Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries.
Journal
IEEE/ACM Trans. Comput. Biology Bioinform.
Journal Volume
12
Journal Issue
3
Pages
712-725
Date Issued
2015
Author(s)
Hsu, Chih-Yuan
Pan, Zhen-Ming
Hu, Rei-Hsing
Chang, Chih-Chun
Cheng, Hsiao-Chun
Lin, Che
Chen, Bor-Sen
Abstract
In this study, robust biological filters with an external control to match a desired input/output (I/O) filtering response are engineered based on the well-characterized promoter-RBS libraries and a cascade gene circuit topology. In the field of synthetic biology, the biological filter system serves as a powerful detector or sensor to sense different molecular signals and produces a specific output response only if the concentration of the input molecular signal is higher or lower than a specified threshold. The proposed systematic design method of robust biological filters is summarized into three steps. Firstly, several well-characterized promoter-RBS libraries are established for biological filter design by identifying and collecting the quantitative and qualitative characteristics of their promoter-RBS components via nonlinear parameter estimation method. Then, the topology of synthetic biological filter is decomposed into three cascade gene regulatory modules, and an appropriate promoter-RBS library is selected for each module to achieve the desired I/O specification of a biological filter. Finally, based on the proposed systematic method, a robust externally tunable biological filter is engineered by searching the promoter-RBS component libraries and a control inducer concentration library to achieve the optimal reference match for the specified I/O filtering response.
Type
journal article