ArticleNucleic acids research2021
Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 58 citations in OpenAlex.
- Site-Specific Protein Bioconjugation Through Cellular Incorporation of Noncanonical Amino Acids.Angewandte Chemie (International ed. in English) · 2026Review
- Site-specific programming characterizes dynamic post-translational acetylation of histone H2B lysine 108 in mouse embryonic stem cells.Nature communications · 2026Article
- Direct phospho-proteoform delivery reveals a degradation-prone monomeric state of 14-3-3.Chemical science · 2026Article
- Bis-Tetrazine Fluorogenic (Silicon)-Rhodamine Dyes for Live-Cell Labeling.Journal of the American Chemical Society · 2026Article
- Fluorescent non-canonical amino acid as a site-specific conformational probe of prion formation.bioRxiv : the preprint server for biology · 2026Article
- Chemical biology approaches to study and target circadian clocks and their components.FEBS letters · 2026Review
- Genetically encoded green-light-responsive photocaged lysine for sequential control of protein function.Chemical science · 2026Article
- Genetic code expansion for single noncanonical amino acid incorporation into SARS-CoV-2 Omicron spike on amber-free lentiviral particles.Methods in enzymology · 2026Article
- Correlating membrane-protein dynamics with function: Integrating bioinformatics, molecular dynamics, and single-molecule FRET.Protein science : a publication of the Protein Society · 2025Article
- Efficient genetic code expansion without host genome modifications.Nature biotechnology · 2025Article
- Fluorescent labeling strategies for molecular bioimaging.Biophysical reports · 2025Review
- Strategies to Expand the Genetic Code of Mammalian Cells.Chemical reviews · 2025Review
- Light-Activatable Ubiquitin for Studying Linkage-Specific Ubiquitin Chain Formation Kinetics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genetic Code Expansion: Recent Developments and Emerging Applications.Chemical reviews · 2025Review
- Genetically Recoding Respiratory Syncytial Virus to Visualize Nucleoprotein Dynamics and Virion Assembly.ACS infectious diseases · 2025Article
- Reaching New Heights in Genetic Code Manipulation with High Throughput Screening.Chemical reviews · 2024Review
- Fluorescent non-canonical amino acid provides insight into the human serotonin transporter.Nature communications · 2024Article
- Activity-Based Acylome Profiling withJournal of the American Chemical Society · 2024Article
- Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming.Chemical reviews · 2024Review
- Fluorescence labeling strategies for cell surface expression of TRPV1.The Journal of general physiology · 2024Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
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