Versatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

多功能的基因表达调控工具对于定制化基因网络的规模和复杂性具有定制响应至关重要。在这里，我们研究并改变了自然界中普遍存在的间接基因调控机制的用途，该机制利用诱骗蛋白质结合DNA位点（称为DNA海绵）来调节大肠杆菌中的靶基因表达。我们证明了合成DNA海绵可以被设计为重塑基因电路的响应曲线，从而提供多方面的调节能力，包括将基础泄漏减少> 20倍，将系统输出幅度增加> 130倍，将动态范围增加> 70倍，并将宿主的生长抑制率降低20％以上。此外，与单层海绵相比，用于对多种调节蛋白进行诱变的多层DNA海绵可对层状回路的响应提供累加的调节效果。我们的工作表明，合成DNA海绵为系统地设计合成基因电路的性能提供了一种简单而可通用的途径，从而扩展了目前用于基因调控的工具包，具有广泛的潜在应用。