Recent Progress in Single-Nucleotide Polymorphism Biosensors

Abstract

Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.

Keywords: SNPs; biosensor; electrochemistry; fluorescence; quartz crystal microbalance (QCM).

Figure 1

Schematic of fluorescence sensing detection strategy based on the multiple primers-mediated rolling circle amplification combined with a graphene oxide (MPRCA-GO) [53]. Copyright 2019 Royal Society of Chemistry.

Figure 2

(a) Schematic explaining the method of the RCA-CRISPR/Cas12a technique for SNV detection; (b) representing the fluorescence intensity and real product photo corresponding to 200 nM mutant and wild-type targets and blank group; (c) showing the fluorescence intensity corresponding to the gap-filling with different nucleotides. Reproduced with permission from [56]. Copyright 2021 Elsevier.

Figure 3

(A) Illustration of PO/IO/WtDNA strands hybridize to form trinucleotide repeat (TR) substrates that were recognized and cleaved by FEN1 and cannot trigger subsequent CHA reactions; (B) Schematic diagram of DNAzyme ligation triggered by CHA-induced invasion detection for ultrasensitive and specific detection of SNPs in the K-ras gene. Reproduced with permission from [63]. Copyright 2022 Elsevier.

Figure 4

(a) Illustration of the universal LNA-integrated X-shaped DNA probes for the fluorescent biosensor; (b,c) fluorescence spectra of no mutDNA (background, curve a), random DNA (curve b), wtDNA (curve c), and mutDNA (curve d). Reproduced with permission from [64]. Copyright 2017 Elsevier.

Figure 5

(a) Illustration of diversified hybridization structures of novel fluorescent molecular probes based on different nanocluster beacons; (b) Fluorescence spectra of NCD-1, NCD-2, NCD-3, and NCD-4 after hybridization; (c) Fluorescence intensities of NCD-1, NCD-2, NCD-3, and NCD-4 after hybridization at maximum emission. Reproduced with permission from [72]. Copyright 2017 Analytical Chemistry.

Figure 6

SMN genotype fluorescence detection based on MIP-RCA reaction with synthesis of poly T-templated CuNCs. Reproduced with permission from [78]. Copyright 2020 Analytica Chimica Acta.

Figure 7

Illustration of the proposed electrochemical biosensor for detecting SNPs in the K-ras gene. Reproduced with permission from [101]. Copyright 2016 Royal Society of Chemistry.

Figure 8

(A) Illustration of the properly matched MT/CS dsDNA was recognized by NsbI and cleaved to initiate the SDA reaction; (B) Schematic diagram of the electrochemical DNA sensor based on NsbI-SDA and four-way DNA junction. Reproduced with permission from [103]. Copyright 2020 Elsevier.

Figure 9

Electrochemical biosensor based on the ligation and ONS engineering for SNP detection method. Reproduced with permission from [104]. Copyright 2013 Elsevier.

Figure 10

Schematic diagram of the process used by the electrochemical DNA biosensor to detect target DNA. Reproduced with permission from [114]. Copyright 2020 American Chemical Society.

Figure 11

Schematic diagram of single-base mutation detection based on QCM strategy. Reproduced with permission from [154]. Copyright 2015 Royal Society of Chemistry.