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List of all the articles of Ribozyme.
Ribozyme publication - export
Year Author Title Ribozyme name Description Journal
2004 Adams, P. L., M. R. Stahley, A. B. Kosek, J. Wang and S. A. Strobel Crystal structure of a self-splicing group I intron with both exons. Group I self-splicing intron Crystal structure of Azoarcus group I intron with both exons Nature 430 (6995): 45-50.
2004 Guo, F., A. R. Gooding and T. R. Cech Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Group I self-splicing intron Crystal structure of an active Tetrahymena ribozyme Mol Cell 16 (3): 351-62.
2005 Golden, B. L., H. Kim and E. Chase Crystal structure of a phage Twort group I ribozyme-product complex. Group I self-splicing intron Crystal structure of phage Twort group I ribozyme-product complex Nat Struct Mol Biol 12 (1): 82-9.
2005 Stahley, M. R. and S. A. Strobel Structural evidence for a two-metal-ion mechanism of group I intron splicing. Group I self-splicing intron Crystal structure of a catalytically active Azoarcus group I intron splicing intermediate Science 309 (5740): 1587-90.
2021 Su, Z., K. Zhang, K. Kappel, S. Li, M. Z. Palo, G. D. Pintilie, R. Rangan, B. Luo, Y. Wei, R. Das and W. Chiu Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 A resolution. Group I self-splicing intron Cryo-EM structures of full-length Tetrahymena ribozyme Nature 596 (7873): 603-607.
1989 Williamson, C. L., N. M. Desai and J. M. Burke Compensatory mutations demonstrate that P8 and P6 are RNA secondary structure elements important for processing of a group I intron. Group I self-splicing intron Verify the existence and importance of P6, P8 Nucleic Acids Res 17 (2): 675-89.
1989 Doudna, J. A., B. P. Cormack and J. W. Szostak RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron. Group I self-splicing intron Conserved UG is an important recognition element for determining guanosine attack sites Proc Natl Acad Sci U S A 86 (19): 7402-6.
1989 Flor, P. J., J. B. Flanegan and T. R. Cech A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing. Group I self-splicing intron The conserved base pair C109-G212 in P4 contributes to the tertiary structure required for self-splicing EMBO J 8 (11): 3391-9.
1982 Kruger, K., P. J. Grabowski, A. J. Zaug, J. Sands, D. E. Gottschling and T. R. Cech Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Group I self-splicing intron Discovery Cell 31 (1): 147-57.
1982 Davies, R. W., R. B. Waring, J. A. Ray, T. A. Brown and C. Scazzocchio Making ends meet: a model for RNA splicing in fungal mitochondria. Group I self-splicing intron Determination of shared secondary structure Nature 300 (5894): 719-24.
1986 Zaug, A. J. and T. R. Cech The intervening sequence RNA of Tetrahymena is an enzyme. Group I self-splicing intron The intervening sequence RNA of Tetrahymena is an enzyme Science 231 (4737): 470-5.
1988 Price, J. V. and T. R. Cech Determinants of the 3' splice site for self-splicing of the Tetrahymena pre-rRNA. Group I self-splicing intron ωG is closely related to the choice of 3' splice site Genes Dev 2 (11): 1439-47.
1990 Michel, F. and E. Westhof Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. Group I self-splicing intron 3D models of group I intron based on comparative sequence analysis J Mol Biol 216 (3): 585-610.
1996 Cate, J. H., A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, C. E. Kundrot, T. R. Cech and J. A. Doudna Crystal structure of a group I ribozyme domain: principles of RNA packing. Group I self-splicing intron Crystal structure of Tetrahymena P4-P6 domain Science 273 (5282): 1678-85.
1998 Golden, B. L., A. R. Gooding, E. R. Podell and T. R. Cech A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Group I self-splicing intron Crystal structure of an engineered, active Tetrahymena ribozyme at 5.0 Å resolution Science 282 (5387): 259-64.
2011 Benz-Moy, T. L. and D. Herschlag Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Group I self-splicing intron Long-range tertiary contacts in RNA exhibit distinct catalytic roles Biochemistry 50 (40): 8733-55.
2022 Liu, D., F. A. Thelot, J. A. Piccirilli, M. Liao and P. Yin Sub-3-A cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Group I self-splicing intron Tetrahymena group I intron at 2.98-Å resolution overall (2.85 Å for the core) Nat Methods 19 (5): 576-585.
1994 Damberger, S. H. and R. R. Gutell A comparative database of group I intron structures. Group I self-splicing intron Comparative database Nucleic Acids Res 22 (17): 3508-10.
2008 Zhou, Y., C. Lu, Q. J. Wu, Y. Wang, Z. T. Sun, J. C. Deng and Y. Zhang GISSD: Group I Intron Sequence and Structure Database. Group I self-splicing intron Sequence and structure database Nucleic Acids Res 36 (Database issue): D31-7.
2009 Vicens, Q. and T. R. Cech A natural ribozyme with 3',5' RNA ligase activity. A natural ribozyme with 3',5' RNA ligase activity Discovery Nat Chem Biol 5(2): 97-9.
2004 J. Proudfoot and A. Akoulitchev Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotes transcription termination. CoTC ribozyme(Beta-globin co-transcriptional cleavage ribozyme) Discovery that the CoTC process in the human beta-globin gene involves an RNA self-cleaving activity Nature 432(7016): 526-530.
2006 Salehi-Ashtiani, K., A. Luptak, A. Litovchick and J. W. Szostak A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. CPEB3 ribozyme A HDV-like sequence in the human CPEB3 gene Science 313 (5794): 1788-92.
2014 Skilandat, M., M. Rowinska-Zyrek and R. K. Sigel Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain. CPEB3 ribozyme NMR solution structure of CPEB3 ribozyme's P4 domain J Biol Inorg Chem 19 (6): 903-12.
2016 Skilandat, M., M. Rowinska-Zyrek and R. K. Sigel Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme. CPEB3 ribozyme NMR studies confirm secondary structure and Mg2+ location in CPEB3 ribozyme RNA 22 (5): 750-63.
2021 Bendixsen, D. P., T. B. Pollock, G. Peri and E. J. Hayden Experimental Resurrection of Ancestral Mammalian CPEB3 Ribozymes Reveals Deep Functional Conservation. CPEB3 ribozyme The functional conservation of CPEB3 ribozyme in mammalian evolution Mol Biol Evol 38 (7): 2843-2853.
2014 Meyer, M., H. Nielsen, V. Olieric, P. Roblin, S. D. Johansen, E. Westhof and B. Masquida Speciation of a group I intron into a lariat capping ribozyme. Lariat capping ribozyme Crystal structures of the precleavage and postcleavage lariat-capping ribozymes Proc Natl Acad Sci U S A 111(21): 7659-7664.
2002 Johansen, S., C. Einvik and H. Nielsen DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique core organization and evolved biological role. Lariat capping ribozyme REVIEW Biochimie 84(9): 905-912.
2002 Vader, A., S. Johansen and H. Nielsen The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis. Lariat capping ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis Eur J Biochem 269(23): 5804-5812.
2014 Tang, Y., H. Nielsen, B. Masquida, P. P. Gardner and S. D. Johansen Molecular characterization of a new member of the lariat capping twin-ribozyme introns. Lariat capping ribozyme Molecular characterization of a new member of the lariat capping twin-ribozyme introns Mob DNA 5: 25.
2021 Pietschmann, M., G. Tempel, M. Halladjian, N. Krogh and H. Nielsen Use of a Lariat Capping Ribozyme to Study Cap Function In Vivo. Lariat capping ribozyme Use of a lariat capping ribozyme to study cap function in vivo Methods Mol Biol 2167: 271-285.
1994 Johansen, S. and V. M. Vogt An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing. Lariat capping ribozyme Sequence discovered Cell 76(4): 725-734.
1995 Decatur, W. A., C. Einvik, S. Johansen and V. M. Vogt Two group I ribozymes with different functions in a nuclear rDNA intron. Lariat capping ribozyme Catalytic RNA element renamed as the group I-like ribozyme, GIR1 EMBO J 14(18): 4558-4568.
2005 Nielsen, H., E. Westhof and S. Johansen An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme. Lariat capping ribozyme GIR1 makes tiny lariats Science 309(5740): 1584-1587.
2008 eckert, B., H. Nielsen, C. Einvik, S. D. Johansen, E. Westhof and B. Masquida Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes. Lariat capping ribozyme Molecular modelling of the GIR1 branching ribozyme EMBO J 27(4): 667-678.
2017 Krogh, N., M. Pietschmann, M. Schmid, T. H. Jensen and H. Nielsen Lariat capping as a tool to manipulate the 5' end of individual yeast mRNA species in vivo. Lariat capping ribozyme Lariat capping as a tool to manipulate the 5' end of mRNA RNA 23(5): 683-695.
2006 Klein, D. and A. Ferré-D'Amaré Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. GlmS ribozyme Crystal structure Science (New York, N.Y.) 313(5794): 1752-1756.
2007 Cochrane, J., S. Lipchock and S. Strobel Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor. GlmS ribozyme Crystal structure Chemistry & biology 14(1): 97-105.
2007 Klein, D., M. Been and A. Ferré-D'Amaré Essential role of an active-site guanine in glmS ribozyme catalysis. GlmS ribozyme Essential role of an active-site guanine G40 in glmS ribozyme catalysis Journal of the American Chemical Society 129(48): 14858-14859.
2017 Schüller, A., D. Matzner, C. Lünse, V. Wittmann, C. Schumacher, S. Unsleber, H. Brötz-Oesterhelt, C. Mayer, G. Bierbaum and G. Mayer Activation of the glmS Ribozyme Confers Bacterial Growth Inhibition. GlmS ribozyme GlcN6P cofactor play a variety of catalytic roles in glmS ribozyme Chembiochem : a European journal of chemical biology 18(5): 435-440.
2004 Winkler, W., A. Nahvi, A. Roth, J. Collins and R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme. GlmS ribozyme Discovery,Secondary structure Nature 428(6980): 281-286.
2006 Soukup, G. Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure. GlmS ribozyme Pseudoknot structure Nucleic acids research 34(3): 968-975.
2007 Collins, J., I. Irnov, S. Baker and W. Winkler Mechanism of mRNA destabilization by the glmS ribozyme. GlmS ribozyme Mechanism of mRNA destabilization by the glms ribozyme Genes & development 21(24): 3356-3368.
2009 Cochrane, J., S. Lipchock, K. Smith and S. Strobel Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme. GlmS ribozyme Chemical Mechanism Biochemistry 48(15): 3239-3246.
2010 Ferré-D'Amaré, A. The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA. GlmS ribozyme Use of a small molecule coenzyme by a gene-regulatory RNA Quarterly reviews of biophysics 43(4): 423-447.
2010 Klawuhn, K., J. Jansen, J. Souchek, G. Soukup and J. Soukup Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding. GlmS ribozyme The role of Mg2+ in active sites Chembiochem : a European journal of chemical biology 11(18): 2567-2571.
2011 Watson, P. and M. Fedor The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. GlmS ribozyme The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo Nature structural & molecular biology 18(3): 359-363.
2011 McCown, P., A. Roth and R. Breaker An expanded collection and refined consensus model of glmS ribozymes. GlmS ribozyme An expanded collection and refined consensus model of glmS ribozymes RNA (New York, N.Y.) 17(4): 728-736.
2012 Viladoms, J. and M. Fedor The glmS ribozyme cofactor is a general acid-base catalyst. GlmS ribozyme The glmS ribozyme cofactor is a general acid-base catalyst Journal of the American Chemical Society 134(46): 19043-19049.
2013 Lau, M. W. L. and A. R. Ferré-D Amaré An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. GlmS ribozyme An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence Journal of the American Chemical Society 134(46): 19043-19049.
2017 Bingaman, J., S. Zhang, D. Stevens, N. Yennawar, S. Hammes-Schiffer and P. Bevilacqua The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. GlmS ribozyme GlcN6P cofactor play a variety of catalytic roles in glmS ribozyme Nature chemical biology 13(4): 439-445.
2018 Cruz-Bustos, T., S. Ramakrishnan, C. Cordeiro, M. Ahmed and R. Docampo A Riboswitch-based Inducible Gene Expression System for Trypanosoma brucei. GlmS ribozyme The glmS ribozyme could be used as a tool to study essential genes in T. brucei The Journal of eukaryotic microbiology 65(3): 412-421.
2020 Andreasson, J., A. Savinov, S. Block and W. Greenleaf Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme. GlmS ribozyme Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme Nature communications 11(1): 1663.
2021 Traykovska, M., K. Popova and R. Penchovsky Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development. GlmS ribozyme The glmS ribozyme is a very suitable target for antibacterial drug development with antisense oligonucleotides ACS synthetic biology 10(11): 3167-3176.
1980 Halbreich, A., P. Pajot, M. Foucher, C. Grandchamp and P. Slonimski A pathway of cytochrome b mRNA processing in yeast mitochondria: specific splicing steps and an intron-derived circular DNA. Group II self-splicing intron "Circular" introns were found to splice out from a mitochondrial gene Cell 19 (2): 321-9.
1982 Michel, F., A. Jacquier and B. Dujon Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Group II self-splicing intron First secondary structure model by comparative sequence analysis Biochimie 64 (10): 867-81.
1986 van der Veen, R., A. C. Arnberg, G. van der Horst, L. Bonen, H. F. Tabak and L. A. Grivell Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Group II self-splicing intron Group II introns form a lariat by self-splicing in vivo Cell 44 (2): 225-34.
1986 Peebles, C. L., P. S. Perlman, K. L. Mecklenburg, M. L. Petrillo, J. H. Tabor, K. A. Jarrell and H. L. Cheng A self-splicing RNA excises an intron lariat. Group II self-splicing intron Group II introns form a lariat by self-splicing in vivo Cell 44 (2): 213-23.
1994 Chanfreau, G. and A. Jacquier Catalytic site components common to both splicing steps of a group II intron. Group II self-splicing intron Common catalytic site to both splicing steps. Cell 178 (3): 612-623.e12.
1995 Peebles, C. L., M. Zhang, P. S. Perlman and J. S. Franzen Catalytically critical nucleotide in domain 5 of a group II intron. Group II self-splicing intron Catalytically critical nucleotide in domain 5 Proc Natl Acad Sci U S A 92 (10): 4422-6.
1995 Boulanger, S. C., S. M. Belcher, U. Schmidt, S. D. Dib-Hajj, T. Schmidt and P. S. Perlman Studies of point mutants define three essential paired nucleotides in the domain 5 substructure of a group II intron. Group II self-splicing intron Three essential paired nucleotides in the domain 5 Mol Cell Biol 15 (8): 4479-88.
1996 Schmidt, U., M. Podar, U. Stahl and P. S. Perlman Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations. Group II self-splicing intron Two-nucleotide bulge in D5 are important RNA 2 (11): 1161-72.
1996 Abramovitz, D. L., R. A. Friedman and A. M. Pyle Catalytic role of 2'-hydroxyl groups within a group II intron active site. Group II self-splicing intron Eight hydroxyl groups in D5 are the key to activity Science 271 (5254): 1410-3.
1997 Costa, M., E. Deme, A. Jacquier and F. Michel Multiple tertiary interactions involving domain II of group II self-splicing introns. Group II self-splicing intron D2 stabilizes the ribozyme core and controls the location of D6 and branching sites J Mol Biol 267 (3): 520-36.
2000 Boudvillain, M., A. de Lencastre and A. M. Pyle A tertiary interaction that links active-site domains to the 5' splice site of a group II intron. Group II self-splicing intron Demonstration of tertiary interactions linking the catalytically critical regions of D1 to D5 and anchoring them at the 5' splice site Nature 406 (6793): 315-8.
2002 Zhang, L. and J. A. Doudna Structural insights into group II intron catalysis and branch-site selection. Group II self-splicing intron Crystal structures of 70-nucleotide RNAs of yeast ai5γ D5 and D6 (3 Å) Science 295 (5562): 2084-8.
2005 Fedorova, O. and A. M. Pyle Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3. Group II self-splicing intron D3 is a functional group important for catalytic activity, and the interaction of D3 and D5 promotes catalysis EMBO J 24 (22): 3906-16.
2005 de Lencastre, A., S. Hamill and A. M. Pyle A single active-site region for a group II intron. Group II self-splicing intron Single active-site region for group II intron catalysis Nat Struct Mol Biol 12 (7): 626-7.
2007 Fedorova, O. and N. Zingler Group II introns: structure, folding and splicing mechanism. Group II self-splicing intron Review: splicing mechanism Biol Chem 388 (7): 665-78.
2008 Toor, N., K. S. Keating, S. D. Taylor and A. M. Pyle Crystal structure of a self-spliced group II intron. Group II self-splicing intron The first 3D structure of the Oceanobacillus iheyensis group IIC intron Science 320 (5872): 77-82.
2010 Pyle, A. M. The tertiary structure of group II introns: implications for biological function and evolution. Group II self-splicing intron Common tertiary structure of the catalytic core Crit Rev Biochem Mol Biol 45 (3): 215-32.
2012 Marcia, M. and A. M. Pyle Visualizing group II intron catalysis through the stages of splicing. Group II self-splicing intron Crystal structures of a group II intron at different stages of catalysis. Cell 151 (3): 497-507.
2014 Robart, A. R., R. T. Chan, J. K. Peters, K. R. Rajashankar and N. Toor Crystal structure of a eukaryotic group II intron lariat. Group II self-splicing intron Crystal structure of the intronic lariat form of eukaryotic group IIB Nature 514 (7521): 193-7.
2016 Qu, G., P. S. Kaushal, J. Wang, H. Shigematsu, C. L. Piazza, R. K. Agrawal, M. Belfort and H. W. Wang Structure of a group II intron in complex with its reverse transcriptase. Group II self-splicing intron Cryo-EM structures of a group Ⅱ intron in complex with its maturase Nat Struct Mol Biol 23 (6): 549-57.
2017 Zhao, C. and A. M. Pyle Structural Insights into the Mechanism of Group II Intron Splicing. Group II self-splicing intron Review: Structural insights into the splicing mechanism Trends Biochem Sci 42 (6): 470-482.
2019 Haack, D. B., X. Yan, C. Zhang, J. Hingey, D. Lyumkis, T. S. Baker and N. Toor Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. Group II self-splicing intron Cryo-EM structures of a group II intron reverse splicing into DNA Cell 178 (3): 612-623.e12.
2020 Liu, N., X. Dong, C. Hu, J. Zeng, J. Wang, J. Wang, H. W. Wang and M. Belfort Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing. Group II self-splicing intron Two cryo-EM structures of group II intron RNPs in their pre-catalytic state Nucleic Acids Res 48 (19): 11185-11198.
2002 Rupert, P., A. Massey, S. Sigurdsson and A. Ferré-D'Amaré Transition state stabilization by a catalytic RNA. Hairpin ribozyme Crystal structure Science (New York, N.Y.) 298(5597): 1421-1424.
2006 Salter, J., J. Krucinska, S. Alam, V. Grum-Tokars and J. Wedekind Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Hairpin ribozyme Crystal structure Biochemistry 45(3): 686-700.
1997 Hampel, A. and J. Cowan A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Hairpin ribozyme Chemical Mechanism Chemistry & biology 4(7): 513-517.
1998 Shippy, R., A. Siwkowski and A. Hampel Mutational analysis of loops 1 and 5 of the hairpin ribozyme. Hairpin ribozyme Loops 1 and 5 of the hairpin ribozyme Biochemistry 37(2): 564-570.
2001 Rupert, P. and A. Ferré-D'Amaré Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Hairpin ribozyme Crystal structure Nature 410(6830): 780-786.
1986 Buzayan, J. M., W. L. Gerlach and G. Bruening Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Hairpin ribozyme Discovery Nature.
1993 Berzal-Herranz, A., S. Joseph, B. Chowrira, S. Butcher and J. Burke Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. Hairpin ribozyme Sequence/Secondary structure The EMBO journal 12(6): 2567-2573.
2001 Pinard, R., K. Hampel, J. Heckman, D. Lambert, P. Chan, F. Major and J. Burke Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. Hairpin ribozyme Essential role of an active-site G8 in hairpin ribozyme catalysis The EMBO journal 20(22): 6434-6442.
2005 Kuzmin, Y., C. Da Costa, J. Cottrell and M. Fedor Role of an active site adenine in hairpin ribozyme catalysis. Hairpin ribozyme Essential role of an active-site A38 in hairpin ribozyme catalysis Journal of molecular biology 349(5): 989-1010.
2012 Kath-Schorr, S., T. Wilson, N. Li, J. Lu, J. Piccirilli and D. Lilley General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. Hairpin ribozyme Catalytic mechanism Journal of the American Chemical Society 134(40): 16717-16724.
2019 Hieronymus, R. and S. Müller Engineering of hairpin ribozyme variants for RNA recombination and splicing. Hairpin ribozyme Engineering of hairpin ribozyme variants Annals of the New York Academy of Sciences 1447(1): 135-143.
2021 Song, E., E. Jiménez, H. Lin, K. Le Vay, R. Krishnamurthy and H. Mutschler Prebiotically Plausible RNA Activation Compatible with Ribozyme-Catalyzed Ligation. Hairpin ribozyme Situ activation of RNA substrates under reaction conditions amenable to catalysis by the hairpin ribozyme Angewandte Chemie (International ed. in English) 60(6): 2952-2957.
2021 Weinberg, C., V. Olzog, I. Eckert and Z. Weinberg Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs. Hairpin ribozyme Expand the number of natural hairpin ribozymes Nucleic acids research 49(11): 6375-6388.
2022 Lee, B., U. Neri, C. Oh, P. Simmonds and E. Koonin ViroidDB: a database of viroids and viroid-like circular RNAs. Hairpin ribozyme ViroidDB: a database of viroids and viroid-like circular RNAs Nucleic acids research 50: D432-D438.
2022 Hieronymus, R., J. Zhu and S. Müller RNA self-splicing by engineered hairpin ribozyme variants. Hairpin ribozyme Engineering of hairpin ribozyme variants Nucleic acids research 50(1): 368-377.
1994 Pley, H. W., K. M. Flaherty and D. B. McKay Three-dimensional structure of a hammerhead ribozyme. Hammerhead ribozyme Crystal structure of type III HHR Nature 372(6501): 68-74.
2008 Chi, Y. I., M. Martick, M. Lares, R. Kim, W. G. Scott and S. H. Kim Capturing hammerhead ribozyme structures in action by modulating general base catalysis. Hammerhead ribozyme Crystal structure PLoS Biol 6(9): e234.
2014 Schultz, E. P., E. E. Vasquez and W. G. Scott Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis. Hammerhead ribozyme Specific base catalysis mechanism Acta Crystallogr D Biol Crystallogr 70(Pt 9): 2256-2263.
2006 Martick, M. and W. G. Scott Tertiary contacts distant from the active site prime a ribozyme for catalysis. Hammerhead ribozyme Crystal structure of typeⅠ HHR Cell 126(2): 309-320.
2013 Anderson, M., E. P. Schultz, M. Martick and W. G. Scott Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure. Hammerhead ribozyme Crystal structure J Mol Biol 425(20): 3790-3798.
1986 Prody, G. A., J. T. Bakos, J. M. Buzayan, I. R. Schneider and G. Bruening Autolytic Processing of Dimeric Plant Virus Satellite RNA. Hammerhead ribozyme Discovery Science 231(4745): 1577-1580.
2015 Weinberg, Z., P. B. Kim, T. H. Chen, S. Li, K. A. Harris, C. E. Lünse and R. R. Breaker New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Hammerhead ribozyme Discover variants of typeⅠHHR Nat Chem Biol 11(8): 606-610.
2017 Lünse, C. E., Z. Weinberg and R. R. Breaker Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers. Hammerhead ribozyme Some variants form dimers to cleave RNA RNA Biol 14(11): 1499-1507.
2017 Ren, A., R. Micura and D. J. Patel Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes. Hammerhead ribozyme Catalytic mechanism Curr Opin Chem Biol 41: 71-83.
2019 Wilson, T. J., Y. Liu, N. S. Li, Q. Dai, J. A. Piccirilli and D. M. J. Lilley Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes. Hammerhead ribozyme The structure is similar with the pistol ribozyme J Am Chem Soc 141(19): 7865-7875.
1986 Hutchins, C. J., P. D. Rathjen, A. C. Forster and R. H. Symons Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Hammerhead ribozyme Discovery Nucleic Acids Research 14(9): 3627-3640.
1986 Hutchins, C. J., P. D. Rathjen, A. C. Forster and R. H. Symons Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Hammerhead ribozyme Secondary structure of type I HHR Nucleic Acids Research 14(9): 3627-3640.
1987 Forster, A. C. and R. H. Symons Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Hammerhead ribozyme Secondary structure of type III HHR Cell 49(2): 211-220.
1991 Pabón-Peña, L. M., Y. Zhang and L. M. Epstein Newt satellite 2 transcripts self-cleave by using an extended hammerhead structure. Hammerhead ribozyme Internal loops are important Mol Cell Biol 11(12): 6109-6115.
1998 Murray, J. B., A. A. Seyhan, N. G. Walter, J. M. Burke and W. G. Scott The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Hammerhead ribozyme Dense positive charge is critical for catalysis Chem Biol 5(10): 587-595.
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1992 Madhani, H. D. and C. Guthrie A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Spliceosome Demonstrate a conserved base-pairing interaction between the U6 and U2 snRNAs that is mutually exclusive with the U4-U6 interaction Cell 71(5): 803-817.
1993 Steitz, T. A. and J. A. Steitz A general two-metal-ion mechanism for catalytic RNA. Spliceosome Proposed that the two phosphotransesterifications of splicing are catalyzed by a two-metal mechanism Proc Natl Acad Sci U S A 90(14): 6498-6502.
1997 Sontheimer, E. J., S. Sun and J. A. Piccirilli Metal ion catalysis during splicing of premessenger RNA. Spliceosome Divalent metals stabilize the leaving group during each step of splicing Nature 388(6644): 801-805.
2000 Yean, S. L., G. Wuenschell, J. Termini and R. J. Lin Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Spliceosome Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome Nature 408(6814): 881-884.
2001 Valadkhan, S. and J. L. Manley Splicing-related catalysis by protein-free snRNAs. Spliceosome U2 and U6 can base-pair and fold in vitro into a structure that catalyzes reactions similar to the two steps of pre-mRNA splicing Nature 413(6857): 701-707.
2009 Mefford, M. A. and J. P. Staley Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps. Spliceosome U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps RNA 15(7): 1386-1397.
2013 Galej, W. P., C. Oubridge, A. J. Newman and K. Nagai Crystal structure of Prp8 reveals active site cavity of the spliceosome. Spliceosome provides crucial insights into the architecture of the spliceosome active site, and reinforces the notion that nuclear pre-mRNA splicing and group II intron splicing have a common origin. Nature 493(7434): 638-643.
2013 Fica, S. M., N. Tuttle, T. Novak, N. S. Li, J. Lu, P. Koodathingal, Q. Dai, J. P. Staley and J. A. Piccirilli RNA catalyses nuclear pre-mRNA splicing. Spliceosome Demonstrate that RNA mediates catalysis within the spliceosome. Nature 503(7475): 229-234.
2015 Yan, C., J. Hang, R. Wan, M. Huang, C. C. Wong and Y. Shi Structure of a yeast spliceosome at 3.6-angstrom resolution. Spliceosome S.p ILS, 3.6 Å
  The first atomic structure of the intact spliceosome		 Science 349(6253): 1182-1191.
2016 Galej, W. P., M. E. Wilkinson, S. M. Fica, C. Oubridge, A. J. Newman and K. Nagai Cryo-EM structure of the spliceosome immediately after branching. Spliceosome The resolution of tri-snRNP, a complex during splice assembly, was increased to 5.9 angstroms Nature 537(7619): 197-201.
2016 Wan, R., C. Yan, R. Bai, G. Huang and Y. Shi Structure of a yeast catalytic step I spliceosome at 3.4 A resolution. Spliceosome S.c C, 3.4 Å
  Active site after branching		 Science 353(6302): 895-904.
2016 Wan, R., C. Yan, R. Bai, L. Wang, M. Huang, C. C. Wong and Y. Shi The 3.8 A structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis. Spliceosome U4/U6.U5 tri-snRNP，3.8Å Science 351(6272): 466-475.
2016 Yan, C., R. Wan, R. Bai, G. Huang and Y. Shi Structure of a yeast activated spliceosome at 3.5 A resolution. Spliceosome B act , 3.5 Å
  Catalytic center is formed		 Science 353(6302): 904-911.
2017 Yan, C., R. Wan, R. Bai, G. Huang and Y. Shi Structure of a yeast step II catalytically activated spliceosome. Spliceosome S.c C*, 4.0 Å Science 355(6321): 149-155.
2017 Fica, S. M., C. Oubridge, W. P. Galej, M. E. Wilkinson, X. C. Bai, A. J. Newman and K. Nagai Structure of a spliceosome remodelled for exon ligation. Spliceosome S.c C*, 3.8 Å Nature 542(7641): 377-380.
2017 Plaschka, C., P. C. Lin and K. Nagai Structure of a pre-catalytic spliceosome. Spliceosome S.c B, 7.2 (3.7) Å
  		 Nature 546(7660): 617-621.
2017 Wan, R., C. Yan, R. Bai, J. Lei and Y. Shi Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae. Spliceosome S.c ILS, 3.5 Å Cell 171(1): 120-132 e112.
2017 Liu, S., X. Li, L. Zhang, J. Jiang, R. C. Hill, Y. Cui, K. C. Hansen, Z. H. Zhou and R. Zhao Structure of the yeast spliceosomal postcatalytic P complex. Spliceosome S.c P, 3.3 Å Science 358(6368): 1278-1283.
2017 Bai, R., C. Yan, R. Wan, J. Lei and Y. Shi Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae. Spliceosome   S.c P, 3.6 Å Cell 171(7): 1589-1598 e1588.
2017 Bertram, K., D. E. Agafonov, O. Dybkov, D. Haselbach, M. N. Leelaram, C. L. Will, H. Urlaub, B. Kastner, R. Luhrmann and H. Stark Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. Spliceosome C*, 5.9 Å
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2017 Zhang, X., C. Yan, J. Hang, L. I. Finci, J. Lei and Y. Shi An Atomic Structure of the Human Spliceosome. Spliceosome C*, 3.8 Å
   The first atomic model of human spliceosom		 Cell 169(5): 918-929 e914.
2017 Bertram, K., D. E. Agafonov, W. T. Liu, O. Dybkov, C. L. Will, K. Hartmuth, H. Urlaub, B. Kastner, H. Stark and R. Luhrmann Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Spliceosome B, 9.9 (4.5) Å
  		 Nature 542(7641): 318-323.
2018 Bai, R., R. Wan, C. Yan, J. Lei and Y. Shi Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation. Spliceosome S.c pre–B, 3.3–4.6 Å
  S.c B, 3.9 Å		 Science 360(6396): 1423-1429.
2018 Plaschka, C., P. C. Lin, C. Charenton and K. Nagai Prespliceosome structure provides insights into spliceosome assembly and regulation. Spliceosome S.c A, 4.9 (4.0) Å Nature 559(7714): 419-422.
2018 Zhan, X., C. Yan, X. Zhang, J. Lei and Y. Shi Structure of a human catalytic step I spliceosome. Spliceosome C, 4.1 Å
  		 Science 359(6375): 537-545.
2018 Haselbach, D., I. Komarov, D. E. Agafonov, K. Hartmuth, B. Graf, O. Dybkov, H. Urlaub, B. Kastner, R. Luhrmann and H. Stark Structure and Conformational Dynamics of the Human Spliceosomal B(act) Complex. Spliceosome Bact , 3.4 Å (core)
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2018 Zhan, X., C. Yan, X. Zhang, J. Lei and Y. Shi Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Spliceosome pre–B (5.7 Å) and B (3.8 Å) Cell Res 28(12): 1129-1140.
2019 Wan, R., R. Bai, C. Yan, J. Lei and Y. Shi Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Spliceosome S.c B*, 2.9–3.8 Å
  Four distinct structures on two different substrates		 Cell 177(2): 339-351 e313.
2019 Fica, S. M., C. Oubridge, M. E. Wilkinson, A. J. Newman and K. Nagai A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Spliceosome P, 3.3 Å
  		 Science 363(6428): 710-714.
2019 Zhang, X., X. Zhan, C. Yan, W. Zhang, D. Liu, J. Lei and Y. Shi Structures of the human spliceosomes before and after release of the ligated exon. Spliceosome P (3.0 Å) and ILS (2.9 Å)
  		 Cell Res 29(4): 274-285.
2019 Charenton, C., M. E. Wilkinson and K. Nagai Mechanism of 5' splice site transfer for human spliceosome activation. Spliceosome pre–B, 3.3 Å
  Mechanism of 5' splice site transfer for human spliceosome activation		 Science 364(6438): 362-367.
2019 Wan, R., R. Bai, C. Yan, J. Lei and Y. Shi Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Spliceosome Mechanism of Branching Cell 177(2): 339-351 e313.
2020 Zhang, Z., C. L. Will, K. Bertram, O. Dybkov, K. Hartmuth, D. E. Agafonov, R. Hofele, H. Urlaub, B. Kastner, R. Luhrmann and H. Stark Molecular architecture of the human 17S U2 snRNP. Spliceosome The structure of 17s U2 snRNP was analyzed and a complete molecular model of 17s U2 snRNP was obtained Nature 583(7815): 310-313.
2020 Townsend, C., M. N. Leelaram, D. E. Agafonov, O. Dybkov, C. L. Will, K. Bertram, H. Urlaub, B. Kastner, H. Stark and R. Luhrmann Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Spliceosome Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation Science 370(6523).
2021 Bai, R., R. Wan, C. Yan, Q. Jia, J. Lei and Y. Shi Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Spliceosome Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2 Science 371(6525).
2022 Tholen, J., M. Razew, F. Weis and W. P. Galej Structural basis of branch site recognition by the human spliceosome. Spliceosome A series of high-resolution (2.0-2.2 Å) U2 snRNP structures were identified Science 375(6576): 50-57.
2019 Yan, C., R. Wan and Y. Shi Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome. Spliceosome Review Cold Spring Harb Perspect Biol 11(1).
2020 Wan, R., R. Bai, X. Zhan and Y. Shi How Is Precursor Messenger RNA Spliced by the Spliceosome? Spliceosome Review Annu Rev Biochem 89: 333-358.
2020 Wilkinson, M. E., C. Charenton and K. Nagai RNA Splicing by the Spliceosome. Spliceosome Review Annu Rev Biochem 89: 359-388.
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