Directed Evolution of Nucleic Acid Enzymes
Abstract
▪ Abstract Just as Darwinian evolution in nature has led to the development of many sophisticated enzymes, Darwinian evolution in vitro has proven to be a powerful approach for obtaining similar results in the laboratory. This review focuses on the development of nucleic acid enzymes starting from a population of random-sequence RNA or DNA molecules. In order to illustrate the principles and practice of in vitro evolution, two especially well-studied categories of catalytic nucleic acid are considered: RNA enzymes that catalyze the template-directed ligation of RNA and DNA enzymes that catalyze the cleavage of RNA. The former reaction, which involves attack of a 2′- or 3′-hydroxyl on the α-phosphate of a 5′-triphosphate, is more difficult. It requires a comparatively larger catalytic motif, containing more nucleotides than can be sampled exhaustively within a starting population of random-sequence RNAs. The latter reaction involves deprotonation of the 2′-hydroxyl adjacent to the cleavage site, resulting in cleaved products that bear a 2′,3′-cyclic phosphate and 5′-hydroxyl. The difficulty of this reaction, and therefore the complexity of the corresponding DNA enzyme, depends on whether a catalytic cofactor, such as a divalent metal cation or small molecule, is present in the reaction mixture.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
A replicator generally has to exhibit exponential growth in order to dominate over a weaker replicator.
“In practice a replicator generally has to exhibit exponential growth in order to dominate over a weaker replicator [5–7].”
From Towards open-ended evolution in self-replicating molecular systems (2017) · cites this paper as [7]
Cites
Selforganization of matter and the evolution of biological macromolecules
Eigen, M. (1971) · Die Naturwissenschaften · doi:10.1007/bf00623322 · Cited by 3,788 · see citing works
The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., & Altman, S. (1983) · Cell · doi:10.1016/0092-8674(83)90117-4 · Cited by 2,684 · see citing works
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900 · see citing works
RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension.
Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., & Bartel, D. P. (2001) · Science · doi:10.1126/science.1060786 · Cited by 768 · see citing works
A self-replicating ligase ribozyme
Paul, N., & Joyce, G. F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202471099 · Cited by 264 · see citing works
Self-citationA ribozyme composed of only two different nucleotides
Reader, J. S., & Joyce, G. F. (2002) · Nature · doi:10.1038/nature01185 · Cited by 100 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Prebiotic chemistry and the origin of the RNA world.
Leslie E., O. (2004) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230490460765 · Cited by 1,124 · see citing works
Prebiotic Systems Chemistry: New Perspectives for the Origins of Life
Ruiz-Mirazo, K., Briones, C., & de la Escosura, A. (2014) · Chemical Reviews · doi:10.1021/cr2004844 · Cited by 930 · see citing works
Self-Sustained Replication of an RNA Enzyme
Lincoln, T. A., & Joyce, G. F. (2009) · Science · doi:10.1126/science.1167856 · Cited by 670 · see citing works
Self-citationOrigins of building blocks of life: A review
Kitadai, N., & Maruyama, S. (2018) · Geoscience Frontiers · doi:10.1016/j.gsf.2017.07.007 · Cited by 464 · see citing works
Ribozyme-catalyzed transcription of an active ribozyme
Wochner, A., Attwater, J., Coulson, A., & Holliger, P. (2011) · Science · doi:10.1126/science.1200752 · Cited by 399 · see citing works
Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature
Sobczak, J.-P. J., Martin, T. G., Gerling, T., & Dietz, H. (2012) · Science · doi:10.1126/science.1229919 · Cited by 285 · see citing works
Wolf, Y. I., & Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-14 · Cited by 235 · see citing works
“It is noteworthy that the main approach to developing ribozymes with desired activities is in vitro selection that, at least conceptually, mimics the Darwinian evolution of ribozymes thought to occur in the primeval RNA world [49,50].”
BackgroundIce as a protocellular medium for RNA replication
Attwater, J., Wochner, A., Pinheiro, V. B., Coulson, A., & Holliger, P. (2010) · Nature Communications · doi:10.1038/ncomms1076 · Cited by 165 · see citing works
Small Molecule Interactions Were Central to the Origin of Life
Shapiro, R. (2006) · The Quarterly Review of Biology · doi:10.1086/506024 · Cited by 180 · see citing works
Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme
Shechner, D. M., Grant, R. A., Bagby, S. C., Koldobskaya, Y., Piccirilli, J. A., & Bartel, D. P. (2009) · Science · doi:10.1126/science.1174676 · Cited by 136 · see citing works
The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers
Briones, C., Stich, M., & Manrubia, S. C. (2009) · RNA · doi:10.1261/rna.1488609 · Cited by 114 · see citing works
Ruff, K. M., Snyder, T. M., & Liu, D. R. (2010) · Journal of the American Chemical Society · doi:10.1021/ja103023m · Cited by 86 · see citing works
Towards open-ended evolution in self-replicating molecular systems
Duim, H., & Otto, S. (2017) · Beilstein Journal of Organic Chemistry · doi:10.3762/bjoc.13.118 · Cited by 72 · see citing works
Müller, U. F. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6047-1 · Cited by 79 · see citing works
New ligase-derived RNA polymerase ribozymes
LAWRENCE, M. S., & BARTEL, D. P. (2005) · RNA · doi:10.1261/rna.2110905 · Cited by 68 · see citing works
Evolution of the division of labor between genes and enzymes in the RNA world
Boza, G., Szilágyi, A., Kun, Á., Santos, M., & Szathmáry, E. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003936 · Cited by 36 · see citing works
Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube
Diaz Arenas, C., & Lehman, N. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-80 · Cited by 25 · see citing works
Intramolecular RNA replicase: Possibly the first self-replicating molecule in the RNA world
Ma, W., & Yu, C. (2006) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-005-9006-1 · Cited by 20 · see citing works
Szilágyi, A., Zachar, I., & Szathmáry, E. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003193 · Cited by 17 · see citing works
- Authors
- Joyce, G. F.
- Affiliations
- Scripps Research Institute (US)
- Corresponding author
- Joyce, Gerald F.
- ORCID
- Joyce, Gerald F.
- Venue
- Annual Review of Biochemistry
- Publisher
- Annual Reviews
- Published
- 2004-06
- Volume
- 73
- Issue
- 1
- Pages
- 791-836
- ISSN
- 0066-4154 (ISSN-L)
- 1545-4509
- OpenAlex
- W2073775872
- Cited by
- 515
- References
- 6
- Citations by year
- 2026: 9 · 2025: 5 · 2024: 13 · 2023: 11 · 2022: 6 · 2021: 18 · 2020: 14 · 2019: 18 · 2018: 14 · 2017: 24 · 2016: 23 · 2015: 28 · 2014: 27 · 2013: 28 · 2012: 20
- FWCI
- 3.11
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
- Keywords
- in vitro evolution, nucleic acid enzymes, ribozymes, RNA ligation, RNA cleavage, 2',3'-cyclic phosphate, divalent metal cations, catalytic motifs
- MeSH terms
- RNA, Catalytic, Directed Molecular Evolution, DNA, Catalytic
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
