Programmable Plasmonic Nanodevice for Structural-State-Encoded Molecular Computation and Dual-MicroRNA Imaging in Living Cells

Abstract

MicroRNAs (miRNAs) are pivotal regulators of gene expression, and their aberrant expression is closely related to tumor initiation and progression. The simultaneous detection and logical discrimination of multiple miRNAs at the single-molecule level remain a significant challenge for precise cancer diagnostics. Herein, we developed a programmable plasmonic nanodevice based on a tetrahedral DNA framework with gold nanoparticle (AuNP) assemblies to achieve structure-state-encoded molecular computation for dual-miRNA analysis. The Au tetramer nanodevice (AuTD) performs a binary half adder logic operation of XOR (Sum) and AND (Carry) gates to process two distinct miRNA inputs simultaneously. Target recognition triggers precise, input-dependent reconfiguration of the AuTD, inducing the controlled disassembly of the AuNP architecture from a tetramer to a trimer or dimer. The structural transitions yield distinct scattering color shifts under dark-field microscopy and translate molecular logic into optical readouts, minimizing false-positive signals through algorithmic verification. The platform exhibits high sensitivity and anti-interference ability, and the limit of detection reached 0.15 fM and 0.69 fM for miRNA-21 and miRNA-155, respectively. Its versatility is further studied through DNA sequence reprogramming for alternative miRNA pairs and material engineering with Au–Ag heterometallic nanostructures for expanded spectral multiplexing. Also, the nanodevice is successfully applied for label-free, real-time imaging and logic-based analysis of endogenous miRNAs in living cells, establishing a robust platform for intelligent biosensing and nanoscale information processing.