Fig. 1: Synthetic logic computation and oscillation.

Recent examples of synthetic logic circuits are shown in (a–e) and oscillators in (f–j). a Four-input AND gates only produce high output signals at the state [1, 1, 1, 1] where four input signals are all present. b The four-input AND gate based on the transcription factor (TF) interaction and layering³⁴. The two-input AND gates relying on the interaction of the transcriptional activator and its cognate chaperone protein are layered into the four-input AND gate. c The four-input AND gate based on recombinase-mediated inversion of promoter and coding sequences, and excision of terminators^4,43. d The four-input AND gate based on the assembly of trigger RNAs of the toehold switch¹². The trigger RNA complex initiates strand displacement and exposes the RBS and start codon to activate translation. e The four-input AND gate based on the chemical-induced protein assembly⁸⁴. Four chemical-induced dimerization domains bridge the TF DNA-binding domain and transcription activation (TA) domain. f Oscillators produce periodic, oscillating outputs. g The oscillator based on the CRISPR-dCas9 system³². The upstream sgRNA binds with dCas9 and represses the transcription of the downstream sgRNA. h The oscillator based on plasmid copy number control⁵³. The activator plasmid encodes a self-activating quorum-sensing LuxI synthase and P_luxI-driven reporter protein. The repressor plasmid encodes a P_luxI-driven endonuclease cleaving the activator plasmid and P_luxI-driven RNA mediating repressor plasmid replication. i The oscillator based on the post-translational coupling of genetic circuits⁸⁵. The quorum clock (driving the yellow protein expression) and constitutively expressed green protein are coupled by sharing ClpXP proteases. j The oscillator based on protein cleavage and degradation⁸⁷. The upstream protease (e.g., TEV protease) exposes the degron fused to the downstream protease (TVMV protease) and reporter proteins, leading to degradation.