Direct RNA Targeting by CRISPR/Cas12: Emerging Mechanisms and Diagnostic Applications

RNA detection is essential for molecular diagnostics because it provides dynamic information on gene expression, pathogen activity, and disease progression. Conventional RNA detection methods, particularly reverse transcription polymerase chain reaction (RT-PCR), remain widely used but require RNA-to-DNA conversion, thermal cycling, and relatively complex workflows, limiting their suitability for rapid and point-of-care testing. In CRISPR diagnostics, Cas13 has traditionally been regarded as the major RNA-targeting system, whereas Cas12 enzymes have been primarily recognized as DNA-targeting nucleases. Recent studies, however, have revealed that several Cas12 variants can directly recognize RNA targets, enabling reverse-transcription-free RNA detection through mechanisms such as RNA-triggered DNase activity. In this review, we summarize the emerging functional diversity of RNA-responsive Cas12 systems, including Cas12a, Cas12a2, Cas12a3, Cas12f, and Cas12g, and discuss their underlying mechanisms for direct RNA sensing. We further highlight strategies for enhancing Cas12-mediated RNA detection, including guide and activator engineering, nanomaterial-assisted readouts, and autocatalytic signal amplification. Finally, we discuss its applications in infectious disease diagnosis, cancer biomarker detection, and environmental monitoring, alongside key challenges and future opportunities for clinical translation and point-of-care testing.