A Modular DNA-Assembled Nanopipette (mDNP) Platform for Spatially Confined Single-Cell Nuclear Detection of Methyltransferase Activity

Single-cell epigenetic regulation relies on spatially organized enzymatic activities within nuclear compartments, which establish DNA methylation patterns that dictate gene expression and cellular identity. Given this spatial organization, we present a modular DNA-assembled nanopipette (mDNP) platform for ultrasensitive detection of DNA methyltransferase 1 (DNMT1) within the nucleus of individual cells. The device incorporates tripartite DNA molecular sentinel probes that undergo methylation-dependent sequence discrimination and initiate rolling circle amplification, producing quantifiable ionic current signals within a confined nanofluidic interface. This system offers high analytical precision and a broad linear range, enabling quantitative evaluation of DNMT1 inhibition and differentiation between malignant and nonmalignant cell populations. The regenerable mDNP device provides an integrated platform for single-cell epigenetic profiling and inhibitor screening at subcellular resolution.