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Background  Nanoparticles have been used for biomedical applications, including drug delivery, diagnosis, and imaging based on their unique properties derived from small size and large surface-to-volume ratio. However, concerns regarding unexpected toxicity due to the localization of nanoparticles in the cells are growing. Herein, we quantified the number of cell-internalized nanoparticles and monitored their cellular localization, which are critical factors for biomedical applications of nanoparticles.    Methods  This study investigates the intracellular trafficking of silica-coated magnetic nanoparticles containing rhodamine B isothiocyanate dye [MNPs@SiO 2 (RITC)] in various live single cells, such as HEK293, NIH3T3, and RAW 264.7 cells, using site-specific direct stochastic optical reconstruction microscopy ( d STORM). The time-dependent subdiffraction-limit spatial resolution of the  d STORM method allowed intracellular site-specific quantification and tracking of MNPs@SiO 2 (RITC).    Results  The MNPs@SiO 2 (RITC) were observed to be highly internalized in RAW 264.7 cells, compared to the HEK293 and NIH3T3 cells undergoing single-particle analysis. In addition, MNPs@SiO 2 (RITC) were internalized within the nuclei of RAW 264.7 and HEK293 cells but were not detected in the nuclei of NIH3T3 cells. Moreover, because of the treatment of the MNPs@SiO 2 (RITC), more micronuclei were detected in RAW 264.7 cells than in other cells.    Conclusion  The sensitive and quantitative evaluations of MNPs@SiO 2 (RITC) at specific sites in three different cells using a combination of  d STORM, transcriptomics, and molecular biology were performed. These findings highlight the quantitative differences in the uptake efficiency of MNPs@SiO 2 (RITC) and ultra-sensitivity, varying according to the cell types as ascertained by subdiffraction-limit super-resolution microscopy.    Graphical AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s12951-021-01147-1.

journal of nanobiotechnology

Quantifying intracellular trafficking of silica-coated magnetic nanoparticles in live single cells by site-specific direct stochastic optical reconstruction microscopy