A Ratiometric Fluorescent DNA Radar Based on Contrary Response of DNA/Silver Nanoclusters and G-Quadruplex/Crystal Violet

Empowering DNA-Based Information Processing: Computation and Data Storage

Information processing is a critical topic in the digital age, as silicon-based circuits face unprecedented challenges such as data explosion, immense energy consumption, and approaching physical limits. Deoxyribonucleic acid (DNA), naturally selected as a carrier for storing and using genetic information, possesses unique advantages for information processing, which has given rise to the emerging fields of DNA computing and DNA data storage. To meet the growing practical demands, a wide variety of materials and interfaces have been introduced into DNA information processing technologies, leading to significant advancements. This review summarizes the advances in materials and interfaces that facilitate DNA computation and DNA data storage. We begin with a brief overview of the fundamental functions and principles of DNA computation and DNA data storage. Subsequently, we delve into DNA computing systems based on various materials and interfaces, including microbeads, nanomaterials, DNA nanostructures, hydrophilic-hydrophobic compartmentalization, hydrogels, metal-organic frameworks, and microfluidics. We also explore DNA data storage systems, encompassing encapsulation materials, microfluidics techniques, DNA nanostructures, and living cells. Finally, we discuss the current bottlenecks and obstacles in the fields and provide insights into potential future developments.

Programmability of dual-color DNA-templated silver nanoclusters for modular design of FRET aptasensors toward multiplexed detection

By exploiting the programmability of DNA, dual-color DNA-templated silver nanoclusters have been synthesized to serve as a label-free fluorescent probe with a G5-linker at the 3' end. This advancement facilitates the modular design of universal FRET-based aptasensors using aptamers with a C5-linker at the 3' end for multiplexed detection, making them easily switch their applications.

Programmable DNA Templates for Silver Nanoclusters Synthesis To Develop On-Demand FRET Aptasensor

DNA-templated silver nanoclusters (AgNCs-DNA) can be synthesized via a one-pot method bypassing the tedious process of biomolecular labeling. Appending an aptamer to DNA templates results in dual-functionalized DNA strands that can be utilized for synthesizing aptamer-modified AgNCs, thereby enabling the development of label-free fluorescence aptasensors. However, a major challenge lies in the necessity to redesign the dual-functionalized DNA strand for each specific target, thus increasing the complexity and hindering widespread application of these aptasensors. To overcome this challenge, we designed six DNA strands (DNA1-DNA6) that incorporate the templates for AgNCs synthesis and A4-linker for further aptamer coupling. Among all the synthesized AgNCs-DNA samples, it was found that both AgNCs-DNA1 and AgNCs-DNA2 stood out for their excellent long-term stability. After capturing the T4-linker that connected with aptamer1 specific for aflatoxin B1 (AFB1), however, we found that only AgNCs-DNA1/aptamer1 maintained excellent long-term stability. This finding highlighted the potential of AgNCs-DNA1 as a versatile label-free fluorescence probe for the development of on-demand fluorescence aptasensors. To emphasize its benefits in aptasensing applications, we utilized AgNCs-DNA1/aptamer1 as the fluorescence probe and MoS2 nanosheets as the quencher to develop a FRET aptasensor for AFB1 detection. This aptasensor demonstrated remarkable sensitivity, enabling the detection of AFB1 within a wide concentration range of 0.03-120 ng/mL, with a limit of detection as low as 3.6 pg/mL (S/N = 3). The versatility of the aptasensor has been validated through the recognition of diverse targets, employing aptamer2 specific for ochratoxin A and aptamer3 specific for zearalenone, thereby showcasing its extensive applicability for on-demand detection. The universal applicability of this aptasensor holds great promise for future applications in diverse fields including food safety, environmental monitoring, and clinical diagnosis.

Topological effect of an intramolecular split G-quadruplex on thioflavin T binding and fluorescence light-up

In this work, the topological effect on binding interaction between a G-quadruplex and thioflavin T (ThT) ligand was systematically investigated on a platform of an intramolecular split G-quadruplex (Intra-SG). Distinct fluorescence changes from ThT were presented in the presence of distinct split modes of Intra-SG structures and an intriguing phenomenon of target-induced fluorescence light-up occurred for split modes 2 : 10, 5 : 7 and 8 : 4. It was validated that hybridization between the Intra-SG spacer and target did not unfold the G-quadruplex, but facilitated the ThT binding. Moreover, the 3' guanine-rich fragment of Intra-SG was very susceptible to topology variation produced by the bound target strand. Additionally, a bioanalytical method was developed for ultrasensitive gene detection, confirming the utility of the ThT/Intra-SG complex as a universal signal transducer. It is believed that the results and disclosed rules will inspire researchers to develop many new DNA-based signal transducers in the future.

A universal approach for synthesis of copper nanoclusters templated by G-rich oligonucleotide sequences and their applications in sensing

Herein, five common G4 sequences have been selected, including three different length of telomere DNA, hemin aptamer, and thrombin aptamer, to synthesize Cu nanoclusters (Cu NCs) in-situ. All G4s are proper templates for Cu NCs with low temperature treatment. The particles (G4-Cu NCs) smaller than 3 nm in diameter were obtained and showed light green fluorescence. This is the first report of metal clusters templated by G4s in-situ. As proof of the concept, hemin and alkaline phosphatase (ALP) were used as the targets to test whether the system can monitor the interaction between G4s and its substrate. The results suggest that G4-Cu NCs can indicate the behavior of G4 and its interaction with hemin, and sensing ALP is achieved with the aid of ATP. The linear ranges of hemin and ALP are 300-4000 nM and 10-500 U/L, respectively, and the corresponding limits of detection as low as 97 nM for hemin and 2.8 U/L for ALP. Moreover, this present system has been successfully applied for the detection of ALP in human serum samples with satisfactory recoveries. This synthesis approach is universal, and it can be easily extended to evaluating the formation of G4, or monitoring the interaction between G4 and its substrate, or selective targeting individual G4, or sensitive detection of other important biomarkers by changing template G4 sequence.

An allosteric DNA switch-mediated catalytic DNA circuit for ratiometric and sensitive nucleic acid detection

Herein, a new allosteric DNA switch-mediated catalytic DNA circuit reaction strategy has been proposed for ratiometric and sensitive nucleic acid detection. The sensing system was based on two DNA hybrid probes, each of which was constructed by annealing a reconfigurable DNA hairpin with single-stranded DNA. Upon target recognition by the first DNA hybrid probe, a reconfigurable DNA switch was liberated, triggering a toehold-mediated strand displacement reaction (TSDR) with the second DNA hybrid probe, which was accompanied by the release of another reconfigurable DNA switch. This released allosteric DNA switch could further interact with the first hybrid DNA probe via the TSDR strategy to form a reciprocal strand displacement network between the two DNA hybrid probes. Theoretically, this reciprocal strand displacement reaction would continue till the complete consumption of the reaction substrates. Thus, it provides a new signal amplification method leading toward target recognition. More interestingly, it creates a ratiometric signal response mode for target recognition, which involves the fluorescence increment of one fluorophore (Cy5) and concurrent decrement of another fluorophore (Cy3) accompanied by the target-triggered reciprocal strand displacement reaction. This process could achieve a low detection limit of about 0.1 pM toward the target nucleic acid and selective discrimination toward different mismatched targets. It could also be applied for detection in a serum sample. Thus, the developed catalytic DNA circuit reaction strategy together with ratiometric signal readout provides a new avenue for programmable, reliable and sensitive detection of nucleic acids and might also pave the way for developing more advanced DNA circuits or biosensors.

CRISPR/Cas Precisely Regulated DNA-Templated Silver Nanocluster Fluorescence Sensor for Meat Adulteration Detection

Meat adulteration can cause consumer fraud, food allergies, and religious issues. Rapid and sensitive detection methods are urgently demanded to supervise meat authenticity. Herein, a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas precisely regulated DNA-templated silver nanocluster (DNA-AgNC) sensor was ingeniously designed to detect meat adulteration. Specific sequence recognition of CRISPR/Cas12a allowed accurate identification of target DNA. The emerging label-free fluorescent probes, DNA-AgNCs, a class of promising fluorophores in biochemical analysis with attractive photostability and remarkably enhanced fluorescence properties, were first introduced as the substrates of CRISPR/Cas12a system, allowing a sensitive output of amplified signals through the precise regulation of the unique target DNA-activated trans-cleavage activity of Cas12a. Based on this specific recognition, efficient signal transduction of CRISPR/Cas12a, and the outstanding fluorescence properties of DNA-AgNCs, the proposed strategy achieved a satisfactory linear range from 10 pM to 1 μM with a limit of detection (LOD) as low as 1.9 pM, which can achieve sensitive detection of meat adulteration.

CRISPR-Cas systems mediated biosensing and applications in food safety detection

Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.

Target Deoxyribonucleic Acid-Recycled Lighting-Up Amplifiable Ratiometric Fluorescence Biosensing of Bicolor Silver Nanoclusters Hosted in a Switchable Deoxyribonucleic Acid Construct

Ratiometric assays of label-free dual-signaling reporters with enzyme-free amplification are intriguing yet challenging. Herein, yellow- and red-silver nanocluster (yH-AgNC and rH-AgNC) acting as bicolor ratiometric emitters are guided to site-specifically cluster in two template signaling hairpins (yH and rH), respectively, and originally, both of them are almost non-fluorescent. The predesigned complement tethered in yH is recognizable to a DNA trigger (T_OC) related to SARS-CoV-2. With the help of an enhancer strand (G₁₅E) tethering G-rich bases (G₁₅) and a linker strand (LS), a switchable DNA construct is assembled via their complementary hybridizing with yH and rH, in which the harbored yH-AgNC close to G₁₅ is lighted-up. Upon introducing T_OC, its affinity ligating with yH is further implemented to unfold rH and induce the DNA construct switching into closed conformation, causing T_OC-repeatable recycling amplification through competitive strand displacement. Consequently, the harbored rH-AgNC is also placed adjacent to G₁₅ for turning on its red fluorescence, while the yH-AgNC is retainable. As demonstrated, the intensity ratio dependent on varying T_OC is reliable with high sensitivity down to 0.27 pM. By lighting-up dual-cluster emitters using one G₁₅ enhancer, it would be promising to exploit a simpler ratiometric biosensing format for bioassays or clinical theranostics.

Exploring the fluorescence enhancement of the split G-quadruplex towards DNA-templated AgNCs and their application in omethoate detection

Based on the enhancement of split G-quadruplex on the fluorescence of DNA-templated AgNCs, a facile label-free and enzyme-free omethoate detection platform has been successfully constructed through the interaction between split G4 with DNA-AgNCs.

Applications of DNA-Functionalized Proteins

As an important component that constitutes all the cells and tissues of the human body, protein is involved in most of the biological processes. Inspired by natural protein systems, considerable efforts covering many discipline fields were made to design artificial protein assemblies and put them into application in recent decades. The rapid development of structural DNA nanotechnology offers significant means for protein assemblies and promotes their application. Owing to the programmability, addressability and accurate recognition ability of DNA, many protein assemblies with unprecedented structures and improved functions have been successfully fabricated, consequently creating many brand-new researching fields. In this review, we briefly introduced the DNA-based protein assemblies, and highlighted the limitations in application process and corresponding strategies in four aspects, including biological catalysis, protein detection, biomedicine treatment and other applications.

Fluorescence and visual immunoassay of HIV-1 p24 antigen in clinical samples via multiple selective recognitions of CdTe QDs

Human immunodeficiency virus (HIV) infection inflicts significant economic and social burdens on many countries worldwide. Given the substantial morbidity and mortality from HIV infection, there is an urgent need for accurate and early detection of the virus. In this study, immunofluorescence and visual techniques are described that detect the HIV-1 p24 antigen, which relied on selective recognition of Ag⁺/Ag nanoparticles (Ag NPs) and Cu²⁺/Cu⁺ using cadmium telluride quantum dots (CdTe QDs). After the sandwich immunoreactions were accomplished, the alkaline phosphatase (ALP) hydrolyzed L-ascorbic acid 2-phosphate (AAP) to form ascorbic acid (AA) that further reduces Ag⁺ and Cu²⁺ to Ag NPs and Cu⁺, respectively. This method was highly sensitive and selective and could detect as low as 1 pg/mL of p24 antigen by naked eyes and had a good linearity in the concentration range 1-100 pg/mL. When using Ag⁺ and Cu²⁺ as media, the limit of detection (LOD) of the new method was 0.3 pg/mL and 0.2 pg/mL, respectively. Compared with clinical electrochemiluminescence immunoassay (ECLIA) results and clinical data, this method demonstrated good consistency for the quantification of HIV-1 p24 antigen in 34 clinical serum samples. In addition, this method could accurately distinguish HIV from other viruses and infections such as hepatitis B virus, systemic lupus erythematosus, hepatitis C virus, Epstein-Barr virus, cytomegalovirus, lipemia, and hemolysis. Therefore, our dual-mode analysis method may provide additional solutions to identify clinical HIV infection. An immunofluorescence and visualization dual-mode strategy for the detection of p24 antigen was constructed based on immune recognition reaction and a phenomenon that cadmium telluride quantum dots (CdTe QDs) can selectively recognize Ag⁺/Ag nanoparticles (Ag NPs) and Cu²⁺/Cu⁺.

Antibody-Responsive Ratiometric Fluorescence Biosensing of Biemissive Silver Nanoclusters Wrapped in Switchable DNA Tweezers

Exploring the ratiometric fluorescence biosensing of DNA-templated biemissive silver nanoclusters (AgNCs) is significant in bioanalysis, yet the design of a stimuli-responsive DNA device is a challenge. Herein, using the anti-digoxin antibody (anti-Dig) with two identical binding sites as a model, a tweezer-like DNA architecture is assembled to populate fluorescent green- and red-AgNCs (g-AgNCs and r-AgNCs), aiming to produce a ratio signal via specific recognition of anti-Dig with two haptens (DigH). To this end, four DNA probes are programmed, including a reporter strand (RS) dually ended with a g-/r-AgNC template sequence, an enhancer strand (ES) tethering two same G-rich tails (G18), a capture strand (CS) labeled with DigH at two ends, and a help strand (HS). Initially, both g-AgNCs and r-AgNCs wrapped in the intact RS are nonfluorescent, whereas the base pairing between RS, ES, CS, and HS resulted in the construction of DNA mechanical tweezers with two symmetric arms hinged by a rigid "fulcrum", in which g-AgNCs are lighted up due to G18 proximity ("green-on"), and r-AgNCs away from G18 are still dark ("red-off"). When two DigHs in proximity recognize and bind anti-Dig, the conformation switch of these tweezers resultantly occurs, taking g-AgNCs away from G18 for "green-off" and bringing r-AgNCs close to G18 for "red-on". As such, the ratiometric fluorescence of r-AgNCs versus g-AgNCs is generated in response to anti-Dig, achieving reliable quantization with a limit of detection at the picomolar level. Based on the fast stimulated switch of unique DNA tweezers, our ratiometric strategy of dual-emitting AgNCs would provide a new avenue for a variety of bioassays.

DNA-Grafted 3D Superlattice Self-Assembly

The exploitation of new methods to control material structure has historically been dominating the material science. The bottom-up self-assembly strategy by taking atom/molecule/ensembles in nanoscale as building blocks and crystallization as a driving force bring hope for material fabrication. DNA-grafted nanoparticle has emerged as a "programmable atom equivalent" and was employed for the assembly of hierarchically ordered three-dimensional superlattice with novel properties and studying the unknown assembly mechanism due to its programmability and versatility in the binding capabilities. In this review, we highlight the assembly strategies and rules of DNA-grafted three-dimensional superlattice, dynamic assembly by different driving factors, and discuss their future applications.

Crystal Violet-Sensitized Direct Z-Scheme Heterojunction Coupled with a G-Wire Superstructure for Photoelectrochemical Sensing of Uracil-DNA Glycosylase

Dye sensitization achieving photoelectrochemical (PEC) signal amplification for ultrasensitive bioanalysis has undergone a major breakthrough. In this proposal, an innovative PEC sensing platform is developed by combining Z-scheme WO₃@SnS₂ photoactive materials and a G-wire superstructure as well as a dye sensitization enhancement strategy. The newly synthesized WO₃@SnS₂ heterojunction with outstanding PEC performance is employed as a photoelectrode matrix. Due to the formation of the Z-scheme heterojunction between WO₃ and SnS₂, the migration dynamics of the photogenerated carrier is evidently augmented. To improve sensitivity, the target excision-driven dual-cycle signal amplification strategy is introduced to output exponential c-myc fragments. Crystal violet is then conjugated into the G-quadruplex to amplify the PEC signal, where crystal violet generates excited electrons by capturing visible light and rapidly injects electrons into the conduction band of SnS₂, suppressing the recombination of the photo-induced carrier. Moreover, the G-wire superstructure acts as a universal amplification pathway, ensuring adequate crystal violet loads. Specifically, the biosensor for uracil-DNA glycosylase quantification displays a wide detection range (0.0005-1.0 U/mL) and a lower detection limit (0.00025 U/mL). Furthermore, the Z-scheme electron migration mechanism and the crystal violet sensitization effect are discussed in detail. The construction of the PEC sensor provides a new consideration for signal amplification and material design.

Recent advances in templated synthesis of metal nanoclusters and their applications in biosensing, bioimaging and theranostics

As a kind of promising nanomaterials, metal nanoclusters (MNCs) generally composed of several to hundreds of metal atoms have received increasing interest owing to their unique properties, such as ultrasmall size (<2 nm), fascinating physical and chemical properties, and so on. Recently, template-assisted synthesis of MNCs (e.g., Au, Ag, Cu, Pt and Cd) has attracted extensive attention in biological fields. Up to now, various templates (e.g., dendrimers, polymers, DNAs, proteins and peptides) with different configurations and spaces have been applied to prepare MNCs with the advantages of facile preparation, controllable size, good water-solubility and biocompatibility. Herein, we focus on the recent advances in the template-assisted synthesis of MNCs, including the templates used to synthesize MNCs, and their applications in biosensing, bioimaging, and disease theranostics. Finally, the challenges and future perspectives of template-assisted synthesized MNCs are highlighted. We believe that this review could not only arouse more interest in MNCs but also promote their further development and applications by presenting the recent advances in this area to researchers from various fields, such as chemistry, material science, physiology, biomedicine, and so on.

DNA Origami-Enabled Biosensors

Biosensors are small but smart devices responding to the external stimulus, widely used in many fields including clinical diagnosis, healthcare and environment monitoring, etc. Moreover, there is still a pressing need to fabricate sensitive, stable, reliable sensors at present. DNA origami technology is able to not only construct arbitrary shapes in two/three dimension but also control the arrangement of molecules with different functionalities precisely. The functionalization of DNA origami nanostructure endows the sensing system potential of filling in weak spots in traditional DNA-based biosensor. Herein, we mainly review the construction and sensing mechanisms of sensing platforms based on DNA origami nanostructure according to different signal output strategies. It will offer guidance for the application of DNA origami structures functionalized by other materials. We also point out some promising directions for improving performance of biosensors.

Targeted DNA-driven catalytic assembly light-up ratiometric fluorescence of biemissive silver nanoclusters for amplified biosensing

We report a ratiometric fluorescence strategy using biemissive silver nanoclusters that are harbored in a functional hairpin beacon for rapid, specific and sensitive detection of specific HIV-related DNA as a model.

Label-free probes using DNA-templated silver nanoclusters as versatile reporters

DNA-templated silver nanoclusters (DNA-AgNCs) have demonstrated pervasive applications in analytical chemistry recently. As a way of signal output in DNA-based detection methods, DNA-AgNCs have prominent advantages: first, the recognition and synthesizing sequences are naturally integrated in one DNA probe without any chemical modification or connection; second, the emissive wavelength of DNA-AgNCs can be adjusted in a wide range by employing different sequences; third, DNA-AgNCs can be utilized for producing not only fluorescence, also electrochemiluminescence and electrochemical signals. Besides, they also show potential applications for cell imaging, and are considered to be one of the most ideal nanomaterials for in-vivo imaging due to their ultra-small particle size. In this review, a brief and comprehensive introduction of DNA-AgNCs is firstly given, then label-free probes using DNA-AgNCs are classified and summarized, lastly concluding perspectives are provided on the defects and application potentials.