公开(公告)号：US20190221281A1

公开(公告)日：2019-07-18

申请号：US16248720

申请日：2019-01-15

Applicant: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY

Inventor： Xiao Wang ,  Qi Zhang ,  Fuqing Wu

IPC: G16B5/00 ,  C12N15/63

CPC classification number: G16B5/00 ,  C12N15/635

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.

公开(公告)号：US11276478B2

公开(公告)日：2022-03-15

申请号：US16248720

申请日：2019-01-15

Applicant: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY

Inventor： Xiao Wang ,  Qi Zhang ,  Fuqing Wu

IPC: G16B5/00 ,  C12N15/63 ,  G16B5/30

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.