DNA condensates with embedded structures, functions, and reaction networks
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Abstract
DNA nanotechnology has traditionally relied on the precise Watson–Crick–Franklin base-pairing interaction for programming synthetic DNA oligonucleotides to construct well-defined nanostructure and nanodevices. The development of toehold-mediated strand displacement reactions further expanded the field into DNA reaction networks for applications in detection, diagnostics, and computation. Nevertheless, DNA nanotechnology faces a challenge in scaling to larger materials and systems. Recently, synthetic long-chain single-stranded DNA polymers have been shown to undergo temperature-induced phase separation, yielding micron-sized DNA condensates that extend the scope of DNA-based materials and open possibilities for new applications. These condensates closely resemble biomolecular condensates found in cells, formed through liquid–liquid phase separation of proteins and nucleic acids. They provide valuable model systems for studying the properties and mechanisms of biomolecular condensates in controlled settings. Meanwhile, their inherent compatibility with DNA nanotechnology and synthetic biology make DNA condensates promising synthetic cell models for integrating structures and functions. Finally, DNA condensates introduce a new hierarchical level of DNA-based materials for constructing complex multiscale architectures and provide a versatile compartmentalization strategy for DNA reaction networks to address challenges in scalability and modularity.
At the intersection of soft matter, supramolecular chemistry, DNA nanotechnology, and synthetic biology, this thesis explores the application of DNA condensates across different research topics:
In the first part of the thesis, DNA condensates are investigated as a model system for biomolecular condensates. They reveal how macromolecular transport within condensates can deviate from classical Fickian diffusion under certain conditions. This study identifies a new transport mechanism, termed ballistic wave diffusion. It emerges from molecular-recognition-mediated transition of condensates from arrested to dynamic states. This mechanism offers a new perspective on macromolecular transport within biomolecular condensates, providing fundamental insights into their behavior in cellular environments.
Beyond serving as model systems for biomolecular condensates, DNA condensates also provide a versatile platform for constructing minimalistic synthetic cells. In the second part of this thesis, they are used to incorporate subcellular structures and transcription function. A co-phase-separation strategy is developed for functionalizing their core with unique single-stranded DNA sequences as recognition barcodes for binding complementary strands. These barcodes enable them to modularly integrate DNA tiles at defined concentrations, enabling the controlled formation of DNA nanotubes inside synthetic cells as artificial cytoskeletons. These cytoskeletons enhance the mechanical stability of synthetic cells and support the formation of a stable synthetic cell-cell interface via cRGD-integrin binding. In parallel, co-phase separation has been leveraged to introduce transcription promoter sequences into DNA condensates, enabling the sequestration of transcription templates and enzymes. This endows the condensates with the ability to locally transcribe RNA nanostar sequences in their cores, which subsequently condense into diverse artificial condensate patterns as intracellular compartments.
This thesis also explores the application of DNA condensates as a compartmentalization strategy for DNA reaction networks. DNA barcodes inside DNA condensates are used to compartmentalize DNA reaction components. In contrast to the global diffusion and reaction observed in solution-based systems, confining DNA reactions within condensates physically isolates sequences from different networks, thereby preventing unwanted diffusion and crosstalk. This allows multiple reaction networks to be independently executed in a single system. Moreover, this approach simplifies design principles and allows the reuse of identical sequence designs for different reactions without interference, facilitating improved scalability and modularity in DNA reaction networks.
From a future perspective, the concepts and approaches developed in this thesis open up opportunities across various research directions. DNA condensates and ballistic wave diffusion could be harnessed to design a gating mechanism that controls the transport of large macromolecules through size-exclusion effects, representing responsive material systems. Their core barcodes could be engineered to integrate multiple functional modules and enable synergistic effects in advanced synthetic cell systems. In addition, DNA condensates can enrich dilute species through barcode recognition and facilitate localized reactions via proximity effects, with potential applications in detection and diagnostics. Of particular interest, DNA condensates may be further developed for compartmentalizing complex DNA reaction networks, such as multi-bit DNA Adder gate arrays, thereby enabling more sophisticated and scalable DNA computing systems capable of addressing challenging tasks.