-
1
-
-
0041305819
-
A common speed limit for r na-cleaving ribozymes and deoxyribozymes
-
Breaker RR, Emilsson GM, Lazarev D, Nakamura S, Puskarz IJ, Roth A, Sudarsan N. 2003. A common speed limit for R NA-cleaving ribozymes and deoxyribozymes. RNA 9: 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
-
2
-
-
4444297561
-
Fast cleavage kinetics of a natural hammerhead ribozyme
-
Canny MD, Jucker FM, Kellogg E, Khvorova A, Jayasena SD, 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
-
3
-
-
33846279049
-
Structural investigation of the glms ribozyme bound to its catalytic cofactor
-
Cochrane JC, Lipchock SV, Strobel SA. 2007. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem Biol 14: 97-105.
-
(2007)
Chem Biol
, vol.14
, pp. 97-105
-
-
Cochrane, J.C.1
Lipchock, S.V.2
Strobel, S.A.3
-
4
-
-
0027400338
-
Metallobiochemistry of RNA. Co(nh3)6 3+ as a probe for mg2+(aq) binding sites
-
Cow an JA. 1993. Metallobiochemistry of RNA. Co(NH3)6 3+ as a probe for Mg2+(aq) binding sites. J Inorg Biochem 49: 171-175.
-
(1993)
J Inorg Biochem
, vol.49
, pp. 171-175
-
-
Cowan, J.A.1
-
5
-
-
0035020626
-
The hammerhead cleavage reaction in monovalent cations
-
Curtis EA, Bartel DP. 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
-
6
-
-
0025998488
-
Role of divalent metal ions in the hammerhead RNA cleavage reaction
-
Dahm SC, Uhlenbeck OC. 1991. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30: 9464-9469.
-
(1991)
Biochemistry
, vol.30
, pp. 9464-9469
-
-
Dahm, S.C.1
Uhlenbeck, O.C.2
-
7
-
-
84906972053
-
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme
-
Eiler D, Wang J, Steitz TA. 2014. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proc Natl Acad Sci 111: 13028-13033.
-
(2014)
Proc Natl Acad Sci
, vol.111
, pp. 13028-13033
-
-
Eiler, D.1
Wang, J.2
Steitz, T.A.3
-
11
-
-
0031194873
-
A unique mechanism for RNA catalysis: The role of metal cofactors in hairpin ribozyme cleavage
-
Hampel A, Cowan JA. 1997. A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem Biol 4: 513-517.
-
(1997)
Chem Biol
, vol.4
, pp. 513-517
-
-
Hampel, A.1
Cowan, J.A.2
-
13
-
-
0018627368
-
Diastereomers of the nucleoside phosphorothioates as probes of the structure of the metal nucleotide substrates and of the nucleotide binding site of yeast hexokinase
-
Jaffe EK, Cohn M. 1979. Diastereomers of the nucleoside phosphorothioates as probes of the structure of the metal nucleotide substrates and of the nucleotide binding site of yeast hexokinase. J Biol Chem 254: 10839-10845.
-
(1979)
J Biol Chem
, vol.254
, pp. 10839-10845
-
-
Jaffe, E.K.1
Cohn, M.2
-
14
-
-
33748325570
-
Structural basis of glms ribozyme activation by glucosamine-6-phosphate
-
Klein DJ, Ferré-D'AmaréAR. 2006. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313: 1752-1756.
-
(2006)
Science
, vol.313
, pp. 1752-1756
-
-
Klein, D.J.1
Ferré-D'Amaré, A.R.2
-
15
-
-
0033575087
-
Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2?-hydroxyl group
-
Li Y, Breaker RR. 1999. Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2?-hydroxyl group. J Am Chem Soc 121: 5364-5372.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 5364-5372
-
-
Li, Y.1
Breaker, R.R.2
-
16
-
-
84906317571
-
Crystal structure and mechanistic investigation of the twister ribozyme
-
Liu Y, Wilson TJ, McPhee SA, Lilley DM. 2014. Crystal structure and mechanistic investigation of the twister ribozyme. Nat Chem Biol 10: 739-744.
-
(2014)
Nat Chem Biol
, vol.10
, pp. 739-744
-
-
Liu, Y.1
Wilson, T.J.2
McPhee, S.A.3
Lilley, D.M.4
-
17
-
-
34547622435
-
In-line attack'conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: A free energy simulation study
-
Min D, Xue S, Li H, YangW. 2007. ' In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study. Nucleic Acids Res 35: 4001-4006.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4001-4006
-
-
Min, D.1
Xue, S.2
Li, H.3
Yang, W.4
-
18
-
-
84890037468
-
InfeRNAl 1.1: 100-fold faster RNA homology searches
-
Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
19
-
-
0021769550
-
Stability constants of mg2+ and cd2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of mgatp and mgadp
-
Pecoraro VL, Hermes JD, Cleland WW. 1984. Stability constants of Mg2+ and Cd2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP. Biochemistry 23: 5262-5271.
-
(1984)
Biochemistry
, vol.23
, pp. 5262-5271
-
-
Pecoraro, V.L.1
Hermes, J.D.2
Cleland, W.W.3
-
20
-
-
79953002042
-
Identification of hammerhead ribozymes in all domains of life reveals novel structural variations
-
Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR. 2011. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol 7: e1002031.
-
(2011)
PLoS Comput Biol
, vol.7
, pp. e1002031
-
-
Perreault, J.1
Weinberg, Z.2
Roth, A.3
Popescu, O.4
Chartrand, P.5
Ferbeyre, G.6
Breaker, R.R.7
-
21
-
-
33846057724
-
Ncbi reference sequences (refseq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt KD,Tatusova T,Maglott DR. 2007 NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 35 D61-D6 5.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D61-D65
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
22
-
-
84922555795
-
In-line alignment and mg2+ coordination at the cleavage site of the env22 twister ribozyme
-
Ren A, Ko͉uticM, Rajashankar KR, Frener M, Santner T, Westhof E, Micura R, Patel DJ. 2014. In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme. Nat Commun 5: 5534.
-
(2014)
Nat Commun
, vol.5
, pp. 5534
-
-
Ren, A.1
Ko͉utic, M.2
Rajashankar, K.R.3
Frener, M.4
Santner, T.5
Westhof, E.6
Micura, R.7
Patel, D.J.8
-
23
-
-
33645462033
-
Characteristics of the glms ribozyme suggest only structural roles for divalent metal ions
-
Roth A, Nahvi A, Lee M, Jona I, Breaker RR. 2006. Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA 12: 607-619.
-
(2006)
RNA
, vol.12
, pp. 607-619
-
-
Roth, A.1
Nahvi, A.2
Lee, M.3
Jona, I.4
Breaker, R.R.5
-
24
-
-
84891008536
-
A widespread self-cleaving ribozyme class is revealed by bioinformatics
-
Roth A, Weinberg Z, Ch en AG, Kim PB, Ames TD, Breaker RR. 2014. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol 10: 56-60.
-
(2014)
Nat Chem Biol
, vol.10
, pp. 56-60
-
-
Roth, A.1
Weinberg, Z.2
Chen, A.G.3
Kim, P.B.4
Ames, T.D.5
Breaker, R.R.6
-
25
-
-
0032831634
-
Relationship between internucleotide linkage geometry and the stability of RNA
-
Soukup GA, Breaker RR. 1999. 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
-
26
-
-
84884235787
-
Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme
-
Thaplyal P, Ganguly A, Golden BL, Hammes-Schiffer S, Bevilacqua PC. 2013. Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Biochemistry 52: 6499-6514.
-
(2013)
Biochemistry
, vol.52
, pp. 6499-6514
-
-
Thaplyal, P.1
Ganguly, A.2
Golden, B.L.3
Hammes-Schiffer, S.4
Bevilacqua, P.C.5
-
27
-
-
0000806492
-
Hydrolytic stability of helical RNA: A selective advantage for the natural 3?,5?-bond
-
Usher DA, McHale AH. 1976. Hydrolytic stability of helical RNA: A selective advantage for the natural 3?,5?-bond. Proc Natl Acad Sci 73: 1149-1153.
-
(1976)
Proc Natl Acad Sci
, vol.73
, pp. 1149-1153
-
-
Usher, D.A.1
McHale, A.H.2
-
28
-
-
80052822183
-
Hdv-like self-cleaving ribozymes
-
Webb CT, Lupták A. 2011. HDV-like self-cleaving ribozymes. RNA Biol 8: 719-727.
-
(2011)
RNA Biol
, vol.8
, pp. 719-727
-
-
Webb, C.T.1
Lupták, A.2
-
29
-
-
78650791283
-
R2r-software to speed the depiction of aesthetic consensus RNA secondary structures
-
Weinberg Z, Breaker RR. 2011. R2R-software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics 12: 3.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 3
-
-
Weinberg, Z.1
Breaker, R.R.2
-
30
-
-
77951606278
-
Comparative genomics reveals 104 candidate structured rnas from bacteria, archaea, and their metagenomes
-
Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. 2010. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 11: R3 1.
-
(2010)
Genome Biol
, vol.11
, pp. R31
-
-
Weinberg, Z.1
Wang, J.X.2
Bogue, J.3
Yang, J.4
Corbino, K.5
Moy, R.H.6
Breaker, R.R.7
-
31
-
-
84937399217
-
New classes of self-cleaving ribozymes revealed by comparative genomics analysis
-
Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lünse CE, Breaker RR. 2015. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol 11: 606-610.
-
(2015)
Nat Chem Biol
, vol.11
, pp. 606-610
-
-
Weinberg, Z.1
Kim, P.B.2
Chen, T.H.3
Li, S.4
Harris, K.A.5
Lünse, C.E.6
Breaker, R.R.7
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