Life’s development and adaption to fluctuating environments are underpinned by DNA–protein interactions, which have also spurred the development of artificial systems ranging from genetic circuits to nanoarchitectures. Nonetheless, in cellulo there remains an untapped design space for DNA–protein systems that are incompatible with the role of DNA as genetic material. Here we engineer retrons to intracellularly express non-genetic small DNAs embedding specific protein-binding sequences. These DNA species are products of genes and therefore their quantitative, spatial and functional control is decoupled from genetic stability, enabling alternative architectures of DNA–protein systems with unique functions. Using synthetic networks of proteins and the engineered retron-DNA, we demonstrated precise, multiplexed gene regulation and construction of feedback circuits for dynamic responses. Further, we developed DNA-based molecular scaffolds and bridges that enable modular, post-translational and spatial control of multiple proteins within cells. Finally, we transformed an allosteric transcription factor into inducible post-translational switches. Our work suggests that the non-genetic DNA–protein systems represent a promising control layer for creating synthetic cellular behaviours.