Methods and systems for quantifying gene expression in synthetic gene circuits and for tuning synthetic gene circuits

Abstract

A method of tuning the performance of a synthetic gene circuit comprising a plurality of genes is disclosed. The method includes quantifying, for each gene, a relative gene expression metric. The metric is quantified by determining a number of nucleotides in a 5' adjacent transcriptional region (ATR) of the gene, a number of nucleotides in a 3′ ATR, a minimum free energy of a mRNA secondary structure around a ribosome binding site of the gene, a total folding energy for the 5′ ATR, and a folding energy for the first 100 nucleotides of the 3′ ATR, and then summing sequence-dependent energy changes, the terms including scaling coefficients and an average energy cost for synthesizing a nucleotide. The method further includes simulating, through application of the relative gene expression metrics of the plurality of genes to a deterministic model, the performance of an intended function of the synthetic gene circuit.