Restriction Endonuclease-Based Assays for DNA Detection and Isothermal Exponential Signal Amplification

Sensitive electrochemical detection of polymorphisms in IL6 and TGFβ1 genes from ovarian cancer DNA patients using EcoRI and DNA hairpin-modified gold electrodes

Two electrochemical bioplatforms were prepared based on thiolated hairpin DNA probes tethered to AuNP-modified screen-printed electrodes to detect T > G and T > C polymorphisms, namely rs1880269 and rs1800469, present the interleukin-6 (IL6) and transforming growth factor β1 (TGFβ1) genes. The electrochemical readout was ensured by the detection of the double-stranded DNA using methylene blue as a redox probe after treatment by EcoRI restrictase. The main parameters influencing the analytical response such as the thiolated DNA probe concentration, incubation time with electrode, DNA hybridization time, EcoRI enzyme load, and its cleavage time were optimized based on the current intensity and signal-to-blank (S/B) ratio as selection criteria. Using spiked buffer solutions, the IL6 and TGFβ1 E-bioplatforms display wide ranges of linearity (1 × 10²-1 × 10⁸ fM and 5 × 10¹-1 × 10⁵ fM, respectively) and limits of detection (47.9 fM and 16.6 fM, respectively). The two bioelectrodes have also good discrimination toward 1-mismatched, two mismatched, and non-complementary sequences, when they were used 30-fold higher than the target sequences. More importantly, the two bioplatforms successfully detected the single nucleotide polymorphisms (SNPs) in scarcely diluted genomic DNA, collected from 52 donors, and showed they can reliably distinguish between heterozygous (TG and TC genotypes) and homozygous (GG and CC genotypes) patients with  respect to the control subjects (TT genotype), where the differences are statistically highly significant (p-value < 0.0001). Thus, the designed devices could be used to conduct large cohort studies targeting these mutations or extended to other SNPs.

A multiplexed circulating tumor DNA detection platform engineered from 3D-coded interlocked DNA rings

Circulating tumor DNA (ctDNA) is a critical biomarker not only important for the early detection of tumors but also invaluable for personalized treatments. Currently ctDNA detection relies on sequencing. Here, a platform termed three-dimensional-coded interlocked DNA rings (3D-coded ID rings) was created for multiplexed ctDNA identification. The ID rings provide a ctDNA recognition ring that is physically interlocked with a reporter ring. The specific binding of ctDNA to the recognition ring initiates target-responsive cutting via a restriction endonuclease; the cutting then triggers rolling circle amplification on the reporter ring. The signals are further integrated with internal 3D codes for multiplexed readouts. ctDNAs from non-invasive clinical specimens including plasma, feces, and urine were detected and validated at a sensitivity much higher than those obtained through sequencing. This 3D-coded ID ring platform can detect any multiple DNA fragments simultaneously without sequencing. We envision that our platform will facilitate the implementation of future personalized/precision medicine.

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A platform termed 3D-coded ID rings was created for multiplexed ctDNA detection.

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This platform was integrated with two schemes: the ID ring scheme and the 3D-coded scheme.

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The platform could achieve multiplexed detection with detection limit of 500 copies per million in non-invasive specimens.

Development of DNA Biosensors Based on DNAzymes and Nucleases

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

Paper-Based Multiplex Surface-Enhanced Raman Scattering Detection Using Polymerase Chain Reaction Probe Codification

We construct a multiplex surface-enhanced Raman scattering (SERS) platform based on a plasmonic paper substrate and a double-labeled probe for the detection of multiple fluorescent dyes at high sensitivity in a single-wavelength light source system. Plasmonic paper, made of silver nanodots on three-dimensional cellulose fibers, enables highly sensitive SERS biosensing based on localized surface plasmon resonance (LSPR). The proposed method enables the identification and quantification of a range of fluorescent dyes ranging from picomolar to millimolar concentrations. The use of 5' fluorescent dyes and 3' biotin-modified probes as SERS-coded probes renders possible the separation of fluorescent dyes with streptavidin-coated magnetic beads (SMBs) and the sensitive detection of multiple dyes after the reverse transcription polymerase chain reaction (RT-PCR). This experimental study reveals the multiplex detection capability of PCR-based SERS under existing PCR conditions without modifying primer and probe sequences. The combination of magnetic bead-based separation and paper SERS platform is efficient, economical, and can be used for the simultaneous detection of two or more pathogens.