Engineering DNA walkers for bioanalysis: A review

A dual-cycle DNA walker sensor for sensitive clinical detection of microRNAs

BACKGROUND

MicroRNAs (miRNAs) play crucial roles in both physiological and pathological processes, and are increasingly recognized as important biomarkers for cancers and other diseases. However, current detection methods for miRNA face challenges, including inadequate sensitivity and the need for temperature-controlled instruments, which hinder their clinical application. It is a pressing need for new strategies suitable for clinical miRNA detection.

RESULTS

We designed a dual-cycle DNA walker sensor (DDWS) by coupling duplex-specific nucleases enzyme-assisted signal amplification (DSNSA) with a DNA walker sensor. In the DSNSA process, the DSN enzyme specifically hydrolyzes DNA in DNA/target miRNA hybrid duplexes to facilitate the target cycling. The DNA walker sensor is activated by the trigger released from the DSNSA process, enabling a DNA walker cycle via the CHA reaction on magnetic microparticles (MMPs). The DDWS exhibited a strong linear relationship over a range of 600 fM to 600 nM and demonstrated excellent specificity for target miRNA. Furthermore, the DDWS was successfully applied to miRNA detection in real samples, including total RNAs extracted in cell samples and clinical papillary thyroid carcinoma (PTC) tissue samples.

SIGNIFICANCE

This DDWS assay holds great potential for evaluating miRNA expression levels across various biological matrices, contributing to the clinical diagnosis and prognosis of cancers.

A triple-helix molecular switch-based fluorescent aptasensor using Klenow fragment-assisted target recycling and Ribonuclease H-powered DNA walker cascade amplification for detection of MRSA

MRSA is an antibiotic resistant bacterium that poses a significant threat to the environment and human health due to its bioaccumulation and potential widespread contamination. The prompt and accurate identification of MRSA is essential for enhancing environmental monitoring and clinical management. Here, we develop a triple-helix molecular switch (THMS) fluorescent aptasensor for the determination of MRSA using Klenow fragment (KF)-assisted target recycling and Ribonuclease H (Rnase H)-powered DNA walker cascade amplification. In this method, the target opens the THMS by specifically binding with the aptamer, resulting in the release of target/aptamer complex and DNA walker. KF then initiates the target recycling process via strand-displacement polymerization reaction under the assistance of carboxyfluorescein (FAM)-labeled primer and dNTPs, creating plenty of double-stranded DNA (dsDNA) products. These dsDNA products show low affinity to graphene oxide (GO) and generate strong fluorescence. This fluorescence is considerably significantly amplified in the presence of SYBR Green I (SGI), attributable to the synergistic interaction between dsDNA and SGI. In the interim, Rnase H drives the released DNA walker to automatically walk on the carboxylated graphene oxide surface by cleaving FAM-labeled RNA signal probe (SP), causing the FAMs to dissociate from the carboxylated graphene oxide (CGO). Therefore, fluorescent signal originating from the two reaction pathways can be detected at excitation/emission wavelengths of 480/514 nm. The target measured by this strategy demonstrates a broad linear working range from 102 colony-forming units (CFU)/mL to 107 CFU/mL, with a detection limit (LOD) of 15 CFU/mL. Moreover, this method performs well in milk and pus sample analysis. These results reveal that this aptasensor is highly specific and sensitive for detecting MRSA and is endowed with good potential for food monitoring and clinical diagnosis applications.

Enzyme-Assisted Solid-Phase Microextraction Coupled with a DNA Nanowalker for Dual-Amplified Detection of Chloramphenicol in Animal-Derived Food Products

Chloramphenicol (CAP), an aminoalcohol antibiotic, exerts its action on bacterial ribosomes, thereby obstructing protein synthesis. However, the use of CAP in husbandry may lead to its excessive accumulation in animal-derived food products. This presents potential risks to consumer health. This study developed a novel dual-amplification fluorescence detection method by integrating enzyme-assisted solid-phase microextraction (SPME) with a Fe3O4@Au NP-based DNA nanowalker for the detection of CAP in food. The combination of a quartz rod-based SPME biosensor and DNA nanowalker effectively eliminated matrix interference, enabling the conversion of CAP and enhancement of detection signals through two cyclic amplification processes. The strategy demonstrated high sensitivity with a limit of detection of 28.1 aM as well as a wide linear range from 0.1 fM to 1 nM (with R2 > 0.99). This method also demonstrates robust stability and accuracy in detecting trace amounts of CAP in both authentic and prepared positive samples.

Signal amplification strategies in photoelectrochemical sensing of carcinoembryonic antigen

Early detection of cancer markers is critical for cancer diagnosis and cancer therapy since these markers may indicate cancer risk, incidence, and disease prognosis. Carcinoembryonic antigen (CEA) is a type of non-specific and broad-spectrum cancer biomarker commonly utilized for early cancer diagnosis. Moreover, it serves as an essential tool to assess the efficacy of cancer treatment and monitor tumor recurrence as well as metastasis, thus garnering significant attention for precise and sensitive CEA detection. In recent years, photoelectrochemical (PEC) techniques have emerged as prominent methods in CEA detection due to the advantages of PEC, such as simple equipment requirements, cost-effectiveness, high sensitivity, low interference from background signals, and easy of instrument miniaturization. Different signal amplification methods have been reported in PEC sensors for CEA analysis. Based on these, this article reviews PEC sensors based on various signal amplification strategies for detection of CEA during the last five years. The advantages and drawbacks of these sensors were discussed, as well as future challenges.

A novel aptasensor based endogenous enzyme-powered DNA walker for ATP imaging in specific living cells

Highly sensitive and specific imaging of ATP in living cells remains a challenge. Here, a novel aptasensor based endogenous enzyme-powered DNA walker for imaging ATP was proposed. The strategy leverages the highly expressed APE1 in tumor cells as the driving force of the DNA walker, achieving high sensitivity and superior imaging contrast. The method can detect ATP as low as 3.43 μM within 1 h. The approach can also effectively monitor intracellular ATP expression fluctuations and successfully differentiate between normal and cancer cells with high contrast.

Screening biotoxin aptamer and their application of optical aptasensor in food stuff: a review

Biotoxins are ranges of toxic substances produced by animals, plants, and microorganisms, which could contaminate foods during their production, processing, transportation, or storage, thus leading to foodborne illness, even food terrorism. Therefore, proposing simple, rapid, and effective detection methods for ensuring food free from biotoxin contamination shows a highly realistic demand. Aptamers are single-stranded oligonucleotides obtained from the systematic evolution of ligands by performing exponential enrichment (SELEX). They can specifically bind to wide ranges of targets with high affinity; thus, they have become important recognizing units in safety monitoring in food control and anti-terrorism. In this paper, we reviewed the technical points and difficulties of typical aptamer screening processes for biotoxins. For promoting the understanding of food control in the food supply chain, the latest progresses in rapid optical detection of biotoxins based on aptamers were summarized. In the end, we outlined some challenges and prospects in this field. We hope this paper could stimulate widespread interest in developing advanced sensing systems for ensuring food safety.

Self-Feedback DNAzyme Motor for Cascade-Amplified Imaging of mRNA in Live Cells and In Vivo

DNA motors have attracted extensive interest in biosensing and bioimaging. However, the amplification capacity of the existing DNA motor systems is limited since the products from the walking process are unable to feedback into the original DNA motor systems. As a result, the sensitivities of such systems are limited in the contexts of biosensing and bioimaging. In this study, we report a novel self-feedback DNAzyme motor for the sensitive imaging of tumor-related mRNA in live cells and in vivo with cascade signal amplification capacity. Gold nanoparticles (AuNPs) are modified with hairpin-locked DNAzyme walker and track strands formed by hybridizing Cy5-labeled DNA trigger-incorporated substrate strands with assistant strands. Hybridization of the target mRNA with the hairpin strands activates DNAzyme and promotes the autonomous walking of DNAzyme on AuNPs through DNAzyme-catalyzed substrate cleavage, resulting in the release of many Cy5-labeled substrate segments containing DNA triggers and the generation of an amplified fluorescence signal. Moreover, each released DNA trigger can also bind with the hairpin strand to activate and operate the original motor system, which induces further signal amplification via a feedback mechanism. This motor exhibits a 102-fold improvement in detection sensitivity over conventional DNAzyme motors and high selectivity for target mRNA. It has been successfully applied to distinguish cancer cells from normal cells and diagnose tumors in vivo based on mRNA imaging. The proposed DNAzyme motor provides a promising paradigm for the amplified detection and sensitive imaging of low-abundance biomolecules in vivo.

The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology

DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.

DNA tetrahedron-mediated triplex molecular switch for extracellular pH monitoring

This study aimed to construct a novel DNA triplex molecular switch modified with DNA tetrahedron (DTMS-DT) with sensitive response to extracellular pH using a DNA tetrahedron as the anchoring unit and DNA triplex as the response unit. The results showed that the DTMS-DT had desirable pH sensitivity, excellent reversibility, outstanding anti-interference ability, and good biocompatibility. Confocal laser scanning microscopy suggested that the DTMS-DT could not only be stably anchored on the cell membrane but also be employed to dynamically monitor the change in extracellular pH. Compared with the reported probes for extracellular pH monitoring, the designed DNA tetrahedron-mediated triplex molecular switch exhibited higher cell surface stability and brought the pH-responsive unit closer to the cell membrane surface, making the results more reliable. In general, developing the DNA tetrahedron-based DNA triplex molecular switch is helpful for understanding and illustrating the pH dependent cell behaviors and disease diagnostics.

DNA Walkers for Biosensing Development

The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer-associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection- of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker-based biosensors are discussed.

A Cancer Cell Membrane Vesicle-packaged DNA Nanomachine for Intracellular microRNAs Imaging

A cancer cell membrane vesicle encapsulated gold nanoparticles with programmable DNA nanomachine was established. Both the homing-targeting ability and fast dynamic response were achieved for amplification analysis of microRNAs in...