ArticleRNA (New York, N.Y.)2013
Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Using structured libraries, selection, and machine learning to rapidly explore the sequence space of a fluorescent deoxyribozyme.Nucleic acids research · 2025Article
- Aurora: a fluorescent deoxyribozyme for high-throughput screening.Nucleic acids research · 2024Article
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.Nature communications · 2022Article
- Supernova: A Deoxyribozyme that Catalyzes a Chemiluminescent Reaction.Angewandte Chemie (International ed. in English) · 2022Article
- Single-round deoxyribozyme discovery.Nucleic acids research · 2021Article
- Secondary Structure Libraries for Artificial Evolution Experiments.Molecules (Basel, Switzerland) · 2021Article
- A combinatorial method to isolate short ribozymes from complex ribozyme libraries.Nucleic acids research · 2020Article
- Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme.Nature communications · 2020Article
- Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA.Journal of the American Chemical Society · 2019Article
- Lipid vesicles chaperone an encapsulated RNA aptamer.Nature communications · 2018Article
- Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code.Transcription · 2018Article
- Rooted tRNAomes and evolution of the genetic code.Transcription · 2018Article
- Information theory, evolutionary innovations and evolvability.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Article
- Altered biochemical specificity of G-quadruplexes with mutated tetrads.Nucleic acids research · 2016Article
- Sex in a test tube: testing the benefits of in vitro recombination.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- High-Throughput Mutational Analysis of a Twister Ribozyme.Angewandte Chemie (International ed. in English) · 2016Article
- Elucidating the molecular architecture of adaptation via evolve and resequence experiments.Nature reviews. Genetics · 2015Review
- Fitness Landscapes of Functional RNAs.Life (Basel, Switzerland) · 2015Review
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2 authors.
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Abstract
The relationship between genotype and phenotype is often described as an adaptive fitness landscape. In this study, we used a combination of recombination, in vitro selection, and comparative sequence analysis to characterize the fitness landscape of a previously isolated kinase ribozyme. Point mutations present in improved variants of this ribozyme were recombined in vitro in more than 10(14) different arrangements using synthetic shuffling, and active variants were isolated by in vitro selection. Mutual information analysis of 65 recombinant ribozymes isolated in the selection revealed a rugged fitness landscape in which approximately one-third of the 91 pairs of positions analyzed showed evidence of correlation. Pairs of correlated positions overlapped to form densely connected networks, and groups of maximally connected nucleotides occurred significantly more often in these networks than they did in randomized control networks with the same number of links. The activity of the most efficient recombinant ribozyme isolated from the synthetically shuffled pool was 30-fold greater than that of any of the ribozymes used to build it, which indicates that synthetic shuffling can be a rich source of ribozyme variants with improved properties.
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