Attomolar Nucleic Acid Detection Using CRISPR EnhancedPhase-Sensitive Surface Plasmon Resonance Imaging

Driven by the growing need for real-time, amplification-free, and label-free nucleic acid detection in clinical diagnostics and pathogen surveillance, traditional methods often fall short due to limited sensitivity, a narrow dynamic range, and difficulties in detecting low-concentration nucleic acids and single-nucleotide mutations. To address these challenges, we developed a clustered regularly interspaced short palindromic repeats (CRISPR) enhanced Phase-interrogation Surface Plasmon Resonance imaging (CRISPR-PSPRi) sensor that employs phase delay modulation for highly sensitive extraction of SPR phase signals and a wavelength scanning strategy to extend its dynamic range. By harnessing CRISPR-Cas12a for target DNA recognition and activating <i>trans</i>-cleavage to cleave ssDNA-linked gold nanoparticle probes, our platform converts extremely weak signals from low-concentration DNA into readily detectable cleavage signals. Achieving a sensitivity of 1.436 × 10^–6 RIU and a dynamic range of 0.0111 RIU, this system successfully detects specific DNA from the SARS-CoV-2 Omicron BA.2 variant and monkeypox virus, and it can detect single-nucleotide mutations down to 1 aM. This breakthrough offers a real-time, high-throughput, and ultrasensitive nucleic acid detection approach, promising significant advancements in clinical diagnostics and pathogen monitoring.