Synthetic frequency-controlled gene circuits unlock expanded cellular states

Abstract: Natural biological systems process environmental information through both amplitude and frequency-modulated signals, yet engineered biological circuits have largely relied on amplitude-based regulation alone. Despite the prevalence of frequency-encoded signals in natural systems, fundamental challenges in designing and implementing frequency-responsive gene circuits have limited their development in synthetic biology. Here we present a Time-Resolved Gene Circuit (TRGC) architecture that enables frequency-to-amplitude signal conversion in engineered biological systems. Through systematic analysis, we establish a theoretical framework that guides the design of synthetic circuits capable of distinct frequency-dependent responses, implementing both high-pass and low-pass filtering behaviors. To enable rigorous characterization of these dynamic circuits, we developed a high-throughput automated platform that ensures stable and reproducible measurements of frequency-dependent r esponses across diverse conditions. Using this platform, we demonstrate that these frequency-modulated circuits can access cellular states unreachable through conventional amplitude modulation, significantly expanding the controllable gene expression space in multi-gene systems. Our results show that frequency modulation expands the range of achievable expression patterns when controlling multiple genes through a single input, demonstrating a new paradigm for engineering cellular behaviors. This work establishes frequency modulation as a powerful strategy for expanding the capabilities of engineered biological systems and enhancing cellular response to dynamic signals.