Computational DNA Droplets Recognizing miRNA Sequence Inputs Based on Liquid–Liquid Phase Separation

Abstract

AbstractPhase‐separated biomolecular droplets are formed in cells to regulate various biological processes. This phenomenon can be applied to constructing self‐assembled dynamic molecular systems such as artificial cells and molecular robots. Recently, programmable phase‐separated droplets called DNA droplets have been reported as a possible method to construct such dynamic molecular systems. This study reports a computational DNA droplet that can recognize a specific combination of tumor biomarker microRNAs (miRNAs) as molecular inputs and output a DNA logic computing result by physical DNA droplet phase separation. A mixed DNA droplet consisting of three DNA nanostructures with orthogonal sticky‐end sequences and two linker DNAs to cross‐bridge the orthogonal DNA nanostructures is proposed. By the hybridization of miRNAs with the linkers, the cross‐bridging ability is lost, causing the phase‐separation of the mixed DNA droplet into three DNA droplets, resulting in executing a miRNA pattern recognition described by a logical expression ((miRNA‐1 ∧ miRNA‐2) ∧ (miRNA‐3 ∧ ¬miRNA‐4)). This experimentally demonstrates that the computational DNA droplets recognize the above specific pattern of chemically synthesized miRNA sequences as a model experiment. In the future, this method will provide potential applications such as diagnosis and therapy with integration to biomolecular robots and artificial cells.