Repurposing Dna-Binding Proteins as Molecular Actuators in Synthetic Systems Through Proximity-Driven DNA Reactions

DNA-binding proteins (DBPs) play central roles in gene regulation by recognizing specific DNA sequences, yet their function in synthetic molecular systems is typically limited to transcriptional control or sequence-specific binding. Here we describe a proximity-driven molecular framework that couples DBP–DNA recognition to DNA strand displacement reactions, enabling DNA-binding proteins to act as sequence-selective inputs for synthetic nucleic acid reaction pathways without modification of the protein scaffold. In our design, protein binding induces spatial colocalization of DNA components, triggering conditional generation of functional nucleic acid outputs through proximity-mediated strand displacement. Using representative DBPs, including EGR1, YY1, and p53, we connect protein recognition to DNA strand displacement, activation of a fluorogenic RNA aptamer, regulation of CRISPR–Cas12a and Cas13 activity, and coordination of multistep CRISPR cascades. A defining feature of this strategy is the decoupling of molecular recognition from downstream function, which avoids structural and thermodynamic constraints associated with switch-based designs. These results demonstrate a general proximity-based approach for integrating DNA-binding proteins into programmable molecular architectures.