-
1
-
-
3042732096
-
Directed evolution of nucleic acid enzymes
-
G.F. Joyce Directed evolution of nucleic acid enzymes Annu Rev Biochem 73 2004 791 836
-
(2004)
Annu Rev Biochem
, vol.73
, pp. 791-836
-
-
Joyce, G.F.1
-
2
-
-
20444502087
-
Structure, folding and mechanisms of ribozymes
-
D.M. Lilley Structure, folding and mechanisms of ribozymes Curr Opin Struct Biol 15 2005 313 323
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 313-323
-
-
Lilley, D.M.1
-
3
-
-
0342313543
-
Evolution of DNA and RNA as catalysts for chemical reactions
-
A. Jäschke, and B. Seelig Evolution of DNA and RNA as catalysts for chemical reactions Curr Opin Chem Biol 4 2000 257 262
-
(2000)
Curr Opin Chem Biol
, vol.4
, pp. 257-262
-
-
Jäschke, A.1
Seelig, B.2
-
4
-
-
20444496805
-
Structure and assembly of group I introns
-
S.A. Woodson Structure and assembly of group I introns Curr Opin Struct Biol 15 2005 324 330
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 324-330
-
-
Woodson, S.A.1
-
6
-
-
20444441572
-
Ribozyme catalysis: Not different, just worse
-
J.A. Doudna, and J.R. Lorsch Ribozyme catalysis: not different, just worse Nat Struct Mol Biol 12 2005 395 402
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 395-402
-
-
Doudna, J.A.1
Lorsch, J.R.2
-
8
-
-
0041305819
-
A common speed limit for RNA-cleaving ribozymes and deoxyribozymes
-
R.R. Breaker, G.M. Emilsson, D. Lazarev, S. Nakamura, I.J. Puskarz, A. Roth, and N. Sudarsan A common speed limit for RNA-cleaving ribozymes and deoxyribozymes RNA 9 2003 949 957
-
(2003)
RNA
, vol.9
, pp. 949-957
-
-
Breaker, R.R.1
Emilsson, G.M.2
Lazarev, D.3
Nakamura, S.4
Puskarz, I.J.5
Roth, A.6
Sudarsan, N.7
-
9
-
-
3242670633
-
Ribozymes in the age of molecular therapeutics
-
S. Bagheri, and M. Kashani-Sabet Ribozymes in the age of molecular therapeutics Curr Mol Med 4 2004 489 506
-
(2004)
Curr Mol Med
, vol.4
, pp. 489-506
-
-
Bagheri, S.1
Kashani-Sabet, M.2
-
10
-
-
3242759845
-
Deoxyribozymes: Cleaving a path to clinical trials
-
C.R. Dass Deoxyribozymes: cleaving a path to clinical trials Trends Pharmacol Sci 25 2004 395 397
-
(2004)
Trends Pharmacol Sci
, vol.25
, pp. 395-397
-
-
Dass, C.R.1
-
11
-
-
1642458402
-
Prospects for antiviral ribozymes and deoxyribozymes
-
A. Peracchi Prospects for antiviral ribozymes and deoxyribozymes Rev Med Virol 14 2004 47 64
-
(2004)
Rev Med Virol
, vol.14
, pp. 47-64
-
-
Peracchi, A.1
-
12
-
-
0037153125
-
Molecular evolution: Booting up life
-
G.F. Joyce Molecular evolution: booting up life Nature 420 2002 278 279
-
(2002)
Nature
, vol.420
, pp. 278-279
-
-
Joyce, G.F.1
-
13
-
-
0142043439
-
Stereoselective synthesis using immobilized Diels-Alderase ribozymes
-
J.C. Schlatterer, F. Stuhlmann, and A. Jäschke Stereoselective synthesis using immobilized Diels-Alderase ribozymes ChemBioChem 4 2003 1089 1092
-
(2003)
ChemBioChem
, vol.4
, pp. 1089-1092
-
-
Schlatterer, J.C.1
Stuhlmann, F.2
Jäschke, A.3
-
15
-
-
0042320360
-
An alcohol dehydrogenase ribozyme
-
7. A minimal catalytic motif only 76 nucleotide long and having identical activity as the wild-type sequence, could be identified.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 713-717
-
-
Tsukiji, S.1
Pattnaik, S.B.2
Suga, H.3
-
17
-
-
0041305988
-
The first example of an RNA urea synthase: Selection through the enzyme active site of human neutrophile elastase
-
D. Nieuwlandt, M. West, X. Cheng, G. Kirshenheuter, and B.E. Eaton The first example of an RNA urea synthase: selection through the enzyme active site of human neutrophile elastase ChemBioChem 4 2003 651 654 Unexpectedly, urea bond formation did not take place at the expected primary amino group tethered to the RNA sequences via a flexible polyethylene glycol spacer.
-
(2003)
ChemBioChem
, vol.4
, pp. 651-654
-
-
Nieuwlandt, D.1
West, M.2
Cheng, X.3
Kirshenheuter, G.4
Eaton, B.E.5
-
19
-
-
0032541654
-
RNA-catalyzed nucleotide synthesis
-
P.J. Unrau, and D.P. Bartel RNA-catalyzed nucleotide synthesis Nature 395 1998 260 263
-
(1998)
Nature
, vol.395
, pp. 260-263
-
-
Unrau, P.J.1
Bartel, D.P.2
-
20
-
-
0141606847
-
Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme
-
K.E. Chapple, D.P. Bartel, and P.J. Unrau Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme RNA 9 2003 1208 1220
-
(2003)
RNA
, vol.9
, pp. 1208-1220
-
-
Chapple, K.E.1
Bartel, D.P.2
Unrau, P.J.3
-
21
-
-
15444362048
-
Ribozyme motif structure mapped using random recombination and selection
-
Q.S. Wang, and P.J. Unrau Ribozyme motif structure mapped using random recombination and selection RNA 11 2005 404 411 This experimental method seems a very efficient way of determining a ribozyme core motif in an unbiased way and it is very likely that it will have a great impact in future research on catalytically active RNA structures.
-
(2005)
RNA
, vol.11
, pp. 404-411
-
-
Wang, Q.S.1
Unrau, P.J.2
-
22
-
-
0035906978
-
RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension
-
W.K. Johnston, P.J. Unrau, M.S. Lawrence, M.E. Glasner, and D.P. Bartel RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension Science 292 2001 1319 1325
-
(2001)
Science
, vol.292
, pp. 1319-1325
-
-
Johnston, W.K.1
Unrau, P.J.2
Lawrence, M.S.3
Glasner, M.E.4
Bartel, D.P.5
-
23
-
-
0042347704
-
Processivity of ribozyme-catalyzed RNA polymerization
-
M.S. Lawrence, and D.P. Bartel Processivity of ribozyme-catalyzed RNA polymerization Biochemistry 42 2003 8748 8755
-
(2003)
Biochemistry
, vol.42
, pp. 8748-8755
-
-
Lawrence, M.S.1
Bartel, D.P.2
-
24
-
-
8844224949
-
Cross-catalytic replication of an RNA ligase ribozyme
-
D.E. Kim, and G.F. Joyce Cross-catalytic replication of an RNA ligase ribozyme Chem Biol 11 2004 1505 1512 The rate of cross-catalytic replication observed for this system was only modest, but the efficiency and specificity of the two-component reactions were sufficient to ensure that the cross-catalytic pathway was dominating over the possible formation of promiscuous products.
-
(2004)
Chem Biol
, vol.11
, pp. 1505-1512
-
-
Kim, D.E.1
Joyce, G.F.2
-
25
-
-
0041629325
-
A versatile tRNA aminoacylation catalyst based on RNA
-
H. Murakami, H. Saito, and H. Suga A versatile tRNA aminoacylation catalyst based on RNA Chem Biol 10 2003 655 662
-
(2003)
Chem Biol
, vol.10
, pp. 655-662
-
-
Murakami, H.1
Saito, H.2
Suga, H.3
-
26
-
-
15544388643
-
Ribozyme-catalyzed aminoacylation from CoA thioesters
-
N. Li, and F. Huang Ribozyme-catalyzed aminoacylation from CoA thioesters Biochemistry 44 2005 4582 4590
-
(2005)
Biochemistry
, vol.44
, pp. 4582-4590
-
-
Li, N.1
Huang, F.2
-
27
-
-
14544275165
-
From peptide-bond formation to cotranslational folding: Dynamic, regulatory and evolutionary aspects
-
D. Baram, and A. Yonath From peptide-bond formation to cotranslational folding: dynamic, regulatory and evolutionary aspects FEBS Lett 579 2005 948 954
-
(2005)
FEBS Lett
, vol.579
, pp. 948-954
-
-
Baram, D.1
Yonath, A.2
-
28
-
-
7544220590
-
Substrate-assisted catalysis of peptide bond formation by the ribosome
-
J.S. Weinger, K.M. Parnell, S. Dorner, R. Green, and S.A. Strobel Substrate-assisted catalysis of peptide bond formation by the ribosome Nat Struct Mol Biol 11 2004 1101 1106
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 1101-1106
-
-
Weinger, J.S.1
Parnell, K.M.2
Dorner, S.3
Green, R.4
Strobel, S.A.5
-
29
-
-
20244375551
-
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation
-
A. Serganov, S. Keiper, L. Malinina, V. Tereshko, E. Skripkin, C. Höbartner, A. Polonskaia, A.T. Phan, R. Wombacher, and R. Micura Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation Nat Struct Mol Biol 12 2005 218 224 The catalytic site architecture reveals that catalysis is achieved by a combination of proximity, complementarity, and electronic effects. Striking structural parallels are observed with the active site of a catalytic antibody evolved for a similar reaction and involving anthracene as the diene. This suggests that common structural principles and catalytic mechanisms are at work in macromolecule-mediated catalysis of Diels-Alder reactions.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 218-224
-
-
Serganov, A.1
Keiper, S.2
Malinina, L.3
Tereshko, V.4
Skripkin, E.5
Höbartner, C.6
Polonskaia, A.7
Phan, A.T.8
Wombacher, R.9
Micura, R.10
-
30
-
-
4644305780
-
Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket
-
S. Keiper, D. Bebenroth, B. Seelig, E. Westhof, and A. Jäschke Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket Chem Biol 11 2004 1217 1227 Unlike many other biopolymeric systems, this ribozyme does not show induced fit recognition upon substrate binding.
-
(2004)
Chem Biol
, vol.11
, pp. 1217-1227
-
-
Keiper, S.1
Bebenroth, D.2
Seelig, B.3
Westhof, E.4
Jäschke, A.5
-
31
-
-
4644272645
-
The effect of mutation on RNA Diels-Alderases
-
T.M. Tarasow, E. Kellogg, B.L. Holley, D. Nieuwlandt, S.L. Tarasow, and B.E. Eaton The effect of mutation on RNA Diels-Alderases J Am Chem Soc 126 2004 11843 11851
-
(2004)
J Am Chem Soc
, vol.126
, pp. 11843-11851
-
-
Tarasow, T.M.1
Kellogg, E.2
Holley, B.L.3
Nieuwlandt, D.4
Tarasow, S.L.5
Eaton, B.E.6
-
32
-
-
2442566895
-
RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles
-
L.A. Gugliotti, D.L. Feldheim, and B.E. Eaton RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles Science 304 2004 850 852
-
(2004)
Science
, vol.304
, pp. 850-852
-
-
Gugliotti, L.A.1
Feldheim, D.L.2
Eaton, B.E.3
-
33
-
-
6344219578
-
Deoxyribozymes: DNA catalysts for bioorganic chemistry
-
S.K. Silverman Deoxyribozymes: DNA catalysts for bioorganic chemistry Org Biomol Chem 2 2004 2701 2706
-
(2004)
Org Biomol Chem
, vol.2
, pp. 2701-2706
-
-
Silverman, S.K.1
-
34
-
-
11444249690
-
Rational modification of a selection strategy leads to deoxyribozymes that create native 3′-5′ RNA linkages
-
R.L. Coppins, and S.K. Silverman Rational modification of a selection strategy leads to deoxyribozymes that create native 3′-5′ RNA linkages J Am Chem Soc 126 2004 16426 16432
-
(2004)
J Am Chem Soc
, vol.126
, pp. 16426-16432
-
-
Coppins, R.L.1
Silverman, S.K.2
-
35
-
-
14344263295
-
Directing the outcome of deoxyribozyme selections to favor native 3′-5′ RNA ligation
-
Y. Wang, and S.K. Silverman Directing the outcome of deoxyribozyme selections to favor native 3′-5′ RNA ligation Biochemistry 44 2005 3017 3023 The substrates used in these selections were related either to the natural sequences of spliceosome substrates or to group II introns. Even an already evolved population of DNAzymes, estimated to contain less than 1% sequences catalyzing 3′-5′ linkages, gave, after only four additional selection cycles, 23 out of 24 isolated clones with the desired 3′- 5′ ligase activity.
-
(2005)
Biochemistry
, vol.44
, pp. 3017-3023
-
-
Wang, Y.1
Silverman, S.K.2
-
36
-
-
1142281951
-
Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme
-
R.P.G. Cruz, J.B. Withers, and Y. Li Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme Chem Biol 11 2004 57 67
-
(2004)
Chem Biol
, vol.11
, pp. 57-67
-
-
Cruz, R.P.G.1
Withers, J.B.2
Li, Y.3
-
37
-
-
0030898510
-
A general purpose RNA-cleaving DNA enzyme
-
S.W. Santoro, and G.F. Joyce A general purpose RNA-cleaving DNA enzyme Proc Natl Acad Sci USA 94 1997 4262 4266
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 4262-4266
-
-
Santoro, S.W.1
Joyce, G.F.2
-
39
-
-
0038209225
-
A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles
-
2+.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 6642-6643
-
-
Liu, J.1
Lu, Y.2
-
41
-
-
4544365768
-
An autonomous DNA nanomotor powered by a DNA enzyme
-
Y. Chen, M. Wang, and C. Mao An autonomous DNA nanomotor powered by a DNA enzyme Angew Chem Int Ed Engl 43 2004 3554 3557
-
(2004)
Angew Chem Int Ed Engl
, vol.43
, pp. 3554-3557
-
-
Chen, Y.1
Wang, M.2
Mao, C.3
-
42
-
-
5644237711
-
Triggering DNAzymes with light: A photoactive C8 thioether-linked adenosine
-
R. Ting, L. Lermer, and D.M. Perrin Triggering DNAzymes with light: a photoactive C8 thioether-linked adenosine J Am Chem Soc 126 2004 12720 12721
-
(2004)
J Am Chem Soc
, vol.126
, pp. 12720-12721
-
-
Ting, R.1
Lermer, L.2
Perrin, D.M.3
-
43
-
-
3843088438
-
Light-regulated catalysis by an RNA-cleaving deoxyribozyme
-
Y. Liu, and D. Sen Light-regulated catalysis by an RNA-cleaving deoxyribozyme J Mol Biol 341 2004 887 892
-
(2004)
J Mol Biol
, vol.341
, pp. 887-892
-
-
Liu, Y.1
Sen, D.2
-
44
-
-
3342955521
-
Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection
-
K. Schlosser, and Y. Li Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection Biochemistry 43 2004 9695 9707
-
(2004)
Biochemistry
, vol.43
, pp. 9695-9707
-
-
Schlosser, K.1
Li, Y.2
-
45
-
-
13544253729
-
Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: A putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation
-
R. Ting, J.M. Thomas, L. Lermer, and D.M. Perrin Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation Nucleic Acids Res 32 2004 6660 6672
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6660-6672
-
-
Ting, R.1
Thomas, J.M.2
Lermer, L.3
Perrin, D.M.4
-
46
-
-
1842618467
-
Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities
-
A.V. Sidorov, J.A. Grasby, and D.M. Williams Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities Nucleic Acids Res 32 2004 1591 1601
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1591-1601
-
-
Sidorov, A.V.1
Grasby, J.A.2
Williams, D.M.3
-
47
-
-
1842607442
-
2+-independent AP-endonuclease mimic
-
2+-independent AP-endonuclease mimic J Am Chem Soc 126 2004 4145 4156 The formation of a Schiff base intermediate between the abasic DNA substrate and a primary amino group carried by the catalyst was inferred by several data including the actual identification of a product-catalyst Schiff base adduct.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 4145-4156
-
-
May, J.P.1
Ting, R.2
Lermer, L.3
Thomas, J.M.4
Roupioz, Y.5
Perrin, D.M.6
-
48
-
-
3042549466
-
A novel strategy for selection of allosteric ribozymes yields RiboReporter sensors for caffeine and aspartame
-
A. Ferguson, R.M. Boomer, M. Kurz, S.C. Keene, J.L. Diener, A.D. Keefe, C. Wilson, and S.T. Cload A novel strategy for selection of allosteric ribozymes yields RiboReporter sensors for caffeine and aspartame Nucleic Acids Res 32 2004 1756 1766
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1756-1766
-
-
Ferguson, A.1
Boomer, R.M.2
Kurz, M.3
Keene, S.C.4
Diener, J.L.5
Keefe, A.D.6
Wilson, C.7
Cload, S.T.8
-
49
-
-
0033797244
-
Nucleic acid aptamers - From selection in vitro to applications in vivo
-
M. Famulok, G. Mayer, and M. Blind Nucleic acid aptamers - from selection in vitro to applications in vivo Acc Chem Res 33 2000 591 599
-
(2000)
Acc Chem Res
, vol.33
, pp. 591-599
-
-
Famulok, M.1
Mayer, G.2
Blind, M.3
-
50
-
-
13844315455
-
Engineered allosteric ribozymes that respond to specific divalent metal ions
-
M. Zivarts, Y. Liu, and R.R. Breaker Engineered allosteric ribozymes that respond to specific divalent metal ions Nucleic Acids Res 33 2005 622 631
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 622-631
-
-
Zivarts, M.1
Liu, Y.2
Breaker, R.R.3
-
51
-
-
0346992203
-
In vitro selection of ribozymes dependent on peptides for activity
-
M.P. Robertson, S.M. Knudsen, and A.D. Ellington In vitro selection of ribozymes dependent on peptides for activity RNA 10 2004 114 127
-
(2004)
RNA
, vol.10
, pp. 114-127
-
-
Robertson, M.P.1
Knudsen, S.M.2
Ellington, A.D.3
-
52
-
-
23044436253
-
Allosterically activated Diels-Alder catalysis by a ribozyme
-
M. Helm, M. Petermeier, B. Ge, R. Fiammengo, and A. Jäschke Allosterically activated Diels-Alder catalysis by a ribozyme J Am Chem Soc 127 2005 10492 10493
-
(2005)
J Am Chem Soc
, vol.127
, pp. 10492-10493
-
-
Helm, M.1
Petermeier, M.2
Ge, B.3
Fiammengo, R.4
Jäschke, A.5
-
53
-
-
14844365734
-
Target-dependent on/off switch increases ribozyme fidelity
-
L.J. Bergeron, and J.-P. Perreault Target-dependent on/off switch increases ribozyme fidelity Nucleic Acids Res 33 2005 1240 1248
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1240-1248
-
-
Bergeron, L.J.1
Perreault, J.-P.2
-
55
-
-
1642586299
-
Control of gene expression by a natural metabolite-responsive ribozyme
-
W.C. Winkler, A. Nahvi, A. Roth, J.A. Collins, and R.R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme Nature 428 2004 281 286 By correlating the in vitro ribozyme activity with the in vivo activity of a β-galactosidase reporter gene, it was possible to show that the ribozyme activity represses the glmS gene, thus keeping the production of GlcN6P under control.
-
(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
-
56
-
-
0038136962
-
Metabolite-binding RNA domains are present in the genes of eukaryotes
-
N. Sudarsan, J.E. Barrick, and R.R. Breaker Metabolite-binding RNA domains are present in the genes of eukaryotes RNA 9 2003 644 647
-
(2003)
RNA
, vol.9
, pp. 644-647
-
-
Sudarsan, N.1
Barrick, J.E.2
Breaker, R.R.3
-
57
-
-
0037013983
-
Glucosamine-6-phosphate synthase - The multi-facets enzyme
-
S. Milewski Glucosamine-6-phosphate synthase - the multi-facets enzyme Biochim Biophys Acta 1597 2002 173 192
-
(2002)
Biochim Biophys Acta
, vol.1597
, pp. 173-192
-
-
Milewski, S.1
|