Co-transcriptional allosteric regulation of synthetic nucleic acid receptors

We present a strategy to control allosterically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be tuned (activated or inhibited) in response to the binding of a specific RNA strand acting as allosteric effector. We then show that the receptor loading/release of ligands can be controlled co-transcriptionally by allosteric RNA regulators produced by rationally designed synthetic genes. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling. The kinetics of our allosteric sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used.