Dual-Site Cooperative Recognition Hybridization Chain Reaction for High-Sensitivity Imaging of lncRNA

Developing highly sensitive and specific imaging strategies for long noncoding RNAs (lncRNAs) is crucial for disease diagnosis and therapeutic research. However, lncRNAs are characterized by long sequence lengths (>200 nt), low abundance, and complex secondary structures, which make their sensitive and specific imaging challenging. To address these challenges, we developed a hybridization chain reaction (HCR) strategy based on dual-site cooperative recognition for lncRNA imaging, termed dual-site cooperative recognition HCR (DCHCR). Through multisite cooperative recognition, the adverse effects of lncRNA secondary structures on probe hybridization are alleviated, thereby significantly improving probe-target binding efficiency and enhancing detection sensitivity and accuracy. Compared with conventional single-site recognition HCR strategies, DCHCR exhibits improved reaction kinetics and higher sensitivity, achieving a detection limit of 47.1 pM. DCHCR also demonstrates strong practical applicability, enabling effective discrimination of lncRNA expression levels between cancer and normal cells at the level of living cells. Furthermore, this strategy enables effective imaging of lncRNAs in tumors of living mice with high contrast. Overall, this strategy is expected to serve as a powerful tool for lncRNA analysis and may contribute to the clinical diagnosis and therapeutic development of lncRNA-related diseases.