Lanthanide Metal–Organic Framework-Integrated CRISPR-Cas Technology for Amplification-free Gene Mutation Assay

Nucleic acid amplification remains a major bottleneck in CRISPR-based molecular diagnostics, limiting assay speed, simplicity, and accuracy. Herein, we report a lanthanide metal-organic framework (Ln-MOF)-integrated CRISPR-Cas12a platform for amplification-free detection of gene mutations with high sensitivity and specificity. In this system, target recognition activates Cas12a trans-cleavage, degrading a single-stranded DNA linker and releasing alkaline phosphatase (ALP). The liberated ALP hydrolyzes p-nitrophenyl phosphate (pNPP) to generate phosphate ions, which interact with Eu-TPTC (TPTC: [1,1':4',1″] terphenyl-3,3″,5,5″-tetracarboxylic acid) MOF sensor, inducing a ratiometric fluorescence change by selectively quenching the Eu3+ emission and enhancing the ligand emission. This mechanism enables quantitative, amplification-free detection of the oncogenic BRAF V600E mutation down to 0.1 pM, with excellent specificity and anti-interference ability. The assay demonstrates full agreement with conventional quantitative PCR when applied to clinical samples, accurately distinguishing mutant from wild-type genotypes. This strategy couples CRISPR-driven enzymatic signaling with Ln-MOF fluorescence modulation, offering an accurate and rapid readout. By eliminating amplification and streamlining workflow, this method holds significant potential for gene mutation analysis in clinical diagnostics.