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

Abstract

Phase‐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.

Chemical reaction motifs driving non-equilibrium behaviors in phase separating materials

“…The analysis of biological CRNs will help formulate hypotheses on how cells manage a multitude of types of condensates with distinct composition, function, structure, and temporal dynamics [21,23,45]. Our results will also provide guidance toward the design of novel materials in the context of a rapidly expanding set of designeable molecular substrates that could be used to implement a variety of CRNs [27,28], as well as a variety of condensates [12,46,47], where chemical reactions could provide instructions to manage condensate formation, dissolution, organization, and other macroscopic properties.…”

“…Amongst the biological questions pertaining phase separation observed in living cells, the interplay between biochemical reactions and phase separation is of particular interest, because it can explain the dynamic nature of biomolecular condensates in the homeostatic cellular environment [7,8]. In parallel, the combination of synthetic phase separating systems and chemical reactions is making it possible to design artificial organelles [9][10][11] and functional materials with precise spatio-temporal responses [12,13]. Chemically active droplets can also be made to self-propel, acting as potential carriers of material [14,15].…”

DNA Droplets: Intelligent, Dynamic Fluid

“…A recent study has employed DNA droplets to detect cancer biomarkers by combining molecular sensing and DNA computing. [13] This computational DNA droplet can recognize specific combinations of tumor biomarker micro-RNAs (miRNAs) as molecular inputs and output the results of logical operations through physical DNA droplet phase separation (Figure 10). The computing is logically controlled by a linker encoding two receptor sequences that recognize two inputs and fulfill the characteristics of an AND gate.…”

“…[9,10] In the context of artificial cell studies, DNA droplets have emerged as a promising biomaterial for the construction of intelligent artificial cells (Figure 1A). [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] DNA droplets are micrometer-scale liquid-like condensate composed purely, or at least mostly, of DNA, a biomolecule in which genetic information is encoded. Since the first report published in 2018, [14] several groups have explored DNA droplets to demonstrate their fundamental functions, properties, and advantages, which are not parallel to other biomolecules.…”

Amphiphiles formed from synthetic DNA-nanomotifs mimic the step-wise dispersal of transcriptional clusters in the cell nucleus

“…This platform has enabled, for example, the construction of a synthetic DNA segregation module that mimics chromosome separation during mitosis [7]. Embedding into DNA-nanomotif droplets has also allowed the combinatorial detection of tumor biomarkers [8]. Further, an up to 20-fold acceleration of DNA-computing operations has been achieved by embedding of DNA-based logic gates within phase-separated droplets [9].…”