Small self-cleaving ribozymes
Open accessAbstract
The hammerhead, hairpin, hepatitis delta virus (HDV), Varkud Satellite (VS), and glmS ribozymes catalyze sequence-specific intramolecular cleavage of RNA. They range between 50 and 150 nucleotides in length, and are known as the "small self-cleaving ribozymes." Except for the glmS ribozyme that functions as a riboswitch in Gram-positive bacteria, they were originally discovered as domains of satellite RNAs. However, recent studies show that several of them are broadly distributed in genomes of organisms from many phyla. Each of these ribozymes has a unique overall architecture and active site organization. Crystal structures have revealed how RNA active sites can bind preferentially to the transition state of a reaction, whereas mechanistic studies have shown that nucleobases can efficiently perform general acid-base and electrostatic catalysis. This versatility explains the abundance of ribozymes in contemporary organisms and also supports a role for catalytic RNAs early in evolution.
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The fidelity of primer extension products resulting from the sequential addition of activated monomers, when catalyzed by activated oligomers, is sufficient to sustain a genome long enough to encode active ribozymes.
“The fidelity of the primer extension products resulting from the sequential addition of activated monomers, when catalyzed by activated oligomers, is sufficient to sustain a genome long enough to encode active ribozymes.”
From Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides (2016) · cites this paper as Ferré-D'Amaré and Scott, 2010
Assuming an error threshold of one mutation per genome, a fidelity of 98% allows for effective genome sizes of 50 nucleotides, long enough to produce functional ribozymes.
“Assuming an error threshold of one mutation per genome (Eigen, 1971), this value of fidelity allows for effective genome sizes of 50 nucleotides, long enough to produce functional ribozymes (Ferré-D'Amaré and Scott, 2010).”
From Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides (2016) · cites this paper as Ferré-D'Amaré and Scott, 2010
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Cites
In Vitro Selection of Functional Nucleic Acids
Wilson, D. S., & Szostak, J. W. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.611 · Cited by 1,209 · see citing works
A general two-metal-ion mechanism for catalytic RNA
Steitz, T. A., & Steitz, J. A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.14.6498 · Cited by 1,171 · see citing works
Three-dimensional structure of a hammerhead ribozyme
Pley, H. W., Flaherty, K. M., & McKay, D. B. (1994) · Nature · doi:10.1038/372068a0 · Cited by 955 · see citing works
Control of gene expression by a natural metabolite-responsive ribozyme
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., & Breaker, R. R. (2004) · Nature · doi:10.1038/nature02362 · Cited by 953 · see citing works
A small catalytic oligoribonucleotide
Uhlenbeck, O. C. (1987) · Nature · doi:10.1038/328596a0 · Cited by 938 · see citing works
Crystal structure of a hepatitis delta virus ribozyme
Ferré-D’Amaré, A. R., Zhou, K., & Doudna, J. A. (1998) · Nature · doi:10.1038/26912 · Cited by 787 · see citing works
Scott, W. G., Finch, J. T., & Klug, A. (1995) · Cell · doi:10.1016/s0092-8674(05)80004-2 · Cited by 688 · see citing works
Self-citationRiboswitches and the RNA WorldPreprint
Breaker, R. R. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003566 · Cited by 679 · see citing works
Autolytic Processing of Dimeric Plant Virus Satellite RNA
Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R., & Bruening, G. E. (1986) · Science · doi:10.1126/science.231.4745.1577 · Cited by 634 · see citing works
Robertson, M. P., & Joyce, G. F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003608 · Cited by 556 · see citing works
Structural Domains of Transfer RNA Molecules
Quigley, G. J., & Rich, A. S. (1976) · Science · doi:10.1126/science.790568 · Cited by 531 · see citing works
Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis
Martick, M. M., & Scott, W. G. (2006) · Cell · doi:10.1016/j.cell.2006.06.036 · Cited by 510 · see citing works
Self-citationNew RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
Barrick, J. E., Corbino, K. A., Winkler, W. C., Nahvi, A., Mandal, M., Collins, J. A., Lee, M. N., Roth, A., Sudarsan, N., Jona, I., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308014101 · Cited by 498 · see citing works
Group II Introns: Mobile Ribozymes that Invade DNAPreprint
Lambowitz, A. M., & Zimmerly, S. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003616 · Cited by 482 · see citing works
Sequence requirements of the hammerhead RNA self-cleavage reaction
Ruffner, D. E., Stormo, G. D., & Uhlenbeck, O. C. (1990) · Biochemistry · doi:10.1021/bi00499a018 · Cited by 470 · see citing works
Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis
Rupert, P. B., & Ferré-D’Amaré, A. R. (2001) · Nature · doi:10.1038/35071009 · Cited by 450 · see citing works
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
Khvorova, A., Lescoute, A., Westhof, É., & Jayasena, S. D. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb959 · Cited by 440 · see citing works
Ribozymes: A Distinct Class of Metalloenzymes
Pyle, A. M. (1993) · Science · doi:10.1126/science.7688142 · Cited by 438 · see citing works
General Acid-Base Catalysis in the Mechanism of a Hepatitis Delta Virus Ribozyme
Nakano, S., Chadalavada, D. M., & Bevilacqua, P. C. (2000) · Science · doi:10.1126/science.287.5457.1493 · Cited by 385 · see citing works
Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage
Sharmeen, L., Kuo, M. Y., Dinter-Gottlieb, G., & Taylor, J. M. (1988) · Journal of Virology · doi:10.1128/jvi.62.8.2674-2679.1988 · Cited by 382 · see citing works
Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate
Klein, D. J., & Ferré-D’Amaré, A. R. (2006) · Science · doi:10.1126/science.1129666 · Cited by 377 · see citing works
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. (1998) · Chemistry & Biology · doi:10.1016/s1074-5521(98)90116-8 · Cited by 374 · see citing works
Self-citationRiboswitches: Structures and MechanismsPreprint
Garst, A. D., Edwards, A. L., & Batey, R. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003533 · Cited by 373 · see citing works
A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA
Perrotta, A. T., & Been, M. D. (1991) · Nature · doi:10.1038/350434a0 · Cited by 344 · see citing works
A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene
Salehi‐Ashtiani, K., Lupták, A., Litovchick, A., & Szostak, J. W. (2006) · Science · doi:10.1126/science.1129308 · Cited by 305 · see citing works
A site-specific self-cleavage reaction performed by a novel RNA in neurospora mitochondria
Saville, B. J., & Collins, R. A. (1990) · Cell · doi:10.1016/0092-8674(90)90480-3 · Cited by 294 · see citing works
Transition State Stabilization by a Catalytic RNA
Rupert, P. B., Massey, A. P., Sigurdsson, S. T., & Ferré-D’Amaré, A. R. (2002) · Science · doi:10.1126/science.1076093 · Cited by 292 · see citing works
Imidazole Rescue of a Cytosine Mutation in a Self-Cleaving Ribozyme
Perrotta, A. T., Shih, I., & Been, M. D. (1999) · Science · doi:10.1126/science.286.5437.123 · Cited by 275 · see citing works
Peripheral regions of natural hammerhead ribozymes greatly increase their self‐cleavage activity
de la Peña, M., Gago‐Zachert, S., & Flores, R. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg530 · Cited by 249 · see citing works
Mechanism of mRNA destabilization by the glmS ribozymePreprint
Collins, J. A., Irnov, I., Baker, S. C., & Winkler, W. C. (2007) · Genes & Development · doi:10.1101/gad.1605307 · Cited by 237 · see citing works
General acid catalysis by the hepatitis delta virus ribozyme
Das, S. R., & Piccirilli, J. A. (2005) · Nature Chemical Biology · doi:10.1038/nchembio703 · Cited by 221 · see citing works
Widespread Occurrence of Self-Cleaving Ribozymes
Webb, C.-H. T., Riccitelli, N. J., Ruminski, D. J., & Lupták, A. (2009) · Science · doi:10.1126/science.1178084 · Cited by 212 · see citing works
Bevilacqua, P. C. (2003) · Biochemistry · doi:10.1021/bi027273m · Cited by 204 · see citing works
A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage
HAMPEL, A. E., & Cowan, J. A. (1997) · Chemistry & Biology · doi:10.1016/s1074-5521(97)90323-9 · Cited by 194 · see citing works
An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
Nesbitt, S., Hegg, L. A., & Fedor, M. J. (1997) · Chemistry & Biology · doi:10.1016/s1074-5521(97)90247-7 · Cited by 191 · see citing works
In vitro evolution suggests multiple origins for the hammerhead ribozyme
Salehi-Ashtiani, K., & Szostak, J. W. (2001) · Nature · doi:10.1038/35102081 · Cited by 183 · see citing works
A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA
Martick, M. M., Horan, L. H., Noller, H. F., & Scott, W. G. (2008) · Nature · doi:10.1038/nature07117 · Cited by 172 · see citing works
Self-citationSchistosome Satellite DNA Encodes Active Hammerhead Ribozymes
Ferbeyre, G., Smith, J. M., & Cedergren, R. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.7.3880 · Cited by 170 · see citing works
Metal Ions Play a Passive Role in the Hairpin Ribozyme Catalysed Reaction
Young, K. J., Gill, F., & Grasby, J. A. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.19.3760 · Cited by 159 · see citing works
The Structure-Function Dilemma of the Hammerhead Ribozyme
Blount, K., & Uhlenbeck, O. C. (2005) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.34.122004.184428 · Cited by 158 · see citing works
Sequences required for self-catalysed cleavage of the satellite RNA of tobacco ringspot virus
Haseloff, J., & Gerlach, W. L. (1989) · Gene · doi:10.1016/0378-1119(89)90028-0 · Cited by 143 · see citing works
Murchie, A. I. H., Thomson, J. B., Walter, F., & Lilley, D. M. J. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80086-6 · Cited by 143 · see citing works
Plant pathogenic RNAs and RNA catalysis
Symons, R. H. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.14.2683 · Cited by 137 · see citing works
Pseudoknots: a new motif in the RNA game
Pleij, C. W. A. (1990) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(90)90214-v · Cited by 132 · see citing works
Nucleobase catalysis in ribozyme mechanism
Bevilacqua, P. C., & Yajima, R. (2006) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.08.014 · Cited by 119 · see citing works
Buzayan, J. M., HAMPEL, A. E., & Bruening, G. E. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.24.9729 · Cited by 113 · see citing works
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions
Roth, A., Nahvi, A., Lee, M. N., Jona, I., & Breaker, R. R. (2006) · RNA · doi:10.1261/rna.2266506 · Cited by 108 · see citing works
Role of an Active Site Adenine in Hairpin Ribozyme Catalysis
Kuzmin, Y. I., Costa, C. P. D., Cottrell, J. W., & Fedor, M. J. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.04.005 · Cited by 105 · see citing works
Wedekind, J. E., & McKay, D. B. (1998) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.27.1.475 · Cited by 105 · see citing works
Reconstitution of Hairpin Ribozyme Activity following Separation of Functional Domains
Butcher, S. E., Heckman, J. E., & Burke, J. M. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.50.29648 · Cited by 98 · see citing works
Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation
Fedor, M. J. (1999) · Biochemistry · doi:10.1021/bi991069q · Cited by 94 · see citing works
Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis
Chi, Y., Martick, M. M., Lares, M. R., Kim, R., Scott, W. G., & Kim, S. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060234 · Cited by 93 · see citing works
Self-citationEssential Role of an Active-Site Guanine in glmS Ribozyme Catalysis
Klein, D. J., Been, M. D., & Ferré-D’Amaré, A. R. (2007) · Journal of the American Chemical Society · doi:10.1021/ja0768441 · Cited by 87 · see citing works
Lilley, D. M. J. (2004) · RNA · doi:10.1261/rna.5217104 · Cited by 85 · see citing works
Klein, D. J., Wilkinson, S. R., Been, M. D., & Ferré-D’Amaré, A. R. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.062 · Cited by 78 · see citing works
Rescue of an Abasic Hairpin Ribozyme by Cationic Nucleobases
Lebruska, L. L., Kuzmine, I., & Fedor, M. J. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00130-8 · Cited by 66 · see citing works
RNA-mediated ligation of self-cleavage products of a Neurospora mitochondrial plasmid transcript.
Saville, B. J., & Collins, R. A. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.19.8826 · Cited by 65 · see citing works
Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme
Liu, L., Cottrell, J. W., Scott, L. G., & Fedor, M. J. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.156 · Cited by 60 · see citing works
Protein Structure, Ribonuclease-S and Nucleotide InteractionsPreprint
Richards, F. M., Wyckoff, H. W., Carlson, W. D., Allewell, N. M., Lee, B., & Mitsui, Y. (1972) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1972.036.01.008 · Cited by 60 · see citing works
Is Counterion Delocalization Responsible for Collapse in RNA Folding?
Murthy, V. L., & Rose, G. D. (2000) · Biochemistry · doi:10.1021/bi001820r · Cited by 57 · see citing works
Efficient Ligation of the Schistosoma Hammerhead Ribozyme
Canny, M. D., Jucker, F. M., & Pardi, A. (2007) · Biochemistry · doi:10.1021/bi062077r · Cited by 53 · see citing works
Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme
Scott, W. G. (1999) · Quarterly Reviews of Biophysics · doi:10.1017/s003358350000353x · Cited by 52 · see citing works
Self-citationThe distribution of RNA motifs in natural sequences
Bourdeau, V., Ferbeyre, G., Pageau, M., Paquin, B., & Cedergren, R. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.22.4457 · Cited by 47 · see citing works
The Neurospora Varkud satellite ribozyme
Collins, R. A. (2002) · Biochemical Society Transactions · doi:10.1042/bst0301122 · Cited by 43 · see citing works
A general two-metal-ion mechanism for catalytic RNA
Steitz, T. A., & STEITZ, J. A. (2020) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789811215865_0070 · Cited by 41 · see citing works
Distribution of Hammerhead and Hammerhead-like RNA Motifs Through the GenBankPreprint
Ferbeyre, G., Bourdeau, V., Pageau, M., Miramóntes, P., & Cedergren, R. (2000) · Genome Research · doi:10.1101/gr.10.7.1011 · Cited by 35 · see citing works
The Loop B Domain Is Physically Separable from the Loop A Domain in the Hairpin Ribozyme
Shin, C., Choi, J. N., Song, S. I., Song, J. T., Ahn, J. H., Lee, J. S., & Choi, Y. D. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.14.2685 · Cited by 33 · see citing works
Jones, F. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.24.5115 · Cited by 28 · see citing works
Blount, K., & Uhlenbeck, O. C. (2002) · Biochemistry · doi:10.1021/bi025596c · Cited by 24 · see citing works
Alternative modes of self-cleavage by newt satellite 2 transcripts
Epstein, L. M., & Pabón‐Peña, L. M. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.7.1699 · Cited by 20 · see citing works
Three-Dimensional Structure of the Hammerhead Ribozyme
McKay, D. B. (1996) · Nucleic acids and molecular biology · doi:10.1007/978-3-642-61202-2_9 · Cited by 9 · see citing works
Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J., & Scott, W. (1998) · Cited by 8 · see citing works
Self-citationScott, W., Finch, J., & Klug, A. (1995) · eScholarship (California Digital Library) · Cited by 2 · see citing works
Self-citation
Flagged first, then by citations
1 of the 74 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- de Gennes P-G 1990 Minimum numer of aminoacids required to build up a specific receptor with a folded polypeptide chain Introduction to Polymer Dynamics Cambridge Cambridge University Press 17 26
- Raines RT 1998 Ribonuclease A Chem Rev 98 1045 1065 11848924
Cited by
Sorted by citations
The eightfold path to non-enzymatic RNA replication
Szostak, J. W. (2012) · Journal of Systems Chemistry · doi:10.1186/1759-2208-3-2 · Cited by 359 · see citing works
Gee, P., Lung, M. S. Y., Okuzaki, Y., Sasakawa, N., Iguchi, T., Makita, Y., Hozumi, H., Miura, Y., Yang, L. F., Iwasaki, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14957-y · Cited by 363 · see citing works
A widespread self-cleaving ribozyme class is revealed by bioinformatics
Roth, A., Zasha Weinberg, A., Chen, A. G. Y., Kim, P. B., Ames, T. D., & Breaker, R. R. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1386 · Cited by 282 · see citing works
Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
Micura, R., & Höbartner, C. (2020) · Chemical Society Reviews · doi:10.1039/d0cs00617c · Cited by 264 · see citing works
Cech, T. R. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a006742 · Cited by 244 · see citing works
New classes of self-cleaving ribozymes revealed by comparative genomics analysis
Zasha Weinberg, A., Kim, P. B., Chen, T. H., Li, S., Harris, K. A., Weinberg, C. E., & Breaker, R. R. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1846 · Cited by 229 · see citing works
Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis
Hu, G., Niu, F., Humburg, B. A., Liao, K., Bendi, V. S., Callen, S. E., Fox, H. S., & Buch, S. J. (2018) · Oncotarget · doi:10.18632/oncotarget.24307 · Cited by 196 · see citing works
Chemistry and Biology of Self-Cleaving Ribozymes
Jimenez, R. M., Polanco, J. A., & Lupták, A. (2015) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.09.001 · Cited by 194 · see citing works
Molecular knots in biology and chemistry
Lim, N. C. H., & Jackson, S. (2015) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/27/35/354101 · Cited by 161 · see citing works
Prywes, N., Blain, J. C., Del Frate, F., & Szostak, J. W. (2016) · eLife · doi:10.7554/elife.17756 · Cited by 141 · see citing works
Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators
Wittmann, A., & Suess, B. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.02.038 · Cited by 158 · see citing works
Role of tautomerism in RNA biochemistry
Singh, V., Fedeles, B. I., & Essigmann, J. M. (2014) · RNA · doi:10.1261/rna.048371.114 · Cited by 149 · see citing works
Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules
Zhang, J., Lau, M. W. L., & Ferré-D’Amaré, A. R. (2010) · Biochemistry · doi:10.1021/bi1012645 · Cited by 146 · see citing works
Panteva, M. T., Giambaşu, G. M., & York, D. M. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b10423 · Cited by 131 · see citing works
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure
Zhang, J., & Landick, R. C. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.12.009 · Cited by 129 · see citing works
In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme
Ren, A., Košutić, M., Rajashankar, K. R., Frener, M., Santner, T., Westhof, É., Micura, R., & Patel, D. J. (2014) · Nature Communications · doi:10.1038/ncomms6534 · Cited by 99 · see citing works
Panteva, M. T., Giambaşu, G. M., & York, D. M. (2015) · Journal of Computational Chemistry · doi:10.1002/jcc.23881 · Cited by 97 · see citing works
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage
Ren, A., Vušurović, N., Gebetsberger, J., Gao, P., Juen, M. A., Kreutz, C., Micura, R., & Patel, D. J. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2125 · Cited by 92 · see citing works
Charged Nucleobases and Their Potential for RNA Catalysis
Wilcox, J. L., Ahluwalia, A. K., & Bevilacqua, P. C. (2011) · Accounts of Chemical Research · doi:10.1021/ar2000452 · Cited by 91 · see citing works
Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs
Lee, B. D., Neri, U., Roux, S., Wolf, Y. I., Camargo, A. P., Krupovìč, M., Peter Simmonds, K., Kyrpides, N. C., Gophna, U., Dolja, V. V., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.039 · Cited by 90 · see citing works
Biochemical analysis of pistol self-cleaving ribozymes
Harris, K. A., Weinberg, C. E., Li, S., Brewer, K. I., & Breaker, R. R. (2015) · RNA · doi:10.1261/rna.052514.115 · Cited by 87 · see citing works
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme
Eiler, D. R., Wang, J., & Steitz, T. A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414571111 · Cited by 85 · see citing works
Long-Range Interactions in Riboswitch Control of Gene Expression
Jones, C. P., & Ferré-D’Amaré, A. R. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-034042 · Cited by 77 · see citing works
TheglmSribozyme: use of a small molecule coenzyme by a gene-regulatory RNA
Ferré-D’Amaré, A. R. (2010) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583510000144 · Cited by 71 · see citing works
Coordinated Activities of Human Dicer Domains in Regulatory RNA Processing
Ma, E., Zhou, K., Kidwell, M. A., & Doudna, J. A. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.06.009 · Cited by 71 · see citing works
Selective amplification and sequencing of cyclic phosphate–containing RNAs by the cP-RNA-seq method
Honda, S., Morichika, K., & Kirino, Y. (2016) · Nature Protocols · doi:10.1038/nprot.2016.025 · Cited by 71 · see citing works
Catalytic RNA, ribozyme, and its applications in synthetic biology
Park, S. V., Yang, J., Jo, H., Kang, B., Oh, S. S., & Jung, G. Y. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.107452 · Cited by 70 · see citing works
Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes
Ren, A., Micura, R., & Patel, D. J. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.09.017 · Cited by 72 · see citing works
Temperature-driven differential gene expression by RNA thermosensors
Krajewski, S. S., & Narberhaus, F. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.03.006 · Cited by 66 · see citing works
Nucleic acids: function and potential for abiogenesis
Wachowius, F., Attwater, J., & Holliger, P. (2017) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583517000038 · Cited by 62 · see citing works
Košutić, M., Neuner, S., Ren, A., Flür, S., Wunderlich, C. H., Mairhofer, E., Vušurović, N., Seikowski, J., Breuker, K., Höbartner, C., et al. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201506601 · Cited by 63 · see citing works
Rock, scissors, paper: How RNA structure informs function
Assmann, S. M., Chou, H., & Bevilacqua, P. C. (2023) · The Plant Cell · doi:10.1093/plcell/koad026 · Cited by 64 · see citing works
Ramia, N. F., Spilman, M. S., Tang, L., Shao, Y., Elmore, J. R., Hale, C. R., Cocozaki, A. I., Bhattacharya, N., Terns, R. M., Terns, M. P., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.11.007 · Cited by 60 · see citing works
The non-coding RNA world of the bacterial pathogenListeria monocytogenes
Mellin, J. R., & Cossart, P. (2012) · RNA Biology · doi:10.4161/rna.19235 · Cited by 60 · see citing works
Cellular Delivery of RNA Nanoparticles
Parlea, L., Puri, A., Kasprzak, W. K., Bindewald, E., Zakrevsky, P., Satterwhite, E. R., Joseph, K., Afonin, K. A., & Shapiro, B. A. (2016) · ACS Combinatorial Science · doi:10.1021/acscombsci.6b00073 · Cited by 59 · see citing works
An expanded collection and refined consensus model of glmS ribozymes
McCown, P. J., Roth, A., & Breaker, R. R. (2011) · RNA · doi:10.1261/rna.2590811 · Cited by 58 · see citing works
Crystal structure of Pistol, a class of self-cleaving ribozyme
Nguyen, L. A., Wang, J., & Steitz, T. A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1611191114 · Cited by 56 · see citing works
Biochemical analysis of hatchet self-cleaving ribozymes
Li, S., Weinberg, C. E., Harris, K. A., & Breaker, R. R. (2015) · RNA · doi:10.1261/rna.052522.115 · Cited by 56 · see citing works
The Hammerhead Ribozyme: A Long History for a Short RNA
de la Peña, M., García‐Robles, I., & Cervera, A. (2017) · Molecules · doi:10.3390/molecules22010078 · Cited by 56 · see citing works
Wong, K. Y., Gu, H., Zhang, S., Piccirilli, J. A., Harris, M. E., & York, D. M. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201104147 · Cited by 54 · see citing works
Thaplyal, P., Ganguly, A., Hammes‐Schiffer, S., & Bevilacqua, P. C. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00190 · Cited by 54 · see citing works
Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration
Zhang, J., & Ferré-D’Amaré, A. R. (2014) · Structure · doi:10.1016/j.str.2014.07.011 · Cited by 52 · see citing works
Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing
Peach, S. E., York, K. T., & Hesselberth, J. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv536 · Cited by 53 · see citing works
Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs
Cervera, A., & de la Peña, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu232 · Cited by 52 · see citing works
O’Flaherty, D. K., Zhou, L., & Szostak, J. W. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b04858 · Cited by 52 · see citing works
Zhang, S., Ganguly, A., Goyal, P., Bingaman, J. L., Bevilacqua, P. C., & Hammes‐Schiffer, S. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510387y · Cited by 51 · see citing works
Metal Binding Motif in the Active Site of the HDV Ribozyme Binds Divalent and Monovalent Ions
Veeraraghavan, N., Ganguly, A., Chen, J.-H., Bevilacqua, P. C., Hammes‐Schiffer, S., & Golden, B. L. (2011) · Biochemistry · doi:10.1021/bi2000164 · Cited by 51 · see citing works
Unwinding the twister ribozyme: from structure to mechanism
Gebetsberger, J., & Micura, R. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1402 · Cited by 50 · see citing works
Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA
Kim, S. C., O’Flaherty, D. K., Zhou, L., Lelyveld, V. S., & Szostak, J. W. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814367115 · Cited by 50 · see citing works
Emerging structural themes in large RNA molecules
Reiter, N. J., Chan, C. W., & Mondragón, A. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.003 · Cited by 49 · see citing works
Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review
Andries, O., Kitada, T., Bodner, K., Sanders, N. N., & Weiss, R. (2015) · Expert Review of Vaccines · doi:10.1586/14760584.2015.997714 · Cited by 50 · see citing works
Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA
Gao, Z., Herrera-Carrillo, E., & Berkhout, B. (2018) · RNA Biology · doi:10.1080/15476286.2018.1551703 · Cited by 47 · see citing works
Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution
Janzen, E., Blanco, C., Peng, H., Kenchel, J., & Chen, I. A. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00620 · Cited by 44 · see citing works
Detection of Low-Abundance Metabolites in Live Cells Using an RNA Integrator
You, M., Litke, J. L., Wu, R., & Jaffrey, S. R. (2019) · Cell chemical biology · doi:10.1016/j.chembiol.2019.01.005 · Cited by 45 · see citing works
Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology
Michelotti, N., Johnson-Buck, A. E., Manzo, A. J., & Walter, N. G. (2011) · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.170 · Cited by 45 · see citing works
The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design
Gaines, C. S., Piccirilli, J. A., & York, D. M. (2019) · RNA · doi:10.1261/rna.071894.119 · Cited by 45 · see citing works
Characterizing excited conformational states of RNA by NMR spectroscopy
Zhao, B., & Zhang, Q. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.02.011 · Cited by 43 · see citing works
Baird, N., & Ferré-D’Amaré, A. R. (2012) · RNA · doi:10.1261/rna.036269.112 · Cited by 42 · see citing works
Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases
Rana, A. K., & Ankri, S. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00099 · Cited by 41 · see citing works
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage
Kapral, G. J., Jain, S., Noeske, J., Doudna, J. A., Richardson, D. C., & Richardson, J. S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku992 · Cited by 41 · see citing works
Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis
Lee, R. T. H., Ng, A. S. M., & Ingham, P. W. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166020 · Cited by 41 · see citing works
Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions
Bou‐Nader, C., & Zhang, J. (2020) · Molecules · doi:10.3390/molecules25122881 · Cited by 41 · see citing works
Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate
Vušurović, N., Altman, R. B., Terry, D. S., Micura, R., & Blanchard, S. C. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b01549 · Cited by 38 · see citing works
Intracellular Imaging with Genetically Encoded RNA-Based Molecular Sensors
Sun, Z., Nguyen, T., McAuliffe, K., & You, M. (2019) · Nanomaterials · doi:10.3390/nano9020233 · Cited by 39 · see citing works
Tupper, A. S., & Higgs, P. G. (2021) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2021.110822 · Cited by 32 · see citing works
Self-Assembly of Informational Polymers by Templated Ligation
Rosenberger, J. H., Göppel, T., Kudella, P. W., Braun, D., Gerland, U., & Altaner, B. (2021) · Physical Review X · doi:10.1103/physrevx.11.031055 · Cited by 38 · see citing works
Veeraraghavan, N., Ganguly, A., Golden, B. L., Bevilacqua, P. C., & Hammes‐Schiffer, S. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp203202e · Cited by 37 · see citing works
The glmS Ribozyme Tunes the Catalytically Critical pKa of Its Coenzyme Glucosamine-6-phosphate
Gong, B., Klein, D. J., Ferré-D’Amaré, A. R., & CAREY, P. R. (2011) · Journal of the American Chemical Society · doi:10.1021/ja205185g · Cited by 37 · see citing works
Crucial Roles of Two Hydrated Mg2+ Ions in Reaction Catalysis of the Pistol Ribozyme
Teplova, M., Falschlunger, C., Krasheninina, O. A., Egger, M., Ren, A., Patel, D. J., & Micura, R. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201912522 · Cited by 36 · see citing works
Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes
Lee, K.-Y., & Lee, B. (2017) · Molecules · doi:10.3390/molecules22040678 · Cited by 35 · see citing works
Ucisik, M. N., Bevilacqua, P. C., & Hammes‐Schiffer, S. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00203 · Cited by 34 · see citing works
de la Peña, M., Ceprián, R., Casey, J. L., & Cervera, A. (2021) · Virus Evolution · doi:10.1093/ve/veab016 · Cited by 34 · see citing works
General Strategies for RNA X-ray Crystallography
Jackson, R. W., Smathers, C. M., & Robart, A. R. (2023) · Molecules · doi:10.3390/molecules28052111 · Cited by 34 · see citing works
Computational Methods for RNA Structure Validation and Improvement
Jain, S., Richardson, D. C., & Richardson, J. S. (2015) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2015.01.007 · Cited by 34 · see citing works
Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins
Aithal, A., Dagar, S., & Rajamani, S. (2023) · ACS Omega · doi:10.1021/acsomega.2c07635 · Cited by 35 · see citing works
NMR characterization of RNA small molecule interactions
Thompson, R. D., Baisden, J. T., & Zhang, Q. (2019) · Methods · doi:10.1016/j.ymeth.2019.05.015 · Cited by 31 · see citing works
Mechanism and Distribution of glmS Ribozymes
McCown, P. J., Winkler, W. C., & Breaker, R. R. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-545-9_8 · Cited by 32 · see citing works
An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence
Lau, M. W. L., & Ferré-D’Amaré, A. R. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1360 · Cited by 31 · see citing works
Mutschler, H., & Holliger, P. (2014) · Journal of the American Chemical Society · doi:10.1021/ja4127714 · Cited by 30 · see citing works
Scarborough, R. J., & Gatignol, A. (2015) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-2432-5_5 · Cited by 29 · see citing works
Yamagami, R., Huang, R., & Bevilacqua, P. C. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00578 · Cited by 28 · see citing works
OLE RNA protects extremophilic bacteria from alcohol toxicity
Wallace, J. G., Zhou, Z., & Breaker, R. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks352 · Cited by 28 · see citing works
Breaker, R. R. (2020) · ACS Chemical Biology · doi:10.1021/acschembio.0c00214 · Cited by 28 · see citing works
Wurmthaler, L. A., Klauser, B., & Hartig, J. S. (2017) · RNA Biology · doi:10.1080/15476286.2017.1397870 · Cited by 27 · see citing works
Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories
Yang, M., Xie, Y., Zhu, L., Li, X., & Xu, W. (2024) · ACS Catalysis · doi:10.1021/acscatal.4c02670 · Cited by 24 · see citing works
Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world
Soslau, G. (2018) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2018.03.021 · Cited by 23 · see citing works
A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes
Doamekpor, S. K., Gozdek, A., Kwaśnik, A., Kufel, J., & Tong, L. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1107 · Cited by 24 · see citing works
Riccitelli, N. J., Delwart, E., & Lupták, A. (2014) · Biochemistry · doi:10.1021/bi401717w · Cited by 24 · see citing works
Many Activities, One Structure: Functional Plasticity of Ribozyme Folds
Lau, M. W. L., & Ferré-D’Amaré, A. R. (2016) · Molecules · doi:10.3390/molecules21111570 · Cited by 24 · see citing works
Posakony, J., & Ferré-D’Amaré, A. R. (2013) · The Journal of Organic Chemistry · doi:10.1021/jo400192e · Cited by 23 · see citing works
Minimal Hammerhead Ribozymes with Uncompromised Catalytic Activity
O’Rourke, S. M., Estell, W., & Scott, W. G. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.05.005 · Cited by 22 · see citing works
Self-citationSocial Networking of Quasi-Species Consortia drive Virolution via Persistence
Villarreal, L. P., Witzany, G., & Telos-Philosophische Praxis, B. (2021) · AIMS Microbiology · doi:10.3934/microbiol.2021010 · Cited by 22 · see citing works
Intronic hammerhead ribozymes in mRNA biogenesis
García‐Robles, I., Sánchez-Navarro, J. Á., & de la Peña, M. (2012) · Biological Chemistry · doi:10.1515/hsz-2012-0223 · Cited by 22 · see citing works
Ferré-D’Amaré, A. R. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0131 · Cited by 22 · see citing works
Huang, M., & York, D. M. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp01050g · Cited by 22 · see citing works
RNA Catalysis, Thermodynamics and the Origin of Life
Scott, W., Szöke, A., Blaustein, J., O’Rourke, S. M., & Robertson, M. P. (2014) · Life · doi:10.3390/life4020131 · Cited by 22 · see citing works
Self-citationMolecular Simulations of RNA 2′- O -Transesterification Reaction Models in Solution
Radak, B. K., Harris, M. E., & York, D. M. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp3084277 · Cited by 21 · see citing works
Göppel, T., Rosenberger, J. H., Altaner, B., & Gerland, U. (2022) · Life · doi:10.3390/life12040567 · Cited by 21 · see citing works
Drogalis, L. K., & Batey, R. (2020) · PLoS ONE · doi:10.1371/journal.pone.0243155 · Cited by 21 · see citing works
Scaling Catalytic Contributions of Small Self‐Cleaving Ribozymes
Egger, M., Bereiter, R., Mair, S., & Micura, R. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202207590 · Cited by 20 · see citing works
- Authors
- Ferre-D'Amare, A. R., & Scott, W. G.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Scott, W. G.
- Venue
- Cold Spring Harbor Perspectives in Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-09-15
- Volume
- 2
- Issue
- 10
- Pages
- a003574-a003574
- ISSN
- 1943-0264 (ISSN-L)
- PMC
- PMC2944367
- OpenAlex
- W2105638515
- Cited by
- 205
- References
- 74
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 8 · 2023: 11 · 2022: 12 · 2021: 10 · 2020: 12 · 2019: 24 · 2018: 7 · 2017: 14 · 2016: 16 · 2015: 25 · 2014: 17 · 2013: 7 · 2012: 15
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cold Spring Harbor Perspectives in Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- W. M. Keck Foundation
- National Institutes of Health (Z99 HL999999)
- National Heart, Lung, and Blood Institute (ZIAHL006102)
- National Institute of General Medical Sciences (GM63576, R01GM063576, R01GM087721)
- National Institute of Allergy and Infectious Diseases (AI043393, R01AI043393, R21AI043393)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- self-cleaving ribozymes, hammerhead ribozyme, hairpin ribozyme, hepatitis delta virus ribozyme, glmS ribozyme, riboswitches, RNA catalysis, crystal structure, ribozyme evolution, satellite RNA
- MeSH terms
- Hepatitis Delta Virus, Models, Molecular, Ribonuclease, Pancreatic, RNA, Catalytic, Catalytic Domain
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