BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts
Fig 4
The idealized models (A, B, and C) do not model the cellular environment; genes and transcripts transcribe and translate catalytically. A. Schematic and simulation of a constituitively active repressor gene repressing a reporter. B. Schematic and simulations of of a toggle switch created by having two genes, A and B, mutually repress each other. C. Schematic and dynamics of a 3-repressor oscillator. The detailed models (D, E, & F) model the cellular environment by including ribosomes, RNAases and background resource competition for cellular resources. D. A dCas9-guideRNA complex binds to the promoter of a reporter and inhibiting transcription. Heatmap shows retroactivity caused by varying the amount of dCas9 and guide-RNA expressed. The sharing of transcription and translational resources gives rise to increases and decreases of reporter even when there is very little repressor. E. A proposed model for a non-transcriptional toggle switch formed by homodimer-RNAase; the homodimer-RNAase made from subunit A selectively degrades the mRNA producing subunit B and visa-versa. F. A model of the Repressillator exploring the effects of multiple ribosomes binding to the same mRNA. G. Histogram comparing the sizes of models A-F and the amount of BioCRNpyler code needed to generate them.