Synthetic nucleic-acid droplets: a bioprogramming platform for designer microliquids

Abstract

Research on biomolecular liquid-state condensates (droplets) in cells has sparked burgeoning interest among synthetic biologists in programmable droplets assembled from synthetic nucleic acids––information-encoding biomolecules amenable to facile synthesis, versatile sequence design, and molecular decoration. Analogous to biological condensates, well-engineered nanostructures consisting of DNA or RNA strands, which are negatively charged, phase-separate into membrane-free droplets via weak multivalent specific interactions or via electrostatic attraction with positively charged peptides. The membraneless compartments of these droplets allow stimuli responsiveness to molecular cues (DNA/RNA, enzymes, etc.). Nucleic acid droplets thus offer a powerful platform for programming their various features, including hierarchical structuring, molecular recognition capabilities, droplet interactions, and physical properties. Specifically, we describe a DNA linker that serves as a programmable surfactant bridging immiscible DNA phases, which, upon molecular inputs, alters their separation level from mixed to divided states. Furthermore, a rational combination of these features can create intelligent liquid-state architectures capable of naturally unachievable functions and dynamics, such as Boolean operations and directional motion. To predict how molecular-level encoding leads to macroscopic characteristics, coarse-grained models, which treat nucleic acids as strings of interacting rigid beads, are widely utilized. This emerging field represents a cross-disciplinary integration of various fields, from biophysics to information science. This Focus Review highlights recent advances in synthetic nucleic-acid droplets and their far-reaching potential, concluding with perspectives on their future directions and challenges. Emerging from DNA/RNA nanoengineering, synthetic nucleic-acid liquid condensates, forming via phase separation of nanostructures, have attracted increasing attention as a powerful platform for synthetic biology and molecular computing. Base-sequence specificity allows for molecular encoding for their organization, functions, and droplet interactions. Authors overview key topics of these programmable droplets, from dynamics programmability to numerical modeling. Additionally, this review highlights cross-linker modules, which enable dynamic compartmentalization and division of droplets triggered by specific molecular input. These modules allow the condensate phase behavior to represent Boolean logic operation.