A simple and programmed DNA tweezer probes for one-step and amplified detection of UO22

Application of DNA-fueled molecular machines in food safety testing

Food is consumed by humans, which is indispensable to human life. Therefore, considerable attention of the whole society has been paid to food safety. Over the last few years, dramatic social development has brought new challenges to food safety, making developing new and quick methods for on-site food safety testing an important necessity. As a result, DNA-fueled molecular machines, characterized by high efficiency, accuracy, and sensitivity in testing, have come into the spotlight, based on which sensors can be constructed to detect toxic and harmful substances in food products. This study reviewed recent research on several DNA-fueled molecular machines, including DNA tweezers, DNA walkers, and DNA origami, for rapidly detecting toxic and harmful substances. Based on the above studies, the sensitivity and timeliness of several DNA molecular machines were summarized and compared, and the development prospect of DNA fuel molecular machines in the field of food safety detection was prospected.

A nicking enzyme-assisted allosteric strategy for self-resetting DNA switching circuits

The self-regulation of biochemical reaction networks is crucial for maintaining balance, stability, and adaptability within biological systems. DNA switching circuits, serving as basic units, play essential roles in regulating pathways, facilitating signal transduction, and processing biochemical reaction networks. However, the non-reusability of DNA switching circuits hinders its application in current complex information processing. Herein, we proposed a nicking enzyme-assisted allosteric strategy for constructing self-resetting DNA switching circuits to realize complex information processing. This strategy utilizes the unique cleavage ability of the nicking enzyme to achieve the automatic restoration of states. Based on this strategy, we implemented a self-resetting DNA switch. By leveraging the reusability of the DNA switch, we constructed a DNA switching circuit with selective activation characteristics and further extended its functionality to include fan-out and fan-in processes by expanding the number of functional modules and connection modes. Furthermore, we demonstrated the complex information processing capabilities of these switching circuits by integrating recognition, translation, and decision functional modules, which could analyze and transmit multiple input signals and realize parallel logic operations. This strategy simplifies the design of switching circuits and promotes the future development of biosensing, molecular computing, and nanomachines.

Multiplexed smFRET Nucleic Acid Sensing Using DNA Nanotweezers

The multiplexed detection of disease biomarkers is part of an ongoing effort toward improving the quality of diagnostic testing, reducing the cost of analysis, and accelerating the treatment processes. Although significant efforts have been made to develop more sensitive and rapid multiplexed screening methods, such as microarrays and electrochemical sensors, their limitations include their intricate sensing designs and semi-quantitative detection capabilities. Alternatively, fluorescence resonance energy transfer (FRET)-based single-molecule counting offers great potential for both the sensitive and quantitative detection of various biomarkers. However, current FRET-based multiplexed sensing typically requires the use of multiple excitation sources and/or FRET pairs, which complicates labeling schemes and the post-analysis of data. We present a nanotweezer (NT)-based sensing strategy that employs a single FRET pair and is capable of detecting multiple targets. Using DNA mimics of miRNA biomarkers specific to triple-negative breast cancer (TNBC), we demonstrated that the developed sensors are sensitive down to the low picomolar range (≤10 pM) and can discriminate between targets with a single-base mismatch. These simple hybridization-based sensors hold great promise for the sensitive detection of a wider spectrum of nucleic acid biomarkers.

Construction and Application of DNAzyme-based Nanodevices

The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.

Recent Advances on DNAzyme-Based Biosensors for Detection of Uranyl

Nuclear facilities are widely used in fields such as national defense, industry, scientific research, and medicine, which play a huge role in military and civilian use. However, in the process of widespread application of nuclear technology, uranium and its compounds with high carcinogenic and biologically toxic cause a lot of environmental problems, such as pollutions of water, atmosphere, soil, or ecosystem. Bioensors with sensitivity and specificity for the detection of uranium are highly demand. Nucleic acid enzymes (DNAzyme) with merits of high sensitivity and selectivity for targets as excellent molecular recognition elements are commonly used for uranium sensor development. In this perspective review, we summarize DNAzyme-based biosensors for the quantitative detection of uranyl ions by integrating with diverse signal outputting strategies, such as fluorescent, colorimetry, surface-enhanced Raman scattering, and electrochemistry. Different design methods, limit of detection, and practical applications are fully discussed. Finally, the challenges, potential solutions, and future prospects of such DNAzyme-based sensors are also presented.

DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects

DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.

Dual-signal amplification electrochemical sensing for the sensitive detection of uranyl ion based on gold nanoparticles and hybridization chain reaction-assisted synthesis of silver nanoclusters

Herein, a dual-signal amplification electrochemical sensing has been proposed for the ultrasensitive detection of uranyl ions (UO₂²⁺) by integration of gold nanoparticles (AuNPs) and hybridization chain reaction (HCR)-assisted synthesis of silver nanoclusters (AgNCs). In this sensing platform, AuNPs are used as an ideal signal amplification carrier, aiming at increasing the loads of UO₂²⁺-specific DNAzyme on the gold electrode. In the presence of UO₂²⁺, UO₂²⁺-specific DNAzyme can be activated, leading to the cleavage of substrate strands (S-DNA). Then, HCR is triggered to produce long dsDNA through hybridization the probe with the ssDNA on the electrode surface. As a result, an amplified electrochemical response can be detected by inserting a large amount of AgNCs generated in situ using dsDNA as template. Featured with amplification efficiency, good specificity and high sensitivity, the strategy could quantitatively detect UO₂²⁺ down to 6.2 pM with a linear calibration range from 20 pM to 5000 pM. The proposed sensing platform has been also successfully demonstrated the practical application of detecting UO₂²⁺, indicating that the developed method has the potential applications and can open up a new avenue for highly sensitive detection of UO₂²⁺ in environmental monitoring.

A novel liquid crystal sensing platform for highly selective UO22+ detection based on a UO22+-specific DNAzyme

A label-free and selective sensor was established for uranyl ion (UO₂²⁺) detection based on a UO₂²⁺-dependent DNAzyme and liquid crystals (LCs). In the presence of UO₂²⁺, the substrate chains can be cleaved at the rA site by the DNAzyme strands. The cleaved products released from the DNAzyme strand will hybridize with the capture probes that are fixed on the LC sensing substrate to form double strands. The formation of double strands would disturb the original orientation and induce the rearrangement of liquid crystal molecules, resulting in the polarization images changing from uniform black to bright. Attributed to the specificity of the DNAzyme and the optical signal of the LC, a highly selective and label-free method was established with a detection limit of 25 nM. This approach showed satisfactory analytical performance and offered an inspiring platform for detecting other radioactive elements.

A "turn-on" and proximity ligation assay dependent DNA tweezer for one-step amplified fluorescent detection of DNA

A "turn-on" and proximity ligation assay dependent DNA tweezer was proposed for one-step amplified fluorescent detection of DNA. Target DNA can anneal with capture probe to form an entire long sequence. The formed long sequence can circularly open the hairpin, resulting the "turn-on" of DNA tweezers. A good linear relationship was shown from 40 pM to 20 nM with limit of detection of 10 pM. In addition, it has been successfully utilized to analysis DNA in human serum, representing a great and practical application future.

Simultaneous detection of aflatoxin B1 and ochratoxin A in food samples by dual DNA tweezers nanomachine

a dual DNA tweezers nanomachine was developed for one-step simultaneous detection of aflatoxin B1 (AFB1) and ochratoxin A (OTA) in food samples. The dual DNA tweezers are locked by the aptamers of mycotoxins, resulting the "turn off" of fluorescent signal. In the presence of AFB1 and OTA, the aptamers can bind with their corresponding targets, resulting the "open" of DNA tweezers and the "turn on" of the fluorescent signals. The limits of detections were 3.5 × 10^-2 ppb for AFB1 and 0.1 ppb for OTA. Moreover, the applicability of the method was further demonstrated by conducting a limited survey on 5 samples collected from various sources. The recoveries of this method change from 90.0% to 110.0% for simultaneous detection of AFB1 or OTA and the RSDs vary from 4.1% to 9.2%. Detection uncertainties were within 5% (with a 95% confidence level).