Robust synthetic gene network design via library-based search method

Abstract

Motivation: Synthetic biology aims to develop the artificial gene networks with desirable behaviors using systematic method. These networks with desired behaviors could be constructed using diverse biological parts, which may limit the development to complex synthetic gene networks. Fortunately, some well-characterized promoter libraries for engineering gene networks are widely available. Thus, a synthetic gene network can be constructed by selecting adequate promoters from promoter libraries to achieve the desired behaviors. However, the present promoter libraries cannot be directly applied to engineer a synthetic gene network. In order to efficiently select adequate promoters from promoter libraries for a synthetic gene network, promoter libraries are needed to be redefined based on the dynamic gene regulation. Results: Based on four design specifications, a library-based search method is proposed to efficiently select the most adequate promoter set from the redefined promoter libraries by a genetic algorithm (GA) to achieve optimal reference tracking design. As the number and size of promoter libraries increase, the proposed method can play an important role in the systematic design of synthetic biology.