A CRISPR/dCas9 mediated electrochemical impedimetric biosensor for sensitive mtDNA detection

The accumulation of mitochondrial DNA (mtDNA) mutations in cells is closely linked to various human diseases. Detection of single-nucleotide variation (SNV) in mtDNA plays a crucial role in understanding the heteroplasmy of mtDNAs that contain pathogenic changes. While conventional nucleic acid sequencing-based methods are instrumental and complex, which hampered their capability in revealing the extensive diversity of mtDNA. In order to realize trace DNA analysis, recent CRISPR/Cas-based detection methods facilitated with target pre-amplification, while raised the risks of non-specific amplification and cross-carryover contamination. Thus, it is imperative to develop new methods for sensitive and precise SNV detection in mtDNA.

This study developed a CRISPR/dCas9 (deactivated Cas9) mediated electrochemical impedimetric biosensor without target pre-amplification for sensitive and specific detection of SNVs in mtDNA. dCas9/sgRNA complexes were immobilized on the surface of indium tin oxide (ITO) electrode to specifically recognize target mtDNA sequences and initiate hybridization chain reaction (HCR) for signal amplification. Subsequently, positively charged polyethylenimine-coated silver nanoparticles (PEI-Ag NPs) were electrostatically deposited onto the HCR-generated long double-stranded DNA (dsDNA) products, leading to a marked decrease in electrochemical impedance due to the high conductivity of the nanoparticles. The concentration of mtDNA was thus quantified by monitoring the impedance change via electrochemical impedance spectroscopy (EIS). The method could distinguish single- and multi-base mismatches with a low detection limit of 67 fM without pre-amplification. It exhibits excellent anti-interference ability and excellent recovery rates of 90.0% to 108.0% in complex matrices (10% human plasma), and enables accurate mtDNA detection in cell lysates.

This free of pre-amplification strategy offers a highly sensitive analytical tool that enables the successfully detection of mtDNA mutation in diverse cells types, and exhibited excellent anti-interference ability in complicated biological specimen. The work presents a viable and promising strategy for the electrochemical detection of cancer-related biomarkers, indicating substantial potential in early clinical diagnosis.