp, P.A.2
-
36
-
-
0034131335
-
Joining of RNAs by splinted ligation
-
Moore, M.J. & Query, C.C. Joining of RNAs by splinted ligation. Methods Enzymol. 317, 109-123 (2000).
-
(2000)
Methods Enzymol
, vol.317
, pp. 109-123
-
-
Moore, M.J.1
Query, C.C.2
-
37
-
-
0035833978
-
Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
-
Nakano, S., Proctor, D.J. & Bevilacqua, P.C. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry 40, 12022-12038 (2001).
-
(2001)
Biochemistry
, vol.40
, pp. 12022-12038
-
-
Nakano, S.1
Proctor, D.J.2
Bevilacqua, P.C.3
-
38
-
-
0030030353
-
Chromatographic properties of cytosine, cytidine and their synthetic analogues
-
Romanova, D. & Novotny, L. Chromatographic properties of cytosine, cytidine and their synthetic analogues. J. Chromatog. B. 675, 9-15(1996).
-
(1996)
J. Chromatog. B.
, vol.675
, pp. 9-15
-
-
Romanova, D.1
Novotny, L.2
-
39
-
-
0029037731
-
Synthesis of 6-aza-pyrimidine and 6-methyl-pyrimidine ribonucleoside phosphoramidites and their incorporation in hammerhead ribozymes
-
Beigelman, L., Karpeisky, A. & Usman, N. Synthesis of 6-aza-pyrimidine and 6-methyl-pyrimidine ribonucleoside phosphoramidites and their incorporation in hammerhead ribozymes. Nucleosides Nucleotides 14, 895-899 (1995).
-
(1995)
Nucleosides Nucleotides
, vol.14
, pp. 895-899
-
-
Beigelman, L.1
Karpeisky, A.2
Usman, N.3
-
40
-
-
0037009368
-
4-thio-U cross-linking identifies the active site of the VS ribozyme
-
Hiley, S.L., Sood, V.D., Fan, J. & Collins, R.A. 4-thio-U cross-linking identifies the active site of the VS ribozyme. EMBO J. 21, 4691-4698 (2002).
-
(2002)
EMBO J
, vol.21
, pp. 4691-4698
-
-
Hiley, S.L.1
Sood, V.D.2
Fan, J.3
Collins, R.A.4
-
41
-
-
1642580826
-
The Varkud satellite ribozyme
-
Lilley, D.M.J. The Varkud satellite ribozyme. RNA 10, 151-158 (2004).
-
(2004)
RNA
, vol.10
, pp. 151-158
-
-
Lilley, D.M.J.1
-
42
-
-
1642586299
-
Control of gene expression by a natural metabolite-responsive ribozyme
-
Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A. & Breaker, R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428,281-286 (2004).
-
(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
-
43
-
-
0024819449
-
Synthesis of small RNAs using T7 RNA polymerase
-
Milligan, J.F. & Uhlenbeck, O.C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51-62 (1989).
-
(1989)
Methods Enzymol
, vol.180
, pp. 51-62
-
-
Milligan, J.F.1
Uhlenbeck, O.C.2
-
44
-
-
0032827799
-
A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase
-
Kao, C., Zheng, M. & Rudisser, S. A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase. RNA 5, 1268-1272 (1999).
-
(1999)
RNA
, vol.5
, pp. 1268-1272
-
-
Kao, C.1
Zheng, M.2
Rudisser, S.3
|