A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits

BMC Bioinformatics

Research

Austin WT Chiang¹  Ming-Jing Hwang¹ 

[1] Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan;Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan;Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan;

关键词: Synthetic Biology;    Ribosome Binding Site;    Efficiency Level;    Gene Circuit;    Computational Pipeline;   

DOI  :  10.1186/1471-2105-14-S16-S5

来源: Springer

【 摘 要 】

BackgroundAn increasing number of genetic components are available in several depositories of such components to facilitate synthetic biology research, but picking out those that will allow a designed circuit to achieve the specified function still requires multiple cycles of testing. Here, we addressed this problem by developing a computational pipeline to mathematically simulate a gene circuit for a comprehensive range and combination of the kinetic parameters of the biological components that constitute the gene circuit.ResultsWe showed that, using a well-studied transcriptional repression cascade as an example, the sets of kinetic parameters that could produce the specified system dynamics of the gene circuit formed clusters of recurrent combinations, referred to as kinetic motifs, which appear to be associated with both the specific topology and specified dynamics of the circuit. Furthermore, the use of the resulting "handbook" of performance-ranked kinetic motifs in finding suitable circuit components was illustrated in two application scenarios.ConclusionsThese results show that the computational pipeline developed here can provide a rational-based guide to aid in the design and improvement of synthetic gene circuits.

【 授权许可】

CC BY   
© Chiang and Hwang; licensee BioMed Central Ltd. 2013