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For: Canny MD, Jucker FM, Pardi A. Efficient ligation of the Schistosoma hammerhead ribozyme. Biochemistry 2007;46:3826-34. [PMID: 17319693 PMCID: PMC3203546 DOI: 10.1021/bi062077r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023;12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
2
Vicino MF, Wuebben C, Kerzhner M, Famulok M, Schiemann O. Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation. Methods Mol Biol 2022;2439:205-221. [PMID: 35226324 DOI: 10.1007/978-1-0716-2047-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
3
Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets. Int J Mol Sci 2021;22:ijms222413526. [PMID: 34948321 PMCID: PMC8707343 DOI: 10.3390/ijms222413526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022]  Open
4
Lihanova Y, Weinberg CE. Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa. RNA Biol 2021;18:1858-1866. [PMID: 33622172 DOI: 10.1080/15476286.2021.1874706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]  Open
5
Cervera A, de la Peña M. Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes. Nucleic Acids Res 2020;48:5054-5064. [PMID: 32198887 PMCID: PMC7229834 DOI: 10.1093/nar/gkaa187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022]  Open
6
Lilley DM. Classification of the nucleolytic ribozymes based upon catalytic mechanism. F1000Res 2019;8:F1000 Faculty Rev-1462. [PMID: 31489181 PMCID: PMC6707401 DOI: 10.12688/f1000research.19324.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/08/2019] [Indexed: 12/29/2022]  Open
7
Maurel MC, Leclerc F, Vergne J, Zaccai G. RNA Back and Forth: Looking through Ribozyme and Viroid Motifs. Viruses 2019;11:E283. [PMID: 30901893 PMCID: PMC6466107 DOI: 10.3390/v11030283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022]  Open
8
O'Rourke SM, Scott WG. Structural Simplicity and Mechanistic Complexity in the Hammerhead Ribozyme. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018;159:177-202. [PMID: 30340787 DOI: 10.1016/bs.pmbts.2018.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
9
Cordero T, Ortolá B, Daròs JA. Mutational Analysis of Eggplant Latent Viroid RNA Circularization by the Eggplant tRNA Ligase in Escherichia coli. Front Microbiol 2018;9:635. [PMID: 29675002 PMCID: PMC5895719 DOI: 10.3389/fmicb.2018.00635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022]  Open
10
Lilley DMJ. How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes. Biochem Soc Trans 2017;45:683-691. [PMID: 28620029 DOI: 10.1042/bst20160158] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 02/11/2024]
11
Liu Y, Wilson TJ, Lilley DM. The structure of a nucleolytic ribozyme that employs a catalytic metal ion. Nat Chem Biol 2017;13:508-513. [PMID: 28263963 PMCID: PMC5392355 DOI: 10.1038/nchembio.2333] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023]
12
de la Peña M, García-Robles I, Cervera A. The Hammerhead Ribozyme: A Long History for a Short RNA. Molecules 2017;22:molecules22010078. [PMID: 28054987 PMCID: PMC6155905 DOI: 10.3390/molecules22010078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 01/22/2023]  Open
13
Daròs JA. Eggplant latent viroid: a friendly experimental system in the family Avsunviroidae. MOLECULAR PLANT PATHOLOGY 2016;17:1170-7. [PMID: 26696449 PMCID: PMC6638527 DOI: 10.1111/mpp.12358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/24/2015] [Accepted: 12/10/2015] [Indexed: 05/22/2023]
14
Gourbal B, Théron A, Grunau C, Duval D, Mitta G. Polymorphic Mucin-Like Proteins in Schistosoma mansoni, a Variable Antigen and a Key Component of the Compatibility Between the Schistosome and Its Snail Host. Results Probl Cell Differ 2016;57:91-108. [PMID: 26537378 DOI: 10.1007/978-3-319-20819-0_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
15
Ligation of RNA Oligomers by the Schistosoma mansoni Hammerhead Ribozyme in Frozen Solution. J Mol Evol 2016;82:81-92. [PMID: 26897022 DOI: 10.1007/s00239-016-9729-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/10/2016] [Indexed: 01/29/2023]
16
Scott WG, Horan LH, Martick M. The hammerhead ribozyme: structure, catalysis, and gene regulation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013;120:1-23. [PMID: 24156940 DOI: 10.1016/b978-0-12-381286-5.00001-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
17
Lee TS, Wong KY, Giambasu GM, York DM. Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013;120:25-91. [PMID: 24156941 PMCID: PMC4747252 DOI: 10.1016/b978-0-12-381286-5.00002-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
18
Kennedy AB, Liang JC, Smolke CD. A versatile cis-blocking and trans-activation strategy for ribozyme characterization. Nucleic Acids Res 2012;41:e41. [PMID: 23155065 PMCID: PMC3553993 DOI: 10.1093/nar/gks1036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Nohales MÁ, Molina-Serrano D, Flores R, Daròs JA. Involvement of the chloroplastic isoform of tRNA ligase in the replication of viroids belonging to the family Avsunviroidae. J Virol 2012;86:8269-76. [PMID: 22623792 PMCID: PMC3421689 DOI: 10.1128/jvi.00629-12] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/15/2012] [Indexed: 11/20/2022]  Open
20
Kaddour H, Vergne J, Hervé G, Maurel MC. High-pressure analysis of a hammerhead ribozyme from Chrysanthemum chlorotic mottle viroid reveals two different populations of self-cleaving molecule. FEBS J 2011;278:3739-47. [PMID: 21824288 DOI: 10.1111/j.1742-4658.2011.08291.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
21
DeAbreu DM, Olive JE, Collins RA. Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme. Nucleic Acids Res 2011;39:6223-8. [PMID: 21507887 PMCID: PMC3152364 DOI: 10.1093/nar/gkr250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
22
Jimenez RM, Delwart E, Lupták A. Structure-based search reveals hammerhead ribozymes in the human microbiome. J Biol Chem 2011;286:7737-7743. [PMID: 21257745 DOI: 10.1074/jbc.c110.209288] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
23
Lee TS, York DM. Computational mutagenesis studies of hammerhead ribozyme catalysis. J Am Chem Soc 2010;132:13505-18. [PMID: 20812715 DOI: 10.1021/ja105956u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
24
Ferré-D'Amaré AR, Scott WG. Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol 2010;2:a003574. [PMID: 20843979 DOI: 10.1101/cshperspect.a003574] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
25
Shepotinovskaya I, Uhlenbeck OC. Enhanced product stability in the hammerhead ribozyme. Biochemistry 2010;49:4494-500. [PMID: 20423112 DOI: 10.1021/bi902025m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
26
Martinsen L, Johnsen A, Venanzetti F, Bachmann L. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae). BMC Evol Biol 2010;10:3. [PMID: 20047671 PMCID: PMC2837043 DOI: 10.1186/1471-2148-10-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 01/04/2010] [Indexed: 11/10/2022]  Open
27
Scott WG, Martick M, Chi YI. Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009;1789:634-41. [PMID: 19781673 DOI: 10.1016/j.bbagrm.2009.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 09/01/2009] [Accepted: 09/13/2009] [Indexed: 01/14/2023]
28
Martínez F, Marqués J, Salvador ML, Daròs JA. Mutational analysis of eggplant latent viroid RNA processing in Chlamydomonas reinhardtii chloroplast. J Gen Virol 2009;90:3057-3065. [PMID: 19675190 DOI: 10.1099/vir.0.013425-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
29
Fedor MJ. Comparative enzymology and structural biology of RNA self-cleavage. Annu Rev Biophys 2009;38:271-99. [PMID: 19416070 DOI: 10.1146/annurev.biophys.050708.133710] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
30
Thomas JM, Perrin DM. Probing general acid catalysis in the hammerhead ribozyme. J Am Chem Soc 2009;131:1135-43. [PMID: 19154176 DOI: 10.1021/ja807790e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
31
Roger E, Grunau C, Pierce RJ, Hirai H, Gourbal B, Galinier R, Emans R, Cesari IM, Cosseau C, Mitta G. Controlled chaos of polymorphic mucins in a metazoan parasite (Schistosoma mansoni) interacting with its invertebrate host (Biomphalaria glabrata). PLoS Negl Trop Dis 2008;2:e330. [PMID: 19002242 PMCID: PMC2576457 DOI: 10.1371/journal.pntd.0000330] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/10/2008] [Indexed: 01/21/2023]  Open
32
Chi YI, Martick M, Lares M, Kim R, Scott WG, Kim SH. Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol 2008;6:e234. [PMID: 18834200 PMCID: PMC2553840 DOI: 10.1371/journal.pbio.0060234] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 08/18/2008] [Indexed: 11/19/2022]  Open
33
Boots JL, Canny MD, Azimi E, Pardi A. Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2008;14:2212-22. [PMID: 18755844 PMCID: PMC2553736 DOI: 10.1261/rna.1010808] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 07/02/2008] [Indexed: 05/20/2023]
34
Shepotinovskaya IV, Uhlenbeck OC. Catalytic diversity of extended hammerhead ribozymes. Biochemistry 2008;47:7034-42. [PMID: 18543946 DOI: 10.1021/bi7025358] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
35
Kisseleva N, Khvorova A, Westhof E, Schiemann O, Wolfson AD. The Different Role of High-Affinity and Low-Affinity Metal Ions in Cleavage by a Tertiary Stabilized Cis Hammerhead Ribozyme from Tobacco Ringspot Virus. Oligonucleotides 2008. [DOI: 10.1089/oli.2008.0129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
36
Nelson JA, Uhlenbeck OC. Hammerhead redux: does the new structure fit the old biochemical data? RNA (NEW YORK, N.Y.) 2008;14:605-615. [PMID: 18287565 PMCID: PMC2271363 DOI: 10.1261/rna.912608] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
37
Hoogstraten CG, Sumita M. Structure-function relationships in RNA and RNP enzymes: recent advances. Biopolymers 2008;87:317-28. [PMID: 17806104 DOI: 10.1002/bip.20836] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
38
Nelson JA, Uhlenbeck OC. Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis. RNA (NEW YORK, N.Y.) 2008;14:43-54. [PMID: 17998291 PMCID: PMC2151028 DOI: 10.1261/rna.717908] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 09/21/2007] [Indexed: 05/25/2023]
39
Przybilski R, Hammann C. Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof. Biol Chem 2007;388:737-41. [PMID: 17570826 DOI: 10.1515/bc.2007.065] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
40
Cottrell JW, Kuzmin YI, Fedor MJ. Functional Analysis of Hairpin Ribozyme Active Site Architecture. J Biol Chem 2007;282:13498-507. [PMID: 17351263 DOI: 10.1074/jbc.m700451200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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