Orthogonal recognition of miRNA and lncRNA enables high-fidelity cancer diagnostics

Recent advances in molecular diagnostics have highlighted the transformative potential of multi-protein response logic gates in enhancing sensitivity and specificity for cancer detection. However, logic gates based on multi-type nucleic acid responses remain underexplored. In this study, we present a dual-biomarker response platform that utilizes nucleic acid logic gates targeting miR-21 (microRNA-21) and lncRNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). Compared to traditional single-target methods, our platform effectively overcomes common challenges, such as expression variability and cross-reactivity, which are inherent in single biomarker approaches, thereby significantly improving both diagnostic sensitivity and specificity. This platform is based on rolling circle amplification (RCA) technology and incorporates two key components: a primer switch and a padlock probe switch. When miR-21 is recognized, a hairpin probe undergoes a shape change, releasing a primer that starts the RCA process. Simultaneously, a MALAT1-specific padlock probe forms a closed circular structure, which is necessary to activate RCA and increase signal detection. Furthermore, the RCA products contain G-quadruplex sequences that can bind to hemin, forming DNAzymes that produce an electrochemical signal. This strategy significantly enhances diagnostic sensitivity and specificity, demonstrating strong potential for early cancer detection and precision oncology.