Recoded Genome 2D: Engineering a Virus-Resistant Microbe

This simulator models genomic recoding, the synthetic-biology strategy (pioneered in E. coli C321.ΔA) that turns a spare stop codon into both a viral firewall and a channel for non-canonical amino acids. Drag the genome ring to rotate it, drag the recoding slider to silently swap TAG stop codons for synonymous TAA across 30 marked genome sites, then decide when it is safe to delete release factor 1 (RF1) — the protein that normally terminates translation at TAG. A live translation-tape panel beneath the ring shows exactly when translation terminates cleanly and when it reads through into a garbled protein. Launch a phage challenge at any point: with RF1 present, invading phage translate and replicate normally; with RF1 gone, their native TAG codons cause translational read-through and every phage protein comes out garbled. Delete RF1 too early, before recoding is complete, and the same read-through wrecks the host's own essential proteins — the live viability readout shows exactly why the ordering of these two steps matters.