A waste-free entropy-driven DNA nanomachine for smartly designed photoelectrochemical biosensing of MicroRNA-155

An electrochemical biosensing platform initiated simultaneously from multi-directions with programmable enzyme-free strategy for DNA variant detection

Single-nucleotide variations (SNVs) represent vital clinical and biological information in the onset and progression of many cancers, but lacking of cost-effective, high-sensitive and reliable SNVs detection method. In this study, we propose a programmable electrochemical biosensing strategy initiated simultaneously from multi-directions by enzyme-free amplifying circuit for high-sensitivity SNVs detection. Through elaborate design, we utilized the power of conventional enzyme-free catalytic reaction to activate a multidirectional initiation self-assembly process, enabling multiple amplification. This innovative cascade strategy significantly improved the amplification performance and detection sensitivity. Subsequently, KRAS gene of cancer cells was used as proof-of concept model for SNVs recognition to demonstrate the capability. With the help of cascade design, the single-base differences between SNV sequence and wild-type sequence (WT) could be differentiated and amplified effectively. Consequently, abundant Y-shaped DNA structure efficiently was induced by DNA variant to generate on the electrode surface, facilitating the incorporation of methylene blue (MB) redox indicator. Therefore, a "signal-on" electrochemical biosensing platform was constructed. Our enzyme-free biosensor achieved a low detection limit of 36 aM and a broader linear range spanning from 100 aM to 1 nM under optimal experimental conditions. The capability of proposed cascaded DNA network to detect DNA variants in complex cancer cells and serum samples indicated the potential applicability in real sample analysis.

A "super-off" photoelectrochemical biosensor based on Cu-BTC nanozyme quenching strategy for the detection of dibutyl phthalate plasticizer

Ultrasensitive detection of phthalic acid (PAEs) is an extremely critical mission in environmental monitoring. We designed a "super-off" photoelectrochemical (PEC) biosensor by using MoO3/Bi2MoO6 as photoanode and copper(II) benzene-1,3,5-tricarboxylate (Cu-BTC) nanozyme as highly efficient signal quencher. It was found that the PEC signal of MoO3/Bi2MoO6 photoelectric material is very sensitive to the concentration of co-reactor H2O2. Therefore, a target-triggered endonuclease-assisted recycle was employed to convert the target DBP into amount of output DNA, which can trigger the assembly of DNA nanonet for the immobilization of Cu-BTC nanozyme. Thanks to the peroxidase-like activity of Cu-BTC, a "super off" photocurrent was observed due to the consumption of electron donor H2O2 in the electrolyte. Compared with the traditional quenching strategies such as steric hindrance and light energy competition, this enzymatic reaction on the electrode interfaces is more effective to induce the distinct decrease of photocurrent for analysis. Ultimately, the constructed PEC sensor exhibited a broad linear range from 1 fM to 100 nM and a detection threshold of 0.3 fM. This work highlights the significance of using peroxide-mimic enzyme as a signal amplifier in PEC sensing platform for environmental monitoring.

Entropy driven-based catalytic biosensors for bioanalysis: From construction to application-A review

The rapid advancement of precision medicine and the continuous emergence of novel pathogens have presented new challenges for biosensors, necessitating higher requirements. Target amplification technology serves as the core component in biosensor construction. Enzyme-based amplification methods are often sensitive and selective but involve relatively complex operational steps, whereas enzyme-free amplification methods offer simplicity but frequently fail to meet both sensitivity and selectivity simultaneously. Existing research has confirmed that entropy-driven catalyst (EDC) biosensors not only fulfills the demands for sensitivity and selectivity concurrently but also offers ease of operation and flexibility in construction. In this review, we summarize the key advantages of EDC, explore how to construct DNA nanomachines based on these advantages to achieve intracellular detection and simultaneous detection of multiple targets, as well as point-of-care testing (POCT) to address practical issues in clinical diagnosis and treatment. We also anticipate potential challenges, propose corresponding solutions, and outline future development directions for EDC-based biosensors in practical clinical applications. We firmly believe that EDC sensors will emerge as a crucial branch within the realm of biosensor development.

Homogeneous electrochemical ratiometric biosensor for MircoRNA detection based on UiO-66-NH2 signal probe and waste-free entropy-driven DNA machine

The construction of efficient methods for highly sensitive and rapid detection of disease markers is essential for the early diagnosis of serious diseases. In this paper, taking advantage of the UiO-66-NH2 signal molecule in combination with a waste-free entropy-driven DNA machine, a novel homogeneous electrochemical ratiometric platform is developed to detect MircoRNA (miRNA). Metal-organic framework materials (UiO-66-NH2 MOF) and ferrocene were utilized as electrochemical signal tags and reference probes, respectively. The target-initiated waste-free three-dimensional (3D) entropy-driven DNA nanomachine is activated in the presence of miRNA, resulting in DNA-labeled-UiO-66-NH2 falling off from the electrode, leading to a decrease in the signal of UiO-66-NH2 at 0.83V. Our strategy can mitigate false positive responses induced by the DNA probes immobilized on electrodes in traditional distance-dependent signal adjustment ratiometric strategies. The proposed ratiometric platform demonstrates superior sensitivity (a detection limit of 9.8 fM), simplified operation, high selectivity, and high repeatability. The ratiometric biosensor is also applied to detect miRNA content in spiked serum samples.

Exploiting epoxy-rich poly(ethylene glycol) films for highly selective ssDNA sensing via electrochemical impedance spectroscopy

This study introduces an alternative approach to immobilize thiolated single-stranded DNA (ssDNA) for the DNA sensing. In contrast to the standard, monomolecular assembly of such moieties on gold substrate, over the thiolate-gold anchors, we propose to use bioinert, porous polyethylene glycol (PEG) films as a 3D template for ssDNA immobilization. The latter process relies on the reaction between the thiol group of the respectively decorated ssDNA and the epoxy groups in the epoxy-rich PEG matrix. The immobilization process and subsequent hybridization ability of the resulting sensing assembly were monitored using cyclic voltammetry and electrochemical impedance spectroscopy, with the latter tool proving itself as the most suitable transduction technique. Electrochemical data confirmed the successful immobilization of thiol-decorated ssDNA probes into the PEG matrix over the thiol-epoxy linkage as well as high hybridization efficiency, selectivity, and sensitivity of the resulting DNA sensor. Whereas this sensor was equivalent to the direct ssDNA assembly in terms of the efficiency, it exhibited a better selectivity and bioinert properties in view of the bioinert character of the PEG matrix. The above findings place PEG films as a promising platform for highly selective ssDNA sensing, leveraging their flexible chemistry, 3D character, and bioinert properties.

The Dual-Response-Single-Amplification Fluorescent Nanomachine for Tumor Imaging and Gastric Cancer Diagnosis

Gastric cancer (GC) is one of the most common tumors worldwide and is the leading cause of tumor-related mortality. Traditional biomarkers and screening methods cannot meet the clinical demands. There is an urgent need for highly sensitive diagnostic markers as well as accurate quantification methods for early gastric cancer (EGC) screening. Here a dual-target cooperatively responsive fluorescent nanomachine by the innovative application of two targets─responsive strand migration system with a single-amplification-cycle element was developed for the simultaneous detection of GC biomarkers miR-5585-5p and PLS3 mRNA, which were selected by next-generation sequencing and RT-qPCR. It was also an RNA extraction-free, PCR-free, and nonenzymatic biosensor to achieve tumor cell imaging and serum diagnosis. Requiring only a 20 μL serum sample and 20 min incubation time, the nanomachine achieved an ultrasensitive detection limit of fM level with a broad linear range from fM to nM. More importantly, a higher AUC value (0.884) compared to the clinically used biomarker CA 72-4 was obtained by the nanomachine to distinguish GC patients successfully. Notably, for the key concerns of diagnosis of EGC patients, the nanomachine also achieved a satisfactory AUC value of 0.859. Taken together, this work has screened and obtained multiple biomarkers and developed a fluorescent nanomachine for combination diagnosis of GC, providing an ingenious design of a functionalized DNA nanomachine and a feasible strategy for the transformation of serum biomarkers into clinical diagnosis.