cShot: spatial dynamic imaging of cell cycle-dependent miRNA heterogeneity using dynamic DNA patterns

Abstract

Profiling cell cycle phase progression and determining how cells respond to external stimuli through miRNA quantification will enable substantial improvements in therapeutic assessment. However, miRNA evaluation is challenging due to its transient nature and the complex cellular environment. Here, we report “cShot” (cell cycle shot), a method for spatial dynamic imaging of miRNA across different cell cycles via dynamic DNA sequences that integrate a pair of competitive probes into a set of static target-binding probes. Compared to traditional irreversible binding probes, cShot enables dynamic binding and dissociation of miRNA through constitutional exchange between two probe sets. Typically, cShot relies on multiple signal outputs, ensuring an accurate signal output through adaptive regulation of the probes. The dynamic behavior of cShot is accompanied by kinetic models, providing a systematic self-checking ability for c-Shot. By tethering DNA tetrahedra to the cShot system and utilizing a hybridization chain reaction, cShot enables real-time monitoring of cell cycle-dependent heterogeneity in synchronized MCF-7 cells under radiomimetic drug stimulation.