Construction of a Homogeneous Enzyme-Free Autocatalytic Nucleic Acid Machinery for High-Performance Intracellular Imaging of MicroRNA

Abstract

Enzyme-free autocatalytic nucleic acidmachinery has been widely used to engineer various self-assembled nanostructures as well as high-performance bioanalysis, yet has rarely been realized in live cells for complicated design, low robustness, and limited reliability. Herein, we constructed simple yet versatile enthalpy-driven autocatalytic hybridization chain reaction (AHCR) machinery with high reliability and robustness for in situ microRNA analysis in live cells. The homogeneous AHCR machine was composed of two differently designed HCR modules, the lead-in HCR-1 amplification module, and the reverse HCR-2 feedback module. After the AHCR amplification system was delivered into live cells, target microRNA stimulated the autonomous cross-invasion of the HCR-1 module and the HCR-2 module for assembling hyperbranched dsDNA nanostructures with synergistically amplified Förster resonance energy transfer readout, thus enabling accurate intracellular micro- RNA imaging. The synergistic AHCR execution was systematically investigated by a series of experimental studies and computer-aided theoretical simulations. The multiple recognition capacity of HCR constituents and the successive signal amplification of the AHCR machine enabled the accurate intracellular microRNA imaging with precise signal localization inside living cells. Based on its intriguing and modular design, the AHCR machinery can be extended for analyzing diverse biomarkers, thus supplementing a powerful toolbox for clinical diagnosis and therapeutic assessment.