High-Affinity DNA Aptamers for Silicate Sensing in Cells

Silicon (Si) participates in diverse biological processes, yet its specific roles remain elusive because of the lack of tools for visualizing silicon in living organisms. In biological contexts, silicon predominantly occurs as silicates with varying polymerization states and structural heterogeneity, posing fundamental challenges for recognition and imaging using existing chemical or analytical methods. Here, we introduce a molecular recognition strategy that leverages single-stranded DNA aptamers selected through a three-dimensional silicified hydrogel screening system, yielding high-affinity binders with nanomolar dissociation constants. We validated these aptamers using electrophoretic mobility shift assays (EMSA) and microscale thermophoresis (MST), and molecular docking revealed the sequence-structure motifs governing silicate recognition. Using these aptamers, we engineered two fluorescent sensors that map intracellular silicate distributions with high specificity. To our knowledge, these are the first aptamers that selectively recognize silicates with distinct polymerization states, providing a powerful tool for real-time visualization of silicon in living cells. This approach opens new avenues for biological imaging and for elucidating the functional roles of biogenic silicon in living organisms.