ArticleProceedings of the National Academy of Sciences of the United States of America2004
De novo synthesis and development of an RNA enzyme.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A cis-acting ligase ribozyme generates circular RNA in vitro for ectopic protein functioning.Nature communications · 2024Article
- Minimizing amplification bias during reverse transcription for in vitro selections.RNA (New York, N.Y.) · 2023Article
- Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit.Biology · 2023Article
- Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations.RNA (New York, N.Y.) · 2022Article
- Article
- Water/Oil Emulsions with Controlled Droplet Sizes forACS omega · 2021Article
- A combinatorial method to isolate short ribozymes from complex ribozyme libraries.Nucleic acids research · 2020Article
- Systematic minimization of RNA ligase ribozyme through large-scale design-synthesis-sequence cycles.Nucleic acids research · 2019Article
- Protocells and RNA Self-Replication.Cold Spring Harbor perspectives in biology · 2018Review
- Crystal structure of a DNA catalyst.Nature · 2016Article
- Landmarks in the Evolution of (t)-RNAs from the Origin of Life up to Their Present Role in Human Cognition.Life (Basel, Switzerland) · 2015Review
- Limits of neutral drift: lessons from the in vitro evolution of two ribozymes.Journal of molecular evolution · 2014Article
- Article
- A ribozyme that triphosphorylates RNA 5'-hydroxyl groups.Nucleic acids research · 2014Article
- RNA nanotechnology for computer design and in vivo computation.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2013Article
- Universal labeling of 5'-triphosphate RNAs by artificial RNA ligase enzyme with broad substrate specificity.Chemical communications (Cambridge, England) · 2013Article
- An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non-GNRA-type tetraloop.Nucleic acids research · 2013Article
- Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation.Journal of molecular evolution · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Arbitrary manipulation of molecular recognition at the atomic level has many applications. However, systematic design and de novo synthesis of an artificial enzyme based on such manipulation has been a long-standing challenge in the field of chemistry and biotechnology. In this report, we developed an artificial RNA ligase by implementing a synthetic strategy that fuses a series of 3D molecular modelings based on naturally occurring RNA-RNA recognition motifs with a small-scale combinatorial synthesis of a modular catalytic unit. The resulting ligase produces a 3'-5' linkage in a template-directed manner for any combinations of two nucleotides at the reaction site. The reaction rate is 10(6)-fold over that of the uncatalyzed reaction with a yield higher than those of previously reported ligase ribozymes. The strategy may be applicable to the synthesis and development of a variety of nonnatural functional RNAs with defined 3D structures.
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