Programming conformational cooperativity to regulate allosteric protein-oligonucleotide signal transduction

Abstract

Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signaling pathways. However, it remains a challenge to develop artificial molecular networks regulated by conformational cooperativity, due to the difficulties in programming and controlling multiple structural interactions. Herein, we develop a cooperative strategy by programming multiple conformational signals, rather than chemical signals, to regulate protein-oligonucleotide signal transduction, taking advantage of the programmability of allosteric DNA constructs. We generate a cooperative regulation mechanism, by which increasing the loop lengths at two different structural modules induced the opposite effects manifesting as down- and up-regulation. We implement allosteric logic operations by using two different proteins. Further, in cell culture we demonstrate the feasibility of this strategy to cooperatively regulate gene expression of PLK1 to inhibit tumor cell proliferation, responding to orthogonal protein-signal stimulation. This programmable conformational cooperativity paradigm has potential applications in the related fields.

A Spatially Controlled Proximity Split Tweezer Switch for Enhanced DNA Circuit Construction and Multifunctional Transduction

“…Currently, [ 22,34 ] signal transduction techniques have garnered considerable interest because of their evolution across a wide range of molecular pathways and signaling networks. [ 35 ] In contrast to the reported cooperative strategy that focuses on programming multiple conformational signals exclusively to regulate protein‐oligonucleotide signal transduction, our design involves two another transduction PST switches based on DNA aptamers for non‐nucleic acid molecules (Figure 3A): tumor progression‐associated adenosine‐5′‐triphosphate (ATP) and arterial thrombosis‐related thrombin (THR) are representative markers of the most studied small molecules and proteins, respectively. When a target molecule binds to the DNT, the proximity effect created by the irregular folding of the target binding sites results in SDR.…”