ArticleNature communications2021
Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 26 citations in OpenAlex.
- Establishing MS2-MCP-based single-molecule RNA visualization in Schizosaccharomyces pombe.Journal of cell science · 2026Article
- Monitoring in vivo transcription with synthetic serum markers.Nature communications · 2026Article
- Establishing MS2-MCP-based single-molecule RNA visualization inbioRxiv : the preprint server for biology · 2026Article
- Post-transcriptional modular synthetic receptors.Nature chemical biology · 2025Article
- Post-Transcriptional Modular Synthetic Receptors.bioRxiv : the preprint server for biology · 2024Article
- Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA.Biophysical journal · 2024Article
- Design of a self-regulating mRNA gene circuit.Scientific reports · 2024Article
- Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects.ACS synthetic biology · 2023Article
- Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes.Nature communications · 2022Article
- Long-term imaging of individual mRNA molecules in living cells.Cell reports methods · 2022Article
- Intelligent host engineering for metabolic flux optimisation in biotechnology.The Biochemical journal · 2021Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP), and Qβ (QCP) to RNA. Using the oligo library, we generate thousands of candidate binding sites for each CP, and screen for binding using a high-throughput dose-response Sort-seq assay (iSort-seq). We then apply a neural network to expand this space of binding sites, which allowed us to identify the critical structural and sequence features for binding of each CP. To verify our model and experimental findings, we design several non-repetitive binding site cassettes and validate their functionality in mammalian cells. We find that the binding of each CP to RNA is characterized by a unique space of sequence and structural determinants, thus providing a more complete description of CP-RNA interaction as compared with previous low-throughput findings. Finally, based on the binding spaces we demonstrate a computational tool for the successful design and rapid synthesis of functional non-repetitive binding-site cassettes.
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