ArticleNature2016
Defining synonymous codon compression schemes by genome recoding.
Article in Nature, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
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Who cites it
113 citing papers in PubMed, 170 citations in OpenAlex.
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- Automated linear DNA assembly of A. thaliana's chloroplast and mitochondrial genome.Nucleic acids research · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
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- Synthetic rewriting technologies in mammalian cells.Nature communications · 2026Review
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- The design and engineering of synthetic genomes.Nature reviews. Genetics · 2025Review
- A diverse single-stranded DNA-annealing protein library enables efficient genome editing across bacterial phyla.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genetic Code Expansion: Recent Developments and Emerging Applications.Chemical reviews · 2025Review
- Engineered CRISPR-Cas9 for Streptomyces sp. genome editing to improve specialized metabolite production.Nature communications · 2025Article
- Restructuring a Complex Genetic Function on Episomal Vectors inACS synthetic biology · 2025Article
- Hierarchical metabolic engineering for rewiring cellular metabolism.FEMS microbiology reviews · 2025Review
- Defining serine tRNA knockout as a strategy for effective repression of gene expression in organisms with a recoded genome.Nucleic acids research · 2025Article
- Reaching New Heights in Genetic Code Manipulation with High Throughput Screening.Chemical reviews · 2024Review
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- Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules.Nucleic acids research · 2024Article
- Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids.Chemical reviews · 2024Review
- De novo engineering of programmable and multi-functional biomolecular condensates for controlled biosynthesis.Nature communications · 2024Article
53 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Synthetic recoding of genomes, to remove targeted sense codons, may facilitate the encoded cellular synthesis of unnatural polymers by orthogonal translation systems. However, our limited understanding of allowed synonymous codon substitutions, and the absence of methods that enable the stepwise replacement of the Escherichia coli genome with long synthetic DNA and provide feedback on allowed and disallowed design features in synthetic genomes, have restricted progress towards this goal. Here we endow E. coli with a system for efficient, programmable replacement of genomic DNA with long (>100-kb) synthetic DNA, through the in vivo excision of double-stranded DNA from an episomal replicon by CRISPR/Cas9, coupled to lambda-red-mediated recombination and simultaneous positive and negative selection. We iterate the approach, providing a basis for stepwise whole-genome replacement. We attempt systematic recoding in an essential operon using eight synonymous recoding schemes. Each scheme systematically replaces target codons with defined synonyms and is compatible with codon reassignment. Our results define allowed and disallowed synonymous recoding schemes, and enable the identification and repair of recoding at idiosyncratic positions in the genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.