Electrical Detection Assay Based on Programmable Nucleic Acid Probe for Efficient Single-Nucleotide Polymorphism Identification

Abstract

The large-scale pandemic and fast evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have triggered an urgent need for an efficient and sensitive on-site nucleic acid testing method with single-nucleotide polymorphism (SNP) identification capability. Here, we report a multiplexed electrical detection assay based on a paperclip-shaped nucleic acid probe (PNprobe) functionalized field-effect transistor (FET) biosensor for highly sensitive and specific detection and discrimination of SARS-CoV-2 variants. The three-stem structure of the PNprobe significantly amplifies the thermodynamic stability difference between variant RNAs that differ in a single-nucleotide mutation. With the assistance of combinatorial FET detection channels, the assay realizes simultaneously the detection and identification of key mutations of seven SARS-CoV-2 variants, including nucleotide substitutions and deletions at single-nucleotide resolution within 15 min. For 70 simulated throat swab samples, the multiplexed electrical detection assay shows an identification accuracy of 97.1% for the discrimination of SARS-CoV-2 variants. Our designed multiplexed electrical detection assay with SNP identification capability provides an efficient tool to achieve scalable pandemic screening.

Materials-Functionalized Point-of-Care Testing Devices for Pathogen Detection

“…We reported a paperclip-shaped nucleic acid probe (PNprobe) to functionalize a field effect transistor (FET) biosensor (Figure 3b). 27 Its unique three-stem structure helps stabilize the probe, which, in turn, amplifies the thermodynamic stability difference between variant RNAs. The probe immobilized on the FET interface could recognize and combine with target viral RNA with negative charges, leading to a change of charge density on the FET biosensing interface.…”

“…(ii and iii) Current responses of PNprobe-functionalized FET biosensors to (ii) the SARS-CoV-2 D614G mutation and (iii) seven mutations. Reproduced with permission from ref . Copyright 2023 American Chemical Society.…”

“…Functional nucleic acid nanomaterials could be advantageous as a probe molecule modified on the electrode interface, underlying specific and reproducible detection of pathogens. We reported a paperclip-shaped nucleic acid probe (PNprobe) to functionalize a field effect transistor (FET) biosensor (Figure b) . Its unique three-stem structure helps stabilize the probe, which, in turn, amplifies the thermodynamic stability difference between variant RNAs.…”

Device-Physics Realization of ZnO–MWCNT Nanostructure-Based Field-Effect Biosensor for Ultrasensitive Simultaneous Genomic Detection of Foodborne Pathogens

“…Quite often, the semiconducting nanomaterial dispersion and thin films act as the active channel for the field-effect-based biosensors. The metallic fingers of the interdigitated micro electrodes (μ-IDEs) constitute the source and drain contacts . In such devices, the electrostatic interactions and thereby, the response signal is largely affected by the variation in the ionic environment of the biological matrix owing to the modulations in the Debye screening length, λ D .…”

Recent Progress in Single-Nucleotide Polymorphism Biosensors

“…Single-nucleotide polymorphisms (SNPs) are the most common form of genetic variations in human genomes [ 1 , 2 , 3 , 4 ]. SNPs were first discovered in 1980; restriction endonuclease assays were used to determine the presence or absence of DNA cleavage sites in the past [ 5 ].…”