Reconstruction of Vesicle Assemblies with DNA Nanorulers for Resolving Heterogeneity of Vesicles in Live Cells

Nanoscale vesicles such as synaptic vesicles play a pivotal role in efficient interneuronal communications in vivo. However, the coexistence of single vesicle and vesicle clusters in living cells increases the heterogeneity of vesicle populations, which largely complicates the quantitative analysis of the vesicles. The high spatiotemporal monitoring of vesicle assemblies is currently incompletely resolved. Here, this work uses synthetic vesicles and DNA nanorulers to reconstruct in vitro the vesicle assemblies that mimic vesicle clusters in living cells. DNA nanorulers program the lateral distance of vesicle assemblies from 3 to 10 nm. This work uses the carbon fiber nanoelectrode (CFNE) to amperometric monitor artificial vesicle assemblies with sub-10 nm interspaces, and obtain a larger proportion of complex events. This work resolves the heterogeneity of individual vesicle release kinetics in PC12 cells with the temporal resolution down to ≈0.1 ms. This work further analyzes the aggregation state of intracellular vesicles and the exocytosis of living cells with electrochemical vesicle cytometry. The results indicate that the exocytosis of vesicle clusters is critically dependent on the size of clusters. This technology has the potential as a tool to shed light on the heterogeneity analysis of vesicle populations.

Construction of Double-enzyme Complexes with DNA Framework Nanorulers for Improving Enzyme Cascade Catalytic Efficiency

Efficient biocatalytic cascade reactions play a crucial role in guiding intricate, specific and selective intracellular transformation processes. However, the catalytic activity of the enzyme cascade reaction in bulk solution was greatly impacted by the spatial morphology and inter-enzyme distance. The programmability and addressability nature of framework nucleic acid (FNA) allows to be used as scaffold for immobilization and to direct the spatial arrangement of enzyme cascade molecules. Here, we used tetrahedral DNA framework (TDF) as nanorulers to assemble two enzymes for constructing a double-enzyme complex, which significantly enhance the catalytic efficiency of sarcosine oxidase (SOx)/horseradish peroxidase (HRP) cascade system. We synthesized four types of TDF nanorulers capable of programming the lateral distance between enzymes from 5.67 nm to 12.33 nm. Enzymes were chemical modified by ssDNA while preserving most catalytic activity. Polyacrylamide gel electrophoresis (PAGE), transmission electron microscopy (TEM) and atomic force microscopy (AFM) were used to verify the formation of double-enzyme complex. Four types of double-enzyme complexes with different enzyme distance were constructed, in which TDF26 (SOx+HRP) exhibited the highest relative enzyme cascade catalytic activity, ~3.11-fold of free-state enzyme. Importantly, all the double-enzyme complexes demonstrate a substantial improvement in enzyme cascade catalytic activity compared to free enzymes.