Cited by 216RNA and protein synthesis mechanismsPhysical Organic Chemistry and Reaction KineticsDNA and Nucleic Acid Chemistry

The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.

Ribozyme speed limits

Open access

EMILSSON, GAIL MITCHELL, NAKAMURA, SHINGO, ROTH, ADAM, BREAKER, RONALD R.·2003·RNA

DOI 10.1261/rna.5680603PMC PMC1370456

Open this paper in CoChat — free account Open PDF

Abstract

The speed at which RNA molecules decompose is a critical determinant of many biological processes, including those directly involved in the storage and expression of genetic information. One mechanism for RNA cleavage involves internal phosphoester transfer, wherein the 2′-oxygen atom carries out an S N 2-like nucleophilic attack on the adjacent phosphorus center (transesterification). In this article, we discuss fundamental principles of RNA transesterification and define a conceptual framework that can be used to assess the catalytic power of enzymes that cleave RNA. We deduce that certain ribozymes and deoxyribozymes, like their protein enzyme counterparts, can bring about enormous rate enhancements.

Integrity signals

Registry

Crossref · 10.1261/rna.5680603

Cites

70 of 70 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Catalysis in chemistry and enzymology
Jencks, W. P. (1969) · Medical Entomology and Zoology · Cited by 3,217
Structure and Mechanism in Protein Science
Fersht, A. (2017) · WORLD SCIENTIFIC eBooks · doi:10.1142/10574 · Cited by 2,053
Why Nature Chose Phosphates
Westheimer, F. H. (1987) · Science · doi:10.1126/science.2434996 · Cited by 1,711 · cited 2×
“Both the stability of phosphate esters and their chemical pliability have been suggested as foremost reasons why a phosphate ester has emerged as the backbone of choice for the molecules responsible for genetic information storage and transfer (Westheimer 1987).”
Background
A general purpose RNA-cleaving DNA enzyme
Santoro, S. W., & Joyce, G. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4262 · Cited by 1,546
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 1,217
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
Ribonuclease A
Raines, R. T. (1998) · Chemical Reviews · doi:10.1021/cr960427h · Cited by 938
Pseudo-rotation in the hydrolysis of phosphate esters
Westheimer, F. H. (1968) · Accounts of Chemical Research · doi:10.1021/ar50003a002 · Cited by 772
Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group
Li, Y., & Breaker, R. R. (1999) · Journal of the American Chemical Society · doi:10.1021/ja990592p · Cited by 587
Self-citation
Relationship between internucleotide linkage geometry and the stability of RNA
Soukup, G. A., & Breaker, R. R. (1999) · RNA · doi:10.1017/s1355838299990891 · Cited by 549
Self-citation

Show all 70 references

Research works printed but not linked: 5

Carlson, W.D. 1976. “X-ray diffraction studies of bovine pancreatic ribonuclease-S and E. coli alkaline phosphatase.” Ph.D. thesis, Yale University, New Haven, CT.
1996, Angew. Chem. Int. Ed. Engl., 35, 707
1995, J. Chem. Soc. Perkin Trans., 2, 1203
March, J. 1992. Acids and bases. In Advanced organic chemistry, 4th ed., pp. 248–272. John Wiley & Sons, New York.
1997, RNA, 3, 914

Sorted by citations

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 976
Self-citation
Chemistry, structure and function of approved oligonucleotide therapeutics
Egli, M., & Manoharan, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad067 · Cited by 909
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 606
The origins of the RNA world
Robertson, M. P., & Joyce, G. F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003608 · Cited by 556
Biosensing with DNAzymes
McConnell, E. M., Cozma, I., Mou, Q., Brennan, J. D., Lu, Y., & Li, Y. (2021) · Chemical Society Reviews · doi:10.1039/d1cs00240f · Cited by 492
Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes
Silverman, S. K. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.04.010 · Cited by 365
Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts
Litke, J. L., & Jaffrey, S. R. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0090-6 · Cited by 352
Protocells and RNA Self-Replication
Joyce, G. F., & Szostak, J. W. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a034801 · Cited by 308
A widespread self-cleaving ribozyme class is revealed by bioinformatics
Roth, A., Weinberg, Z., Chen, A. G. Y., Kim, P. B., Ames, T. D., & Breaker, R. R. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1386 · Cited by 287
Self-citation
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 265
Drug delivery of siRNA therapeutics: potentials and limits of nanosystems
Reischl, D., & Zimmer, A. (2008) · Nanomedicine Nanotechnology Biology and Medicine · doi:10.1016/j.nano.2008.06.001 · Cited by 256
Synthetic metallonucleases for RNA cleavage
Morrow, J. R., & Iranzo, O. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.02.006 · Cited by 223
The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition
Polacek, N., & Mankin, A. S. (2005) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230500326334 · Cited by 218
Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme
Canny, M. D., Jucker, F. M., Kellogg, E. A., Khvorova, A., Jayasena, S. D., & Pardi, A. (2004) · Journal of the American Chemical Society · doi:10.1021/ja046848v · Cited by 205
Catalytic DNA (deoxyribozymes) for synthetic applications—current abilities and future prospects
Silverman, S. K. (2008) · Chemical Communications · doi:10.1039/b807292m · Cited by 186
Deoxyribozymes: Selection Design and Serendipity in the Development of DNA Catalysts
Silverman, S. K. (2009) · Accounts of Chemical Research · doi:10.1021/ar900052y · Cited by 182
Deoxyribozymes: useful DNA catalysts in vitro and in vivo
Baum, D. A., & Silverman, S. K. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-8029-y · Cited by 174
DNA Catalysis: The Chemical Repertoire of DNAzymes
Hollenstein, M. (2015) · Molecules · doi:10.3390/molecules201119730 · Cited by 172
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 155
An efficient method for long-term room temperature storage of RNA
Fabre, A.-L., Colotte, M., Luis, A., Tuffet, S., & Bonnet, J. (2014) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.145 · Cited by 151
A common speed limit for RNA-cleaving ribozymes and deoxyribozymes
Breaker, R. R., Emilsson, G. M., Lazarev, D. S., Nakamura, S., Puskarz, I., Roth, A., & Sudarsan, N. (2003) · RNA · doi:10.1261/rna.5670703 · Cited by 151
Self-citation
Structure, folding and mechanisms of ribozymes
Lilley, D. M. J. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.05.002 · Cited by 148
A Versatile Endoribonuclease Mimic Made of DNA: Characteristics and Applications of the 8–17 RNA‐Cleaving DNAzyme
Schlosser, K., & Li, Y. (2010) · ChemBioChem · doi:10.1002/cbic.200900786 · Cited by 142
Crystal structure and mechanistic investigation of the twister ribozyme
Liu, Y., Wilson, T. J., McPhee, S. A., & Lilley, D. M. J. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1587 · Cited by 142
The Effect of Formaldehyde Fixation on RNA
Evers, D. L., Fowler, C. B., Cunningham, B. R., Mason, J. T., & O’Leary, T. J. (2011) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2011.01.010 · Cited by 127
Design Principles for Riboswitch Function
Beisel, C. L., & Smolke, C. D. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000363 · Cited by 125
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
Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology
Weis, S., Llenos, I. C., Dulay, J. R., Elashoff, M. R., Martínez-Murillo, F., & Miller, C. L. (2007) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2007.06.001 · Cited by 118
DNA and RNA Can Be Equally Efficient Catalysts for Carbon−Carbon Bond Formation
Chandra, M., & Silverman, S. K. (2008) · Journal of the American Chemical Society · doi:10.1021/ja7111965 · Cited by 115
Selection of ribozymes that catalyse multiple-turnover Diels–Alder cycloadditions by using in vitro compartmentalization
Agresti, J. J., Kelly, B. T., Jäschke, A., & Griffiths, A. D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503733102 · Cited by 114
Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight
Lönnberg, H. (2011) · Organic & Biomolecular Chemistry · doi:10.1039/c0ob00486c · Cited by 111
Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution
Zeng, J., Giese, T. J., Ekesan, Ş., & York, D. M. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00201 · Cited by 112
RNA Stability: A Review of the Role of Structural Features and Environmental Conditions
Корниенко, И. В., Арамова, О. Ю., Tishchenko, A. A., Rudoy, D. V., & Chikindas, M. L. (2024) · Molecules · doi:10.3390/molecules29245978 · Cited by 127
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 110
Self-citation
Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination
Teixeira, A., Tahiri‐Alaoui, A., West, S., Thomas, B., Ramadass, A., Martianov, I., Dye, M., James, W., Proudfoot, N. J., & Akoulitchev, A. V. (2004) · Nature · doi:10.1038/nature03032 · Cited by 110
Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function
Weinberg, C. E., Weinberg, Z., & Hammann, C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz737 · Cited by 105
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
Self-citation
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
Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions
Ryckelynck, M., Baudrey, S., Rick, C., Marin, A., Coldren, F., Westhof, É., & Griffiths, A. D. (2015) · RNA · doi:10.1261/rna.048033.114 · Cited by 85
DNA Catalysis: Potential, Limitations, Open Questions
Peracchi, A. (2005) · ChemBioChem · doi:10.1002/cbic.200500098 · Cited by 78
Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme
Bonaccio, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh250 · Cited by 77
The Novel Chemical Mechanism of the Twister Ribozyme
Wilson, T. J., Liu, Y., Domnick, C., Kath‐Schorr, S., & Lilley, D. M. J. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.5b11791 · Cited by 78
Phosphodiester models for cleavage of nucleic acids
Mikkola, S., Lönnberg, T., & Lönnberg, H. (2018) · Beilstein Journal of Organic Chemistry · doi:10.3762/bjoc.14.68 · Cited by 80
Nucleic acid enzymes
Fiammengo, R., & Jäschke, A. (2005) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2005.10.006 · Cited by 74
Exploring RNA structure and dynamics through enhanced sampling simulations
Mlýnský, V., & Bussi, G. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.01.004 · Cited by 71
The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids
Higgs, P. (2016) · Life · doi:10.3390/life6020024 · Cited by 64
Catalytic DNA with phosphatase activity
Chandrasekar, J., & Silverman, S. K. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221946110 · Cited by 64
Engineered allosteric ribozymes that respond to specific divalent metal ions
Zivarts, M. V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki182 · Cited by 64
Nucleic acids: function and potential for abiogenesis
Wachowius, F., Attwater, J., & Holliger, P. (2017) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583517000038 · Cited by 63
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes
Bevilacqua, P. C., Harris, M. E., Piccirilli, J. A., Gaines, C. S., Ganguly, A., Kostenbader, K., Ekesan, Ş., & York, D. M. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.9b00202 · Cited by 65
Metal Ion-Dependent DNAzymes and Their Applications as Biosensors
Lan, T., & Lu, Y. (2011) · Metal ions in life sciences · doi:10.1007/978-94-007-2172-2_8 · Cited by 63
Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics
Banáš, P., Walter, N. G., Šponer, J., & Otyepka, M. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp9109699 · Cited by 58
Catalysis and Rational Engineering of trans‐Acting pH6DZ1, an RNA‐Cleaving and Fluorescence‐Signaling Deoxyribozyme with a Four‐Way Junction Structure
Shen, Y., Chiuman, W., Brennan, J. D., & Li, Y. (2006) · ChemBioChem · doi:10.1002/cbic.200600195 · Cited by 57
Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
Ganguly, A., Weissman, B. P., Giese, T. J., Li, N., Hoshika, S., Rao, S. A., Benner, S. A., Piccirilli, J. A., & York, D. M. (2020) · Nature Chemistry · doi:10.1038/s41557-019-0391-x · Cited by 57
The spliceosome: a ribozyme at heart?
Valadkhan, S. (2007) · Biological Chemistry · doi:10.1515/bc.2007.080 · Cited by 57
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
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 59
Self-citation
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
PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase
Blanga‐Kanfi, S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl415 · Cited by 54
Exceptionally fast self-cleavage by a Neurospora Varkud satellite ribozyme
Zamel, R., Poon, A., Jaikaran, D. C. J., Andersen, A. A., Olive, J. E., Abreu, D. D., & Collins, R. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0305753101 · Cited by 54
Insights into DNA catalysis from structural and functional studies of the 8-17 DNAzyme
Cepeda‐Plaza, M., & Peracchi, A. (2020) · Organic & Biomolecular Chemistry · doi:10.1039/c9ob02453k · Cited by 55
Ribozyme Catalysis Revisited: Is Water Involved?
Walter, N. G. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.12.001 · Cited by 51
Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity
Rosenbach, H., Victor, J., Etzkorn, M., Steger, G., Riesner, D., & Span, I. (2020) · Molecules · doi:10.3390/molecules25133100 · Cited by 52
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
The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme
Bingaman, J. L., Zhang, S., Stevens, D. R., Yennawar, N. H., Hammes‐Schiffer, S., & Bevilacqua, P. C. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2300 · Cited by 51
Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution
Ekesan, Ş., & York, D. M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz773 · Cited by 50
The structural basis of RNA-catalyzed RNA polymerization
Shechner, D. M., & Bartel, D. P. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2107 · Cited by 48
Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community
Müller, R., Betsou, F., Barnes, M., Harding, K., Bonnet, J., Kofanova, O. A., Crowe, J. H., & A Review from the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group (2016) · Biopreservation and Biobanking · doi:10.1089/bio.2015.0022 · Cited by 47
SPEED LIMITS FOR ARTIFICIAL RIBONUCLEASES
Morrow, J. R. (2008) · Comments on Inorganic Chemistry · doi:10.1080/02603590802551801 · Cited by 47
Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base
Harris, M. E., Dai, Q., Gu, H., Kellerman, D. L., Piccirilli, J. A., & Anderson, V. E. (2010) · Journal of the American Chemical Society · doi:10.1021/ja103550e · Cited by 48
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery
Zeng, J., Tao, Y., Giese, T. J., & York, D. M. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c01172 · Cited by 49
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
Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme
Xin, Y., & Hamelberg, D. (2010) · RNA · doi:10.1261/rna.2334110 · Cited by 45
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
Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites
Seith, D. D., Bingaman, J. L., Veenis, A. J., Button, A. C., & Bevilacqua, P. C. (2017) · ACS Catalysis · doi:10.1021/acscatal.7b02976 · Cited by 44
Metal Ions: Supporting Actors in the Playbook of Small Ribozymes
Johnson-Buck, A. E., McDowell, S. E., & Walter, N. G. (2011) · Royal Society of Chemistry eBooks · doi:10.1039/9781849732512-00175 · Cited by 44
Zn 2+ -Dependent Deoxyribozymes That Form Natural and Unnatural RNA Linkages
Manthei, K. A., Purtha, W. E., Wolf, A. C., Flynn-Charlebois, A., & Silverman, S. K. (2005) · Biochemistry · doi:10.1021/bi050146g · Cited by 43
Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions
Giese, T. J., Zeng, J., Ekesan, Ş., & York, D. M. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00151 · Cited by 42
Evidence of a General Acid–Base Catalysis Mechanism in the 8–17 DNAzyme
Cepeda‐Plaza, M., McGhee, C. E., & Lu, Y. (2018) · Biochemistry · doi:10.1021/acs.biochem.7b01096 · Cited by 40
The glmS Ribozyme Cofactor is a General Acid–Base Catalyst
Viladoms, J., & Fedor, M. J. (2012) · Journal of the American Chemical Society · doi:10.1021/ja307021f · Cited by 39
Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup
Vaidya, N., Walker, S. I., & Lehman, N. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.01.007 · Cited by 39
Catalytic Diversity of Extended Hammerhead Ribozymes
Shepotinovskaya, I. V., & Uhlenbeck, O. C. (2008) · Biochemistry · doi:10.1021/bi7025358 · Cited by 38
An Active-Site Guanine Participates in glmS Ribozyme Catalysis in Its Protonated State
Viladoms, J., Scott, L. G., & Fedor, M. J. (2011) · Journal of the American Chemical Society · doi:10.1021/ja207426j · Cited by 38
Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations
McDowell, S. E., Jun, J. M., & Walter, N. G. (2010) · RNA · doi:10.1261/rna.1829110 · Cited by 38
How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes
Lilley, D. M. J. (2017) · Biochemical Society Transactions · doi:10.1042/bst20160158 · Cited by 39
Targeting BACE with small inhibitory nucleic acids - a future for Alzheimer's disease therapy?
Nawrot, B. (2004) · Acta Biochimica Polonica · doi:10.18388/abp.2004_3582 · Cited by 38
Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation
Kellerman, D. L., York, D. M., Piccirilli, J. A., & Harris, M. E. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.06.010 · Cited by 38
Hatchet ribozyme structure and implications for cleavage mechanism
Zheng, L., Falschlunger, C., Huang, K., Mairhofer, E., Yuan, S., Wang, J., Patel, D. J., Micura, R., & Ren, A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1902413116 · Cited by 37
Reinventing the Wheel: Synthetic Circular RNAs for Mammalian Cell Engineering
Costello, A., Lao, N. T., Barron, N., & CLYNES, M. M. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.07.008 · Cited by 39
Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes
Lee, K.-Y., & Lee, B. (2017) · Molecules · doi:10.3390/molecules22040678 · Cited by 36
Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications
Liczner, C., Duke, K., Juneau, G., Egli, M., & Wilds, C. J. (2021) · Beilstein Journal of Organic Chemistry · doi:10.3762/bjoc.17.76 · Cited by 34
Raman crystallography of RNA
Gong, B., Chen, J.-H., Yajima, R., Chen, Y., Chase, E. S., Chadalavada, D. M., Golden, B. L., CAREY, P. R., & Bevilacqua, P. C. (2009) · Methods · doi:10.1016/j.ymeth.2009.04.016 · Cited by 34
QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester A N + D N Associative Mechanism with an O2′ H Internal Proton Transfer
Elsässer, B., Fels, G., & Weare, J. H. (2013) · Journal of the American Chemical Society · doi:10.1021/ja406122c · Cited by 33
Impact of mixing and shaking on mRNA-LNP drug product quality characteristics
Matthessen, R., Pottelberge, R. V., Goffin, B., & Winter, G. (2024) · Scientific Reports · doi:10.1038/s41598-024-70680-4 · Cited by 32
Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology
Gaines, C. S., Giese, T. J., & York, D. M. (2019) · ACS Catalysis · doi:10.1021/acscatal.9b01155 · Cited by 32
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
Self-citation
The ionic environment determines ribozyme cleavage rate by modulation of nucleobase p K a
Smith, M. D., Mehdizadeh, R., Olive, J. E., & Collins, R. A. (2008) · RNA · doi:10.1261/rna.1102308 · Cited by 32
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
Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme
Ganguly, A., Weissman, B. P., Piccirilli, J. A., & York, D. M. (2019) · ACS Catalysis · doi:10.1021/acscatal.9b02035 · Cited by 31
Opportunities for innovation: Building on the success of lipid nanoparticle vaccines
Huang, J. Y., Yuen, D., Mintern, J. D., & Johnston, A. P. R. (2021) · Current Opinion in Colloid & Interface Science · doi:10.1016/j.cocis.2021.101468 · Cited by 31

Authors: EMILSSON, G. M., NAKAMURA, S., ROTH, A., & BREAKER, R. R.
Affiliations: Yale University (US)
Corresponding author: BREAKER, RONALD R.
ORCID: NAKAMURA, SHINGO
BREAKER, RONALD R.
Venue: RNA
Publisher: Cold Spring Harbor Laboratory
Published: 2003-07-17
Volume: 9
Issue: 8
Pages: 907-918
ISSN: 1355-8382 (ISSN-L)
1469-9001
DOI: 10.1261/rna.5680603
PMC: PMC1370456
OpenAlex: W2160498409
Cited by: 216
References: 70
Citations by year: 2026: 4 · 2025: 5 · 2024: 11 · 2023: 6 · 2022: 11 · 2021: 18 · 2020: 7 · 2019: 16 · 2018: 9 · 2017: 16 · 2016: 8 · 2015: 6 · 2014: 5 · 2013: 10 · 2012: 5
FWCI: 0.68
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: RNA (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: David and Lucile Packard Foundation
National Institutes of Health (5r01gm057500-03)
National Institute of General Medical Sciences (GM559343, GM57500)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Physical Sciences › Chemistry › Organic Chemistry › Physical Organic Chemistry and Reaction Kinetics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords: ribozymes, deoxyribozymes, RNA cleavage, catalytic rate enhancement
MeSH terms: Esterification, Hydrolysis, Oxygen, RNA, RNA, Catalytic, Hydroxyl Radical

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Ribozyme speed limits

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks