Automated and Programmable Cell-Free Systems for Scalable Synthetic Biology with a Focus on Biofoundry Integration

Abstract

Cell-free protein synthesis (CFPS) has been used as a transformative technology in synthetic biology, providing a programmable, scalable, and automation-compatible platform for biological engineering. Freed from the limitations of cell viability and growth, CFPS enables rapid design iteration, precise control of reaction conditions, and high-throughput experimentation. Recent integration of CFPS with biofoundries-automated, high-throughput biological engineering platforms-has dramatically accelerated the Design-Build-Test-Learn cycle, facilitating applications such as enzyme engineering, metabolic pathway prototyping, biosensor development, and remote biomanufacturing. Advances in automation technologies, including liquid-handling robotics and digital microfluidics, have further enhanced the scalability and reproducibility of CFPS workflows. Additionally, coupling CFPS with machine learning has enabled predictive optimization of genetic constructs and biosynthetic systems. This review highlights the technological innovations driving the convergence of CFPS and automated biofoundries, outlining current capabilities, challenges, and future directions toward programmable, scalable, and distributed biological engineering.

Keywords: Cell-free protein synthesis; automation; biofoundry; high-throughput screening; programmable biological engineering; synthetic biology.

Fig. 1. Major components of cell-free protein synthesis (CFPS).

A CFPS reaction consists of DNA templates, transcription (TX)-translation (TL) machineries, nucleotides, amino acids, energy regeneration systems, and cofactors/buffers. These elements work together in cell-free environments to drive gene expression independent of living cells.

Fig. 2. General applications of CFPS.

CFPS supports a broad range of applications, including metabolic pathway prototyping, enzyme engineering, antibody screening, genetic circuit testing, and biosensor development. Its open and tunable environment enables rapid and flexible prototyping across synthetic biology, diagnostics, and biomanufacturing.

Fig. 3. Integration of CFPS into the Design-Build-Test-Learn (DBTL) cycle.

CFPS enables rapid prototyping and high throughput testing within the DBTL workflow by decoupling gene expression from living cells. Its compatibility with automation, programmability, and reproducibility accelerates synthetic biology research and biofoundry operations.