title: Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries.
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.
authors.forename: Chih-Yuan
authors.initials: CY
authors.lastname: Hsu
authors.forename: Zhen-Ming
authors.initials: ZM
authors.lastname: Pan
authors.forename: Rei-Hsing
authors.initials: RH
authors.lastname: Hu
authors.forename: Chih-Chun
authors.initials: CC
authors.lastname: Chang
authors.forename: Hsiao-Chun
authors.initials: HC
authors.lastname: Cheng
authors.forename: Che
authors.initials: C
authors.lastname: Lin
authors.forename: Bor-Sen
authors.initials: BS
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D001665:Binding Sites / Q000235:genetics; D015723:Gene Library; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics; D058615:Synthetic Biology / Q000379:methods*