Dual-Channel Surface Plasmon Resonance for Quantification of ApoE Gene and Genotype Discrimination in Unamplified Genomic DNA Extracts

DNA tetrahedron-based dual-signal fluorescence detection of apoE4 gene sites on a microplate reader

As a neurodegenerative disorder, Alzheimer's disease (AD) is characterized by cognitive dysfunction and behavioral impairment. Among the various genetic risk factors for AD, apoE4 gene plays a pivotal role in the onset and progression of AD, and detection of apoE4 gene holds significance for prevention and early diagnosis of AD. Herein, dual-signal fluorescence detection of fragments associated with apoE ε4 allele near codon 112 (Tc1) and codon 158 (Tc2) was achieved using DNA tetrahedron nanostructure (DTN). The Förster resonance energy transfer (FRET) process in the DTN was initiated in which the nucleic acid intercalating dye thiazole orange (TO) served as the donor and the cyanine dyes of cyanine3 (Cy3) and cyanine5 (Cy5) at the two vertices of DTN served as the acceptors. In the presence of Tc1 and Tc2, the FRET process between TO and the cyanine dyes was hindered by the enzymatic cleavage reaction, which ensures the dual-signal fluorescence assay of apoE4 gene sites. The limit of detection for Tc1 and Tc2 was estimated to be 0.82 nM and 0.77 nM, respectively, and the whole assay was accomplished within 1 h on a microplate reader. The proposed method thus possesses the advantages of easy operation, short detection time, and high-throughput capability.

Fluorescence detection of apolipoprotein E gene polymorphisms based on oligonucleotide ligation and magnetic separation

Alzheimer's disease is a progressive neurodegenerative condition that causes brain cell death and is the leading cause of dementia. Most patients with Alzheimer's disease are diagnosed with late-onset Alzheimer's disease (LOAD), with apolipoprotein E (APOE) genotypes being highly associated with the frequency of LOAD risk. A fluorescence detection system coupled with oligonucleotide ligation and magnetic separation was developed to identify two single-nucleotide polymorphisms (SNPs) for the APOE gene and recognize APOE alleles for LOAD. The system utilized a fluorescence probe with one base-discriminating nucleoside for SNP (F probe) and a perfectly complementary biotin-modified sequence against the target DNA (P probe). When the F and P probes matched the target DNA sequences, DNA ligation occurred, and ligation products were produced. Streptavidin magnetic beads were subsequently employed to remove the ligation products, and a decrease in fluorescence intensity was observed in the supernatant compared to when there was no target DNA. This system detected two SNPs of APOE alleles, namely rs429358 and rs7412. The results indicated that the R-values ((F0 - F1)/F0) for rs429358 were 0.92 ± 0.002 for the T/T target, 0.47 ± 0.004 for the T/C target and 0.11 ± 0.004 for the C/C target, respectively. The R-values for rs7412 were 0.73 ± 0.009 for the C/C target, 0.42 ± 0.001 for the C/T target and 0.16 ± 0.007 for the T/T target, respectively. F0 and F1 represent the fluorescence intensity of the F probe without and with target DNA, respectively. Based on fluorescence intensity, the fluorescence detection system was able to identify the genotypes of the APOE gene accurately to evaluate the risk of Alzheimer's disease.

Recent Progress in Single-Nucleotide Polymorphism Biosensors

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.

Application of Nanotechnology for Sensitive Detection of Low-Abundance Single-Nucleotide Variations in Genomic DNA: A Review

Single-nucleotide polymorphisms (SNPs) are the simplest and most common type of DNA variations in the human genome. This class of attractive genetic markers, along with point mutations, have been associated with the risk of developing a wide range of diseases, including cancer, cardiovascular diseases, autoimmune diseases, and neurodegenerative diseases. Several existing methods to detect SNPs and mutations in body fluids have faced limitations. Therefore, there is a need to focus on developing noninvasive future polymerase chain reaction (PCR)-free tools to detect low-abundant SNPs in such specimens. The detection of small concentrations of SNPs in the presence of a large background of wild-type genes is the biggest hurdle. Hence, the screening and detection of SNPs need efficient and straightforward strategies. Suitable amplification methods are being explored to avoid high-throughput settings and laborious efforts. Therefore, currently, DNA sensing methods are being explored for the ultrasensitive detection of SNPs based on the concept of nanotechnology. Owing to their small size and improved surface area, nanomaterials hold the extensive capacity to be used as biosensors in the genotyping and highly sensitive recognition of single-base mismatch in the presence of incomparable wild-type DNA fragments. Different nanomaterials have been combined with imaging and sensing techniques and amplification methods to facilitate the less time-consuming and easy detection of SNPs in different diseases. This review aims to highlight some of the most recent findings on the aspects of nanotechnology-based SNP sensing methods used for the specific and ultrasensitive detection of low-concentration SNPs and rare mutations.

Toehold-Mediated Strand Displacement Reaction for Dual-Signal Electrochemical Assay of Apolipoprotein E Genotyping

Apolipoprotein E (apoE) polymorphic genes are one of the main genetic determinants of Alzheimer's disease (AD) risk. Relying on the toehold-mediated strand displacement reaction (SDR), the dual-signal electrochemical assay of apoE genotyping with potential applications in the early diagnosis of AD has been achieved. The displacement of the surface-confined methylene blue- and ferrocene-capped detection probe-modified gold nanoparticles (AuNPs) by the complementary sequences (Tc 1 and Tc 2, fragment of allele ε4 at codon 112 and that of allele ε3 or ε4 at codon 158, respectively), triggered by the highly specific SDR, results in decreased voltammetric signals. In contrast, partial strand displacement caused by the single mismatched sequences (Tsm 1 and Tsm 2, fragment of allele ε2 or ε3 at codon 112 and that of allele ε2 at codon 158, respectively) produces larger voltammetric signals. The proposed method serves as a versatile platform for the discrimination of six apoE genotypes, including three homozygotes (ε2/2, ε3/3, and ε4/4) and three heterozygotes (ε2/3, ε2/4, and ε3/4), and for the quantification of apoE ε3/3 from genomic DNA extracts of AD patients.

Surface plasmon resonance biosensors for detection of Alzheimer's biomarkers; an effective step in early and accurate diagnosis

The rapid and direct detection of biomarkers in biofluids at clinically relevant concentrations faces serious limitations to develop diagnostic criteria for neurodegenerative diseases such as Alzheimer's disease (AD). In this regard, the early detection of biomarkers correlated with AD using novel modalities and instruments is at the center of attention. Recently, some newly invented optical-based biosensors namely Surface Plasmon Resonance (SPR) has been extensively investigated for the detection of biomarkers using a label-free method or by checking interaction between ligand and analyte. These approaches can sense a very small amount of target molecules in the blood and cerebrospinal fluids samples. In this review, the different hypothesis related to AD, and the structural properties of AD biomarkers was introduced. Also, we aim to highlight the specific role of available SPR-based sensing methods for early detection of AD biomarkers such as aggregated β-amyloid and tau proteins. Efforts to better understand the accuracy and efficiency of optical-based biosensors in the field of neurodegenerative disease enable us to accelerate the advent of novel modalities in the clinical setting for therapeutic and diagnostic purposes.

Electrochemical immunosensor based on AuBP@Pt nanostructure and AuPd-PDA nanozyme for ultrasensitive detection of APOE4

An ultrasensitive sandwich-type electrochemical immunosensor based on AuBP@Pt nanostructures and AuPd-PDA nanozyme was developed for the detection of apolipoprotein E4 (APOE4) which was an important risk factor for Alzheimer's disease (AD). In this work, gold nanobipyramid coated Pt (AuBP@Pt) nanostructures were prepared and applied to electrochemical immunosensors as a substrate material. AuBP@Pt nanostructures have advantages of electrical conductivity and large electroactive area, which could greatly increase electron transfer rate. In previous work, we designed AuPd alloy modified polydopamine (AuPd-PDA) nanozyme which catalyzed the decomposition of hydrogen peroxide (H₂O₂). AuPd-PDA nanozyme was used to label detection antibody due to excellent catalytic capability and stability in this new paper. And the concentration of APOE4 could be detected quantitatively by variation for transient current. As a result, the electrochemical immunosensor based on AuBP@Pt and AuPd-PDA exhibited a wide linear range from 0.05 to 2000 ng mL⁻¹ and low detection limit of 15.4 pg mL⁻¹ (S/N = 3). Furthermore, the designed biosensor displayed good selectivity in phosphate buffer saline (PBS) buffer solution or commercial goat serum, which provided a promising tool for early diagnosis of AD.

An ultrasensitive sandwich-type electrochemical immunosensor based on AuBP@Pt nanostructures and AuPd-PDA nanozyme was developed for the detection of apolipoprotein E4 (APOE4) which was an important risk factor for Alzheimer's disease (AD).

Bioactivity-Protected Electrochemiluminescence Biosensor Using Gold Nanoclusters as the Low-Potential Luminophor and Cu2S Snowflake as Co-reaction Accelerator for Procalcitonin Analysis

The expansion of electrochemiluminescence (ECL) technology to immunoassay at the core of care emphasizes all immune molecules will not be inactivated in the analysis process. That poses a major challenge to ECL-based biosensors due to the deoxynucleotide sequences of an antigen or antibody could be oxidized through a route of excessive cyclic potential. Herein, an ultrasensitive ECL biosensor was developed based on a novel bioactivity-protected sensing strategy utilizing Au nanoclusters (Au NCs) as low-potential luminophor for detection of procalcitonin (PCT). Bovine serum albumin (BSA)-templated Au NCs exhibited a low-potential anodic ECL signal in triethylamine (TEA) solution at 0.87 V, where it is suitable for the survival of immune molecules. Taking advantage of good conductivity and high surface area, a Cu₂S snowflake not only functions as a satisfying substrate for connecting immune molecules but also acts as co-reaction accelerator to produce more cationic radicals TEA^•+, which could improve the ECL intensity needed to meet the requirements of trace analysis. Otherwise, HWRGWVC (HC-7) heptapeptide as specific antibody immobilizer for site-oriented fixation was introduced to further maintain the bioactivity of an antibody. In view of the preceding discussion, the obtained biosensor exhibited ultrahigh immune recognition to targets so that the detection limit was as low as an unprecedented value of 2.36 fg/mL, which will be of great significance to the application and development of a biosensor in the future.