The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model

Yanhong Sun; Fengyu Zhang; Qi Ouyang; Chunxiong Luo

doi:10.1016/j.isci.2024.109142

The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model

iScience. 2024 Feb 5;27(3):109142. doi: 10.1016/j.isci.2024.109142. eCollection 2024 Mar 15.

Authors

Yanhong Sun^{1

2}, Fengyu Zhang³, Qi Ouyang^{1

2}, Chunxiong Luo^{1

2

3}

Affiliations

¹ The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China.
² Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
³ Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China.

Abstract

Differential equation models are widely used to describe genetic regulations, predict multicomponent regulatory circuits, and provide quantitative insights. However, it is still challenging to quantitatively link the dynamic behaviors with measured parameters in synthetic circuits. Here, we propose a dynamic delay model (DDM) which includes two simple parts: the dynamic determining part and the doses-related steady-state-determining part. The dynamic determining part is usually supposed as the delay time but without a clear formula. For the first time, we give the detail formula of the dynamic determining function and provide a method for measuring all parameters of synthetic elements (include 8 activators and 5 repressors) by microfluidic system. Three synthetic circuits were built to show that the DDM can notably improve the prediction accuracy and can be used in various synthetic biology applications.

Keywords: Biological sciences; Genetics.