Current Application of Modeling and Cell-Free System for Synthetic Gene Circuit Design

作者：Thales R. Spartalis, Andres Lizano, Caroline E. Copeland, Yong‐Chan Kwon, Xun Tang · 发表于：Synthetic biology and engineering · 年份：2024 · DOI：10.35534/sbe.2024.10013 · 被引用次数：2 · 研究领域：Gene Regulatory Network Analysis、Viral Infectious Diseases and Gene Expression in Insects、Microfluidic and Capillary Electrophoresis Applications

The desire to harness nature’s capability of precise gene expression regulation has motivated the pursuit of synthetic gene circuits. However, designing and building novel synthetic gene circuits with predictable dynamics is nontrivial. To facilitate the design, cell-free systems have emerged as an effective alternative testbed to living biological systems in characterizing and prototyping synthetic gene regulatory networks, given its relative simplicity and designability in terms of cellular contents. Meanwhile, as parameterizing and analyzing first principle-based models can shed light on the required kinetic parameter values, thus the specific regulatory components, for the desired dynamics, coupling mathematical modeling with cell-free experiments has become an effective approach in exploring novel synthetic gene circuits. In this mini-review, we provide an overview of current progress on using deterministic first principle-based mathematical modeling in conjunction with cell-free systems, in designing and characterizing novel gene circuits, as well as the standing challenges and issues with this approach.