ArticleRNA (New York, N.Y.)2005
Ribozyme motif structure mapped using random recombination and selection.
Article in RNA (New York, N.Y.), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- On the roles of function and selection in evolving systems.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A GTP-synthesizing ribozyme selected by metabolic coupling to an RNA polymerase ribozyme.Science advances · 2021Article
- Secondary Structure Libraries for Artificial Evolution Experiments.Molecules (Basel, Switzerland) · 2021Article
- In vitro selections with RNAs of variable length converge on a robust catalytic core.Nucleic acids research · 2021Article
- A combinatorial method to isolate short ribozymes from complex ribozyme libraries.Nucleic acids research · 2020Article
- Extensive libraries of gene truncation variants generated by in vitro transposition.Nucleic acids research · 2017Article
- 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
- RNA synthesis by in vitro selected ribozymes for recreating an RNA world.Life (Basel, Switzerland) · 2015Review
- Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme.RNA (New York, N.Y.) · 2013Article
- Functional information and the emergence of biocomplexity.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Discovery of a mRNA mitochondrial localization element in Saccharomyces cerevisiae by nonhomologous random recombination and in vivo selection.Nucleic acids research · 2007Article
- Modular evolution and increase of functional complexity in replicating RNA molecules.RNA (New York, N.Y.) · 2007Article
- Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server.BMC bioinformatics · 2006Article
- Recombination during in vitro evolution.Journal of molecular evolution · 2005Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Isolating the core functional elements of an RNA is normally performed during the characterization of a new RNA in order to simplify further biochemical analysis. The removal of extraneous sequence is challenging and can lead to biases that result from the incomplete sampling of deletion variants. An impartial solution to this problem is to construct a library containing a large number of deletion constructs and to select functional RNA isolates that are at least as efficient as their full-length progenitors. Here, we use nonhomologous recombination and selection to isolate the catalytic core of a pyrimidine nucleotide synthase ribozyme. A variable-length pool of approximately 10(8) recombinant molecules that included deletions, inversions, and translocations of a 271-nucleotide-long ribozyme isolate was constructed by digesting and randomly religating its DNA genome. In vitro selection for functional ribozymes was then performed in a size-dependent and a size-independent manner. The final pools had nearly equivalent catalytic rates even though their length distributions were completely different, indicating that a diverse range of deletion constructs were functionally active. Four short sequence islands, requiring as little as 81 nt of sequence, were found within all of the truncated ribozymes and could be folded into a secondary structure consisting of three helix-loops. Our findings suggest that nonhomologous recombination is a highly efficient way to isolate a ribozyme's core motif and could prove to be a useful method for evolving new ribozyme functions from pre-existing sequences in a manner that may have played an important role early in evolution.
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