Probing the self-assembly process of amphiphilic tetrahedral DNA frameworks

Probing Cell Membrane Tension Using DNA Framework-Encoded Vibration-Induced Emission Molecular Assemblies

Mechanosensitive fluorescent probes are valuable tools for detecting changes in cellular mechanics and viscosity. While numerous mechanosensitive probes have been developed, the construction of molecular assemblies for probing cellular mechanics remains largely unexplored, possibly due to the challenges of designing assemblies with synergistic and integrated functionalities. Here, we report the design and synthesis of mechanosensitive molecular assemblies by integrating DNA frameworks with vibration-induced emission (VIE) probes to enable live-cell membrane tension imaging. The molecular assemblies consist of a rigid tetrahedral DNA framework anchored with prescribed numbers of VIE probes. We find that VIE probes on the DNA framework retain their ratiometric fluorescence response characteristics in aqueous systems and on lipidic model membranes. Importantly, VIE assemblies exhibit distinct cell membrane targeting behaviors depending on the number of contact points between the molecular assemblies and the cell membrane. Especially, trivalent molecular assemblies can inhibit the internalization of the probes by the cells, a property absent in free VIE and mono/divalent molecular assemblies, thereby achieving targeted and prolonged retention on the cell membrane. Using the trivalent molecular assemblies, we successfully achieve ratiometric fluorescence imaging of cell membrane tension using confocal laser scanning microscopy, revealing the potential of such multifunctional mechanical-sensitive probes for live-cell applications.

Directing the Encapsulation of Single Cells with DNA Framework Nucleator-Based Hydrogel Growth

Encapsulating individual mammalian cells with biomimetic materials holds potential in ex vivo cell culture and engineering. However, current methodologies often present tradeoffs between homogeneity, stability, and cell compatibility. Here, inspired by bacteria that use proteins stably anchored on their outer membranes to nucleate biofilm growth, we develop a single-cell encapsulation strategy by using a DNA framework structure as a nucleator (DFN) to initiate the growth of DNA hydrogels under cell-friendly conditions. We find that among the tested structures, the tetrahedral DFN can evenly and stably reside on cell membranes, effectively initiating hybridization chain reactions which generate homogeneously dense yet flexible single-cell encapsulation for diverse cell lines. The encapsulation persists for up to 72 hours in a serum-containing cell culture environment, representing a ~70-fold improvement compared to encapsulations mediated by single-stranded DNA nucleators. The metabolism and proliferation of the encapsulated cells are suppressed, but can be restored to the original efficiencies upon release, suggesting the superior cell compatibility of the encapsulation. We also find that compared to naked cells, the encapsulated cells exhibit a lower autophagy level after undergoing mechanical stress, suggesting the protective effect of the DNA encapsulation. This method may provide a new tool for ex vivo cell engineering.

MnO2@Au nanostructures supported colorimetric biosensing with duplex-specific nuclease-assisted DNA structural transition

Manganese dioxide (MnO₂) nanosheets are regarded as a new class of two-dimensional nanomaterials with several attractive properties with enormous progress in biomedical fields. Gold nanoparticles (AuNPs) are also important biocompatible nanomaterials with unusual optical properties. Hetero-nanostructure of MnO₂ and AuNPs with the medium of DNA is an interesting topic. In this work, the protection of the hetero-nanostructure from salt-induced aggregation is systematically investigated including the effects of sequence length, reagents concentrations, incubation time and temperature. The MnO₂@Au nanostructures are thus applied for the analysis of miRNA. Duplex-specific nuclease (DSN) catalyzed digestion, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are utilized for signal amplification. By finally analyzing the optical responses of the nanocomponents, highly sensitive analysis of target miRNA can be achieved. Excellent analytical performances are attributed to the unique features of MnO₂@Au nanostructures and signal amplification designs. They are promising basis for the construction of novel biosensors for clinical applications.