Insight into the Sensing Behavior of DNA Probes Based on MOF-Nucleic Acid Interaction for Bioanalysis

A novel and universal dual-channel signal amplification aptasensing platform for ultrasensitive and rapid detection of cardiac biomarkers based on the mutual regulation of bimetallic organic framework and silver nanoclusters

Cardiac troponin I (cTnI) is a key biomarker for diagnosing myocardial infarction caused by myocardial injury. The accurate and rapid monitoring of ultralow levels of cTnI is crucial for early diagnosis and risk warning of myocardial injury. Herein, a novel dual-channel signal amplification aptasensor for cTnI detection was developed utilizing the mutual regulation of bimetallic organic framework (MOFs) and silver nanoclusters (AgNCs) with the assistance of catalytic hairpin assembly (CHA). Rationally designed triple-helix molecular switch (THMS) and two hairpin probes (HP1 and HP2) containing AgNCs and a guanine-rich DNA sequence could be adsorbed onto the surface of bimetallic Cu, Mo-MOFs, enhancing the catalytic activity and reducing the fluorescence signal. The target cTnI specifically binds to the aptamer in the THMS, releasing the signal transduction probe which triggers CHA to desorb HP1-AgNCs and HP2, thereby restoring the fluorescence and decreasing the catalytic activity as well as initiating cycling. This enables dual-channel fluorescence and colorimetric detection of cTnI. The linear fluorescence and colorimetric response ranges were 0.001-20 ng/mL with LOD of 0.48 pg/mL and 0.001-10 ng/mL with LOD of 0.69 pg/mL, respectively. The aptasensor significantly increases the detection sensitivity and reduces the time required for cTnI detection in human serum, with excellent anti-interference capability. Moreover, the aptasensor shows promise for the construction of universal dual-channel aptasensors for multiple targets by altering the aptamer in THMS.

Redefining Metal Organic Frameworks in Biosensors: Where Are We Now?

As a broad class of porous nanomaterials, metal organic frameworks (MOFs) exhibit unique properties, such as broad tunability, high stability, atomically well-defined structure, and ordered uniform porosity. These features facilitate the rational design of MOFs as an outstanding nanomaterial candidate in biosensing, therapeutics delivery, and catalysis applications. Recently, novel modifications of the MOF nanoarchitecture and incorporation of synergistic guest materials have been investigated to achieve well-tailored functional design, gradually bridging the fundamental gap between structure and targeted activity. Specifically, the burgeoning studies of MOF-based high-performance biosensors have aimed to achieve high sensitivity, selectivity, and stability for a large variety of analytes in different sensing matrices. In this review, we elaborate the key roles of MOF nanomaterials in biosensors, including their high stability as a protective framework for biomolecules, their intrinsic sensitivity-enhancing functionalities, and their contribution of catalytic activity as a nanozyme. By examining the main structures of MOFs, we further identify varied structural engineering approaches, such as precursor tuning and guest molecule incorporation, that elucidate the concept of the structure-activity relationship of MOFs. Furthermore, we highlight the unique applications of MOF nanomaterials in electrochemical and optical biosensors for enhanced sensor performances. Finally, the challenges and future perspectives of developing next-generation MOF nanomaterials for biosensor applications are discussed.

The aggregation-caused quenching effect and fluorescence enhancement features of ZIF-90 and their feasibility for the detection and imaging of ATP in cells

Herein, two new or overlooked features of ZIF-90 were identified and investigated. Imidazole-2-carboxaldehyde is fluorescent, but its fluorescence in ZIF-90 is quenched by an ACQ effect. ZIF-90 can enhance the fluorescence of Cy5, but quench that of 6-FAM. The applicability of the two newly identified features in biosensing was explored.

Targeted Enrichment of Nucleic Acid Bionic Arms Enhances the Hydrolysis Activity of Nanozymes for Degradation and Real-Time Monitoring of Organophosphorus Pesticides in Water

Organophosphorus pesticides (OPs) pose significant environmental and health risks, and their detoxification through catalytic hydrolysis using zirconium-based metal-organic frameworks (Zr-MOFs) has attracted considerable interest due to the strong Lewis acid metal ions. Albeit important, the defects of the materials for OP hydrolysis (e.g., poor degradation efficiency, rate, and selectivity) limit their further application. Herein, a nucleic acid bionic arm-modified biomimetic nanozyme (MOF-808-Apt) was designed through a Zr-MOF and a specific aptamer against OPs, which was employed for the efficient and selective degradation of OPs. At the system, the functionalized biomimetic nanozyme can continuously capture trace OPs onto its catalytic sites for degradation with the fabricated nucleic acid bionic arms, significantly improving their catalytic activities compared to bare MOF-808 using paraoxon as a model of OPs, providing better performances including (i) an excellent degradation efficiency, boosting from 4 to over 60% within 6 min; (ii) a satisfactory catalytic rate (the pseudo-first-order rate constants of paraoxon hydrolysis improved from 0.09 to 0.14 min-1); and (iii) good selective degradation because of aptamers used. Besides, this dynamic degradation process could be visually recorded in real time with high sensitivity (limit of detection, 0.18 μM) because of the obvious color change of the reaction solution and signal amplification ascribed to increasing local concentrations of targets by the nucleic acid bionic arms. Summarily, this work provides a new strategy for the effective and selective degradation of typical OPs and concurrent monitoring of their dynamic degradation process.

Enhancing reliability for AFB1 analysis in food: Ratiometric fluorescence/colorimetric dual-modal analysis platform using multifunctional GO-Fe3O4

Adsorption of DNA fluorescent probes on GO-Fe3O4 is a promising strategy for establishing fluorescent bioassays, often using magnetic separation or fluorescence quenching to generate signals. However, there is a lack of systematic understanding of ssDNA-regulated changes in the enzyme-mimetic activity of GO-Fe3O4, and the accuracy of the results of single-mode fluorescence analysis is susceptible to environmental interference. These limit the rational design and scope of application of the methods. Herein, the force and the catalytic mechanism of ssDNA/GO-Fe3O4 interactions were explored in detail. On this basis, a ratiometric fluorescence/colorimetric dual-modal analysis platform was constructed based on the superparamagnetism and DNA controllable peroxidase-like activity of GO-Fe3O4. The ratiometric fluorescent signal was generated by combining 7-amino-4-methyl-3-coumarinylacetic acid (AMCA) labeled aptamer (AMCA-aptamer) with AT hairpin-synthesized copper nanoparticles, which has built-in correction and resistance to environmental interference. The aptamer-modulated peroxidase-like activity of GO-Fe3O4 generated the colorimetric signal. Two signals correct each other to further enhance the reliability of the results. The analytical platform performed satisfactorily for AFB1 detection in the range of 0.1-150 μg/L, and was successfully applied to real samples (peanut, milk powder, and wheat flour). With the support of ImageJ software, quantitative detection was achieved by RGB channel analysis for real-color images, which provides a potential pathway for the rapid detection of food safety.

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

DNA-functionalized cryogel based colorimetric biosensor for sensitive on-site detection of aflatoxin B1 in food samples

Hydrogel biosensors present numerous advantages in food safety analysis owing to their remarkable biocompatibility, cargo-loading capabilities and optical properties. However, the current drawbacks (slow target responsiveness and poor mechanical strength) restricted their further utilization at on-site detection of targets. To address these challenges, a DNA-functionalized cryogel with hierarchical pore structures is constructed to improve the reaction rate and the robustness of hydrogel biosensor. During cryogel preparation, ice crystals serve as templates, shaping interconnected hierarchical microporous structures to enhance mass transfer for faster responses. Meanwhile, in the non-freezing zone, concentrated monomers create a dense cross-linked network, strengthening cryogel matrix strength. Accordingly, a colorimetric biosensor based on DNA cryogel has been developed as a proof of concept for rapid detection of aflatoxin B1 (AFB1) in food samples, and an excellent analytical performance was obtained under the optimized conditions with a low detection limit (1 nM), broad detection range (5-100 nM), satisfactory accuracy and precision (recoveries, 81.2-112.6 %; CV, 2.75-5.53 %). Furthermore, by integrating with a smartphone sensing platform, a portable device was created for rapid on-site measurement of target within 45 min, which provided some insight for hydrogel biosensors design.

Programmable Lanthanide Metal-Organic Framework for Ultra-Efficient Nucleic Acids Extraction and Interaction Analysis

Efficient, mild, and reversible adsorption of nucleic acids onto nanomaterials represents a promising analytical approach for medical diagnosis. However, there is a scarcity of efficient and reversible nucleic acid adsorption nanomaterials. Additionally, the lack of comprehension of the molecular mechanisms governing their interactions poses significant challenges. These issues hinder the rational design and analytical applications of the nanomaterials. Herein, we propose an ultra-efficient nucleic acid affinity nanomaterial based on programmable lanthanide metal-organic frameworks (Ln-MOFs). Through experiments and density functional theory calculations, a rational design guideline for nucleic acid affinity of Ln-MOF was proposed, and a modular and flexible preparation scheme was provided. Then, Er-TPA (terephthalic acid) MOF emerged as the optimal candidate due to its pore size-independent adsorption and desorption capabilities for nucleic acids, enabling ultra-efficient adsorption (about 150% mass ratio) within 1 min. Furthermore, we elucidate the molecular-level mechanisms underlying the Ln-MOF adsorption of single- and double-stranded DNA and G4 structures. The affinity nanomaterial based on Ln-MOF exhibits robust nucleic acid extraction capability (4-fold higher than commercial reagent kits) and enables mild and reversible CRISPR/Cas9 functional regulation. This method holds significant promise for broad application in DNA/RNA liquid biopsy and gene editing, facilitating breakthroughs in analytical chemistry, pharmacy, and medical research.

"On-On-Off" Recyclable Fluorescence Battery for Direct and Selective Detection of Glyphosate and Cu2

Residues of environmental organophosphorus pesticides (OPs) will seriously endanger human health. Most reported OP sensors utilized the restrictions capacity of OPs on the catalytic capacity of acetylcholinesterase (AChE) to acetylthiocholine chloride (ATCh), which suffers from high costs, weak stability, long reaction time, and unrecyclable. Herein, a recyclable strategy was proposed for selective and sensitive detection of glyphosate (Gly). The weak fluorescence of UIO-66-NH2 at 450 nm was enhanced almost 10-fold after reacting with Gly because of the rotation-restricted emission enhancement mechanism. Moreover, inspired by the process of charging and discharging the batteries, we introduced Cu2+ to chelate with Gly. Because of the strong chelation between Cu2+ and Gly, the Gly was removed from UIO-66-NH2, which resulted in the quenching of fluorescence intensity and making UIO-66-NH2 recycle. This method proposed is fast, recyclable, easily conducted, and with a low 0.33 μM LOD in dd H2O based on 3σ/S. The recovery rates of Gly in tap water ranged from 93.07 to 104.35% within a satisfied 7.75% RSD. The Cu2+ LOD is 0.01 mM based on 3σ/S and 94.37-118.34% recovery rates within 6.48% RSD in tap water. We believe that the findings in this work provide a meaningful and promising strategy to detect Gly and Cu2+ in real samples. This sensor first successfully achieves the recycling use of the material in OP fluorescence detection, which greatly decreases the cost of the designed sensor and reduces the possibility of secondary pollution to the environment, broadens a new circulation dimension of fluorescence detection methods in detecting OPs, and has the potential to remove glyphosate from water. It also provides a method to utilize functionalized metal-organic frameworks to establish various sensors.

Morphology Control of Zr-Based Luminescent Metal-Organic Frameworks for Aflatoxin B1 Detection

Metal-organic frameworks (MOFs) have gained significant prominence as sensing materials owing to their unique properties. However, understanding the correlation between the morphology, properties, and sensing performance in these MOF-based sensors remains a challenge, limiting their applications and potential for improvement. In this study, Zr-MOF was chosen as an ideal model to explore the impact of the MOF morphology on the sensing performance, given its remarkable stability and structural variability. Three luminescent MOFs (namely rod-like Zr-LMOF, prismoid-like Zr-LMOF, and ellipsoid-like Zr-LMOF) were synthesized by adjusting the quantities of the benzoic acid and the reaction time. More importantly, the sensing performance of these Zr-LMOFs in response to aflatoxin B1 (AFB1) was thoroughly examined. Notably, the ellipsoid-like Zr-LMOF exhibited significantly higher sensitivity compared to other Zr-LMOFs, attributed to its large specific surface area and pore volume. Additionally, an in-depth investigation into the detection mechanism of AFB1 by Zr-LMOFs was conducted. Building upon these insights, a ratiometric fluorescence sensor was developed by coordinating Eu3+ with ellipsoid-like Zr-LMOF, achieving a remarkably lower detection limit of 2.82 nM for AFB1. This study contributes to an improved comprehension of the relationship between the MOF morphology and the sensing characteristics while presenting an effective approach for AFB1 detection.

A dual-signal aptasensor based on cascade amplification for ultrasensitive detection of aflatoxin B1

Aflatoxin B1 (AFB1) is considered as a serious carcinogenic mycotoxin that was widely detected in grains and foods, and its sensitive analysis is of key importance to avoid the health threats for consumers. In this study, a dual-signal aptasensor based on cascade of entropy-driven strand displacement reaction (ESDR) and linear rolling circle amplification (LRCA) was fabricated for ultrasensitive determination of AFB1. At the sensing system, the complementary strand would be released after the aptamer combined with AFB1, which will bring about the functional domains exposed, triggering the subsequent ESDR. Meanwhile, the two strands that were outputted by ESDR would incur the downstream LRCA reaction to produce a pair of long strands to assist in the generation of fluorescence and absorbance signals. Under the optimized conditions, the proposed aptasensor could achieve excellent sensitivity (limit of detection, 0.427 pg/mL) with satisfactory accuracy (recoveries, 92.8-107.9 %; RSD, 2.4-5.0 %), mainly ascribed to the cascade amplification. Importantly, owing to the flexibility design of nucleic acid primer, this analytical method can be applied in monitoring various hazardous substances according to the specific requirements. Our strategy provides some novel insights at signal amplification for rapid detection of AFB1 and other targets.

Aptamer tuned nanozyme activity of nickel-metal-organic framework for sensitive electrochemical aptasensing of tetracycline residue

It is urgently needed to develop high-performance method for tetracycline (TC) analysis to meet the growing concerns about food safety. Herein, a MOF of Ni2+-2,3,6,7,10,11-hexahydroxytriphenylene (Ni-HHTP) with peroxidase activity has been prepared and coated on a screen printing electrode, followed by non-covalent adsorption of tetracycline aptamer (TC-Apt) through the π-stacking. The spectroscopic and electrochemical assays show that TC-Apt can effectively enhance the nanozyme activity of Ni-HHTP using 3,3',5,5'-tetramethylbenzidine (TMB)/H2O2 as the probe. Upon binding with TC, the configuration of TC-Apt is changed and desorbs from the Ni-HHTP, resulting in the decrease of the nanozyme activity of aptasensor. Based on this principle, the target TC can be analyzed in concentrations ranging from 10 pM to 1.0 μM, with a detection limit of 1.9 pM. The aptsensor is also applicable for TC analysis in fresh Ctenopharyngodon idella meat and milk, which provides a new approach for TC residue monitoring in food.

Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1

Traditional hybridization chain reaction (HCR) as a popular isothermal amplification technique shows some inevitable disadvantages in bioanalysis due to its relatively slow kinetics, which could be markedly promoted when the HCR initiator occurs under tension. Herein, a poly DNA tetrahedrons (pTDNs)-mediated HCR was successfully constructed to make its initiator in a stretched state by long-range electrostatic forces owing to the superimposed electrostatic interactions derived from the synthesized pTDNs, and it was hypothesized that it could remarkably enhance HCR performance, which was testified by theoretical simulations and experimental studies. Consequently, pTDNs-mediated HCR was applied to develop a novel immunoassay for rapid and sensitive detection of aflatoxin B1 as a proof-of-concept, and its signal amplification was attributed to the increased G4 DNAzyme that loaded on the second antibody. Our work paves a promising way using simple DNA frameworks alone to heighten HCR kinetics for reaction speed improvement and signal amplification in bioanalysis.