Construction of Molecular Sensing and Logic Systems Based on Site-Occupying Effect-Modulated MOF-DNA Interaction

Ratiometric Electrochemical DNAzyme Biosensor for Sensitive Detection of Salmonella in Urban Water Source

Accurate, precise detection of Salmonella typhimurium (Salmonella) is crucial for maintaining water safety and preventing outbreaks of foodborne diseases. Bacterial culture, the gold standard for Salmonella detection, is time-consuming and cumbersome. Herein, a novel ratiometric electrochemical biosensing platform was constructed for Salmonella detection based on combining the electrochemical signals of a DNAzyme and metal-organic framework (MOF) and programmed DNA assembly amplification by target-specific cleavage of catalyzed hairpin assembly (CHA). DNAzyme is used to identify and detect S. typhimurium (ST) due to its release of RNase H2 (STH2) which specifically cleaves the rA site in DNAzyme, causing a subsequent reaction. To achieve proportional dual signaling strategy, the electrochemical signaling tag, ferrocene (Fc), was modified onto the DNA sequence H1, and Fe-MOF, an electrochemical indicator with high redox potential separation, was selected as the signaling probe. The prepared ratiometric electrochemical biosensor was analyzed via alternating current voltammetry (ACV). Salmonella detection in urban water source samples using the novel biosensor yielded essentially the same results as commercial Salmonella test strips, with even higher sensitivity, confirming the accuracy and usefulness of this sensing strategy. This study describes a valuable platform for highly specific, ultrasensitive Salmonella detection in aqueous environments.

Ultrasensitive Detection of Extracellular Vesicles Based on Metal-Organic Framework DNA Biobarcodes Triggered G-Quadruplex Coupled with Rolling Circle Amplification Assay

Extracellular vesicles (EVs), as liquid biopsy markers for accurate tumor diagnosis, are considered to hold great promise. However, effectively isolating and sensitively detecting EVs with convenience still face challenges. Herein, we propose a highly sensitive and specific platform for EV detection by integrating a metal-organic framework (MOF)-based DNA biobarcodes strategy with a rolling circle amplification (RCA)/G-quadruplex system. In this study, first, Zr-MOFs act as signal converters by comodification with DNA barcodes and antibodies, converting and amplifying the abundance of EVs into DNA barcodes. Second, the released DNA can trigger RCA, followed by G-quadruplex formation to further amplify the signal. Consequently, this approach significantly enhances the sensitivity for EV biomarker detection, achieving a low limit of detection of 100 EVs mL-1. Furthermore, the strategy offers high sensitivity, specificity, accuracy, and simplicity, highlighting its potential for clinical applications in noninvasive EV detection.

A Phototautomeric 3D Covalent Organic Framework for Ratiometric Fluorescence Humidity Sensing

Photoinduced proton transfer is an essential photochemical process for designing photocatalysts, white light emitters, bioimaging, and fluorescence sensing materials. However, deliberate control of the excited/ground states and meticulous manipulation of the excited state intramolecular proton transfer (ESIPT) pathway constitute a significant challenge in liquids and dense solids. Here, we present the integration of a hydronaphthoquinone fluorophore into a crystalline, porous, phototautomeric dynamic 3D covalent organic framework (COF) to show guest-induced fluorescence turn-on, emission redshift enhancement, and shortened lifetimes for ratiometric fluorescence humidity sensing. Theoretical and spectroscopic studies provide mechanistic insights into the conformational dynamics, charge transfer coupled with local excitation, and ground-state uphill regulation for the multiple tautomers. We illustrate the sensitive, rapid, steady, and self-calibrated ratiometric fluorescence sensing for a wide range of humidity benefiting from the architectural and chemical robustness and crystallinity of such a phototautomeric 3D COF. These findings provide molecular insights into the design of functional porous materials that integrate host-guest mutual recognition and photoelectronic response for multiplex molecular sensing for environmental monitoring and biomedical diagnostics applications.

Highly sensitive fluorescence detection of chloramphenicol based on product catalysis of tetrahedral DNA framework and fluorescent quenching of MIL-101(Fe)

An ultrasensitive fluorescence detection strategy of chloramphenicol (CAP) was developed based on product catalysis of tetrahedral DNA framework (TDF) and fluorescent quenching of MIL-101(Fe). The product was used to catalyze the reaction. As the concentration of catalyst increased, the reaction time was significantly shorted to 21 min which was much shorter than other isothermal amplification technologies. Moreover, the multiple fluorophores of TDF and high efficient quenching ability of MIL-101(Fe) provided better performance with a linear range for CAP detecting from 1.6 pM to 80 pM and the limit of detection (LOD) as low as 0.67 pM. In addition, it also demonstrated good specificity and resistance to interference from other related antibiotics. Importantly, this strategy exhibited satisfactory relative standard deviation and recovery results for practical application, exhibiting a favorable application prospect in CAP analysis.

Surface engineering of metal-organic framework nanoparticles-based miRNA carrier: Boosting RNA stability, intracellular delivery and synergistic therapy

MicroRNAs (miRNAs) are small noncoding RNAs that are critical for the regulation of multiple physiological and pathological processes, thus holding great clinical potential. However, the therapeutic applications of miRNAs are severely limited by their biological instability and poor intracellular delivery. Herein, we describe a dual-layers surface engineering strategy to design an efficient miRNA delivery nanosystem based on metal-organic frameworks (MOFs) incorporating lipid coating. The resulting nanoparticle system was demonstrated to protect miRNA from ribonuclease degradation, enhance cellular uptake and facilitate lysosomal escape. These ensured effective miRNA mediated gene therapy, which synergized with MOF-specific photodynamic therapy and pre-encapsulated doxorubicin (Dox) chemotherapy to provide a multifunctional with therapeutic effectiveness against cencer cells The mechanisms of miRNA binding and Dox loading were revealed, demonstrating the potential of the present MOFs surface-engineered strategy to overcome their inherent pore-size restriction for macromolecular miRNA carrying, enableefficient co-delivery. In vitro studies revealed the potential of our multifunctional system for miRNA delivery and the demonstrated the therapeutic effectiveness against cancer cells, thereby providing a versatile all-in-one MOFs strategy for delivery of nucleic acids and diverse therapeutic molecules in synergistic therapy.

Bio-MOFs Based on Natural Phenolic, Hematoxylin Leverages Biomedical Applications: Enzyme Inhibition, Antioxidant, and Antibacterial Properties

Here, using natural hematoxylin (HT) as linker, metal-organic frameworks (MOFs) from Cu(II), Fe(II), and Fe(III) ions was prepared. The SEM images and DLS analyses revealed HT-based MOFs are Collapse

Key Words

• Antimicrobial/antioxidant MOFs
• Biocompatible MOFs
• Hematoxylin
• Phenolic Metal-Organic Frameworks
• α-glucosidase inhibitors

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MESH Headings

• Metal-Organic Frameworks/chemistry
• Metal-Organic Frameworks/pharmacology
• Metal-Organic Frameworks/chemical synthesis
• Anti-Bacterial Agents/pharmacology
• Anti-Bacterial Agents/chemistry
• Anti-Bacterial Agents/chemical synthesis
• Antioxidants/pharmacology
• Antioxidants/chemistry
• Antioxidants/chemical synthesis
• Microbial Sensitivity Tests
• Humans
• Staphylococcus aureus/drug effects
• Phenols/pharmacology
• Phenols/chemistry
• Escherichia coli/drug effects
• Glycoside Hydrolase Inhibitors/pharmacology
• Glycoside Hydrolase Inhibitors/chemistry
• alpha-Glucosidases/metabolism
• Biological Products/chemistry
• Biological Products/pharmacology
• Cell Survival/drug effects
• Dose-Response Relationship, Drug
• Copper/chemistry
• Copper/pharmacology
• Structure-Activity Relationship
• Molecular Structure

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Grants

• 1059B192201458 BİDEB-2219 Postdoctoral Research Program
• Scientific and Technological Research Council of Turkey

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Affiliation(s)

Mehtap Sahiner Department of Bioengineering, Faculty of Engineering, Canakkale Onsekiz Mart University, Terzioglu Campus, Canakkale, 17100, Turkey
Zhi Tian Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
Sahin Demirci Department of Chemistry, Faculty of Science and Arts, Canakkale Onsekiz Mart University, Terzioglu Campus, 17100, Canakkale, Turkey
Aydin Sunol Department of Chemical and Biomedical Engineering, Materials Science and Engineering Program, University of South Florida, Tampa, FL, 33620, USA
Diane S Allen-Gipson Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA Division of Allergy and Immunology, Department of Internal Medicine, College of Medicine, University of South Florida, Tampa, FL, 33612, USA
Nurettin Sahiner Department of Chemistry, Faculty of Science and Arts, Canakkale Onsekiz Mart University, Terzioglu Campus, 17100, Canakkale, Turkey Department of Ophthalmology, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, MDC21, Tampa, FL, 33612>, USA Department of Bioengineering, U.A. Whittaker College of Engineering, Florida Gulf Coast University, Fort Myers, FL, 33965, USA

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Bioinspired Spatial Compartment of Substrate Molecules and Catalytic Counting Entities in Hierarchical MOFs Initiated for a Dual-Mode Glycoprotein Assay

Living cell systems possess multiple isolated compartments that can spatially confine complex substances and shield them from each other to allow for feedback reactions. In this work, a bioinspired design of metal-organic frameworks (MOFs) with well-defined multishelled matrices was fabricated as a hierarchical host for multiple guest substances including fluorogenic molecules and catalytic nanoparticles (NPs) at the separated locations for the development of a dual-mode glycoprotein assay. The multispatial-compartmental zeolitic imidazolate framework-8 (ZIF-8) constituents were synthesized via epitaxial shell-by-shell overgrowth to guide the integration and spatial organization of host guests. The specific property toward glycoprotein recognition was guaranteed by both the antibody-antigen recognition and covalent bonding through boronate-glycan affinity, and the immediate signal responses were initiated by textural collapse of the ZIF-8 integrity. In addition, the inner micropore and the enclosed space of ZIF-8 can avoid the surpassed contact between molecular substances and catalytic entities, inherently. Furthermore, multishelled ZIF-8 can function as a hierarchical matrix for hosting abundant fluorogenic substrates and a large number of catalytic Pt-shelled Au (AuPt) NPs, which can signify its signal amplification means, while upon the stimuli-responsive framework collapse, the signal generators can be harvested in the on-demand manner. Besides, endowing Pt shells on inert plasmonic NPs can not only mimic peroxidase-like catalytic behavior involved in a fluorogenic catalytic reaction to generate fluorescence signals but also function as scattering signal reporters, which can also signify the dynamic light scattering output signals. Collectively, our proposed method may provide a new thought in combining the well-defined multishelled MOF matrices for dual-signal generators in a stimuli-responsive manner, which can also reinforce the accurate detection capability for the glycoprotein assay.

Detecting telomerase activity at the single-cell level using a CRISPR-Cas12a-based chip

The intimate association between telomerase activity and cancer has driven the exploration of diverse methodologies for its precise detection. However, detecting telomerase activity at the single-cell level remains a significant challenge. Herein, we present a MOF-DNA barcode-amplified CRISPR-Cas12a strategy integrated with a single-cell microfluidic chip for ultrasensitive detection of telomerase activity. DNA-functionalized UiO-66 nanoparticles act as signal transducers, effectively converting telomerase activity into DNA activation strands, which subsequently trigger the trans-cleavage activity of CRISPR-Cas12a. This amplification-based assay could be integrated with a microfluidic chip to enable highly sensitive detection of telomerase activity at the single-cell level, offering promising advancements in early cancer diagnosis.

A fluorescent aptasensor for deoxynivalenol detection based on Nb.BbvCI-assisted targeted-responsive three-way junctions integrated DNA walking machine

Deoxynivalenol (DON) contamination in cereals is a widespread issue with global implications, necessitating the development of efficient detection methods. Here, a fluorescent aptasensor integrating target-responsive DNA three-way junction (TWJ) and DNA walking machine was developed to detect DON. The DON-specific aptamer (Apt) and the walker (Walker DNA) are integrated into TWJs. TWJs initiate the DNA walking machine with the assistance of Nb.BbvCI to provide signal amplification for sensing events. The constructed fluorescent aptasensor selectively recognizes and detects DON. Additionally, the sensing platform explored the quantitative relationship between fluorescence signal changes and DON concentration, achieving a limit of detection (LOD) of 0.009 ng/mL. Ultimately, the method performed well in the detection of cornmeal samples with recoveries ranging from 95.49 % to 100.82 %. The method demonstrates good stability and is expected to be a potential candidate for the accurate detection of DON in grains.

The integration platform for exosome capture and colorimetric detection: Site occupying effect-modulated MOF-aptamer interaction and aptamer-Au NPs-dopamine interaction

Exosomes are extracellular vesicles of 30-200 nm in diameter that inherit molecular markers from their parent cells, including proteins, lipids, nucleic acids, and glycoconjugates. The detection and protein profiling of exosome could provide noninvasive access to disease diagnosis and treatment. In recent years, it has been found that Zr-MOFs can capture exosomes by forming Zr-O-P bonds through the phospholipid bilayer of exosomes. In addition, gold nanoparticles with optical response are used for colorimetric biological analysis, such as proteins, peptides, DNA. In this work, we proposed an aptasensor for exosome capture and sensitive colorimetric detection. The Zr-MOF (PCN-224) is innovatively used to capture exosome by Zr-O-P bond, and sodium tripolyphosphate (STPP) is used to block the non-specific adsorption of DNA aptamers on the surface of PCN-224 by site occupying effect. The aptamer binds to exosome immunity, and the remaining aptamer binds to Au NPs, resulting in an increase in steric hindrance and electrostatic repulsion, which makes the dispersion of Au NPs better and avoids the aggregation of Au NPs induced by dopamine (DA). The ratio of absorbance A650/A520 represents the aggregate degree of Au NPs, which correlates with the concentration of exosomes, and achieves sensitive colorimetric detection of exosomes with a linear range of 1.0 × 105-1.0 × 107 particles/mL. Further studies reveal that our work has excellent selectivity and anti-interference, breast cancer patients and healthy individuals can be distinguished by analyzing the differences in the expression of CD63 protein on exosome. The proposed biosensor integrates the capture and detection of exosomes, the multiple colors of Au NPs changed significantly from red to gray, which was conducive to the naked-eye identification of exosome detection.

Portable smartphone-based RecJf exonuclease-modulated enhanced ratiometric fluorescence bioplatform for rapid visual detection of As3

Arsenite (As3+), a highly carcinogenic heavy metal ion and widely distributed in nature, can have serious health implications even with minimal exposure. Herein, a portable smartphone device-based ratiometric fluorescence platform was established for sensitive detection of As3+. The work relied on the use of metal-organic framework-tagged cDNA (PCN-224-cDNA), with high adsorption capability and fluorescence properties, as an internal reference to quench the fluorescence of FAM-anchored aptamer (FAM-Apt) via hybridization. In the presence of As3+, FAM-Apt specifically bound to As3+ leading to conformational changes, which detached from the PCN-224-cDNA surface. Interestingly, a smartphone-based readout equipment engineered using a 3D-printed hardware device administered the portable detection of As3+. The limit of detection (LOD) for the proposed ratiometric biosensor was calculated to be 0.021 ng/mL, significantly below WHO's safety threshold. Hence, it demonstrates significant potential for large-scale screening of As3+ residues in food and the environment.

Recent Advances on the Metal-Organic Frameworks-Based Biosensing Methods for Cancer Biomarkers Detection

Sensitive and selective detection of cancer biomarkers is crucial for early diagnosis and treatment of cancer, one of the most dangerous diseases in the world. Metal-organic frameworks (MOFs), a class of hybrid porous materials fabricated through the assembly of metal ions/clusters and organic ligands, have attracted increasing attention in the sensing of cancer biomarkers, due to the advantages of adjustable size, high porosity, large surface area and ease of modification. MOFs have been utilized to not only fabricate active sensing interfaces but also arouse a variety of measurable signals. Several representative analytical technologies have been applied in MOF-based biosensing strategies to ensure high detection sensitivity toward cancer biomarkers, such as fluorescence, electrochemistry, electrochemiluminescence, photochemistry and colorimetric methods. In this review, we summarized recent advances on MOFs-based biosensing strategies for the detection of cancer biomarkers in recent three years based on the categories of metal nodes, and aimed to provide valuable references for the development of innovative biosensing platform for the purpose of clinical diagnosis.

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.

A novel dual-signal output strategy for POCT of CEA based on a smartphone electrochemical aptasensing platform

A smartphone-based electrochemical aptasensing platform was developed for the point-of-care testing (POCT) of carcinoembryonic antigen (CEA) based on the ferrocene (Fc) and PdPt@PCN-224 dual-signal labeled strategy. The prepared PdPt@PCN-224 nanocomposite showed a strong catalytic property for the reduction of H2O2. Phosphate group-labeled aptamer could capture PdPt@PCN-224 by Zr-O-P bonds to form PdPt@PCN-224-P-Apt. Therefore, a dual signal labeled probe was formed by the hybridization between Fc-DNA and PdPt@PCN-224-P-Apt. The presence of CEA forced PdPt@PCN-224-P-Apt to leave the electrode surface due to the specific affinity, leading to the decrease of the reduction current of H2O2. At the same time, the Fc-DNA strand changed to hairpin structure, which made Fc closer to the electrode and resulted in the increase of the oxidation current of Fc. Thus, CEA can be accurately determined through both signals: the decrease of H2O2 reduction current and the increase of Fc oxidation current, which could avoid the false positive signal. Under the optimal conditions, the prepared aptasensor exhibited a wide linear range from 1 pg·mL-1 to 100 ng·mL-1 and low detection limits of 0.98 pg·mL-1 and 0.27 pg·mL-1 with Fc and PdPt@PCN-224 as signal labels, respectively. The aptasensor developed in this study has successfully demonstrated its capability to detect CEA in real human serum samples. These findings suggest that the proposed sensing platform will hold great potential for clinical tumor diagnosis and monitoring.

A generalizable sensing platform based on molecularly imprinted polymer-aptamer double recognition and nanoenzyme assisted photoelectrochemical-colorimetric dual-mode detection

Developing highly sensitive and selective methods that incorporate specific recognition elements is crucial for detecting small molecules because of the limited availability of small molecule antibodies and the challenges in obtaining sensitive signals. In this study, a generalizable photoelectrochemical-colorimetric dual-mode sensing platform was constructed based on the synergistic effects of a molecularly imprinted polymer (MIP)-aptamer sandwich structure and nanoenzymes. The MIP functionalized peroxidase-like Fe3O4 (Fe3O4@MIPs) and alkaline phosphatase mimic Zr-MOF labeled aptamer (Zr-mof@Apt) were used as the recognition elements. By selectively accumulating dibutyl phthalate (DBP), a small molecule target model, on Fe3O4@MIPs, the formation of Zr-MOF@Apt-DBP- Fe3O4@MIPs sandwich structure was triggered. Fe3O4@MIPs oxidized TMB to form blue-colored oxTMB. However, upon selective accumulation of DBP, the catalytic activity of Fe3O4@MIPs was inhibited, resulting in a lighter color that was detectable by the colorimetric method. Additionally, Zr-mof@Apt effectively catalyzed the hydrolysis of L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AAPS), generating ascorbic acid (AA) that could neutralize the photogenerated holes to decrease the photocurrent signals for PEC sensing and reduce oxTMB for colorimetric testing. The dual-mode platform showed strong linearity for different concentrations of DBP from 1.0 pM to 10 μM (PEC) and 0.1 nM to 0.5 μM (colorimetry). The detection limits were 0.263 nM (PEC) and 30.1 nM (colorimetry) (S/N = 3), respectively. The integration of dual-signal measurement mode and sandwich recognition strategy provided a sensitive and accurate platform for the detection of small molecules.

Textural Precursor Compositions Harvested for Independent Signal Generators: Scaling Micron-Sized Flower-Like Metal-Organic Frameworks as Amplifying Units for Dual-Mode Glycoprotein Assay

In this work, a micron-sized flower-like metal-organic frameworks (MOFs)-based boronate-affinity sandwich-type immunoassay was fabricated for the dual-mode glycoprotein assay. For proof of concept, the flower-like MOFs were synthesized from transition Cu nodes and tetrakis (4-carboxyphenyl) porphyrin (TCPP) ligands by spontaneous standing assembly. In addition, the specificity toward glycoprotein involved the antigen recognition as well as covalent bonding via the boronate-glycan affinity, and the immediate signal responses were initiated by textural decomposition of the flower-like MOFs. Intriguingly, Cu nodes, of which the valence state is dominant by CuI species, can endow the Fenton-like catalytic reaction of the fluorogenic substrate for generating fluorescence signals. For benefits, TCPP ligands, in which each TCPP molecule has four guest donors, can provide multiple valences for the assembly of cyclodextrin-capped gold nanoparticles via host-guest interaction for colorimetry output. Albeit important, the scaling micrometer patterns for the flower-like MOFs carrying numerous Cu nodes and TCPP ligands can also function as amplifying units, signifying the output signal. The detection limit of the dual-mode glycoprotein assay can reach 10.5 nM for the fluorescence mode and 18.7 nM for the colorimetry mode, respectively. Furthermore, the merits of harvesting different signal generators toward the multimodal readout patterns can allow the mutual verification and make the analytical results more reliable. Collectively, our proposed assay may offer a new idea in combining the inherent textural merits from MOFs for dual signal generators, which can also emphasize accurate detection capability for glycoprotein assay.

Mo5N6 nanosheets for fluorescent quenching and target recognition: Highly selectively sensing of sodium hexametaphosphate

Typical fluorescent biosensors use fluorescently labeled ssDNA for target recognition and nanomaterials for signal transduction. Herein, we propose a reverse sensing strategy that Mo5N6 nanosheets are used for target recognition while fluorescein (FAM)-labeled ssDNA only serves for signal generation. We discover that Mo5N6 nanosheets show high fluorescence quenching ability (>95%) and selective recognition for sodium hexametaphosphate (SHMP). After FAM-labeled ssDNA is adsorbed on Mo5N6 nanosheets, the fluorescence is quenched due to the photoinduced electron transfer (PET) effect between FAM and Mo5N6 nanosheets. SHMP can specifically displace the adsorbed FAM-labeled ssDNA from Mo5N6 nanosheets, resulting in more than 80% fluorescence recovery on addition of 5 μmol L-1 SHMP. This biosensor can sensitively detect SHMP down to 150 nmol L-1 and selectively recognize SHMP over glucose, lactose, common amino acids, Zn2+, Mg2+, Ca2+ and other phosphates (such as Na2HPO4, sodium pyrophosphate, sodium tripolyphosphate). This biosensor also shows great potential for the detection of SHMP in bacon sample. This work not only provides a facile sensitive and selective biosensor for SHMP but also exploits the application of transition metal nitrides in the field of sensing and biosensing.

Principal component analysis-assisted zirconium-based metal-organic frameworks/DNA biosensor for the analysis of various phosphates

Considering the diversity of phosphates and their pivotal roles in physiological processes, detection of various phosphates related to their metabolism is urgent but challenging. Herein, we design a biosensor with zirconium-based MOFs (Zr-MOFs) and fluorophore-modified single-stranded DNA (F-ssDNA) for the analysis of phosphates. Relying on the interaction between Zr clusters and phosphate backbone, F-ssDNA is anchored on the surface of Zr-MOFs, inducing fluorescence resonance energy transfer (FRET) and subsequently quenching the fluorescence of F-ssDNA. Meanwhile, phosphates with different numbers of phosphate groups, molecular structures and coordination environments are able to adjust the FRET between Zr-MOFs and F-ssDNA via a site-occupying effect, recovering the fluorescence of F-ssDNA in distinct cases, which may result in diverse fluorescence signals. Consequently, seventeen phosphates and four phosphate mixtures are discriminated with the assistance of principal component analysis. These results provide new insight into the application of Zr-MOFs and broaden the path for the development of analytical methods for phosphates.

Weak Value Amplification-Based Biochip for Highly Sensitive Detection and Identification of Breast Cancer Exosomes

Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of the parent cell. The highly sensitive detection of exosomes is a crucial prerequisite for the diagnosis of cancer. In this study, we report an exosome detection system based on quantum weak value amplification (WVA). The WVA detection system consists of a reflection detection light path and a Zr-ionized biochip. Zr-ionized biochips effectively capture exosomes through the specific interaction between zirconium dioxide and the phosphate groups on the lipid bilayer of exosomes. Aptamer-modified gold nanoparticles (Au NPs) are then used to specifically recognize proteins on exosomes to enhance the detection signal. The sensitivity and resolution of the detection system are 2944.07 nm/RIU and 1.22 × 10-5 RIU, respectively. The concentration of exosomes can be directly quantified by the WVA system, ranging from 105-107 particles/mL with the detection limit of 3 × 104 particles/mL. The use of Au NPs-EpCAM for the specific enhancement of breast cancer MDA-MB-231 exosomes is demonstrated. The results indicate that the WVA detection system can be a promising candidate for the detection of exosomes as tumor markers.

Colorimetric and fluorescent dual-biosensor based on zirconium and preasodium metal-organic framework (zr/pr MOF) for miRNA-191 detection

MicroRNAs (miRNAs) are associated with certain types of cancer, tumor stages, and responses to treatment, thus efficient methods are required to identify them quickly and accurately. Abnormal expression of microRNA-191 (miR-191) has been linked to particular cancers and several other health conditions, such as diabetes and Alzheimer's disease. In this study, a new dual-biosensor based on the zirconium and preasodium-based metal-organic framework (Zr/Pr MOF) was developed for the rapid, ultrasensitive, and selective detection of miRNA-191. The synthesized Zr/Pr MOF exhibited peroxidase-like activity and fluorescence properties. Our dual method involves monitoring the fluorescence and peroxidase activity of metal-organic frameworks (MOFs) in the presence of miRNAs. The Zr/Pr MOF can catalyze hydrogen peroxide (H2O2) to oxidize the chromogenic substrate 3, 3', 5, 5'-tetramethylbenzidine (TMB) to produce blue oxidized TMB (oxTMB), which exhibits ultraviolet absorption at 660 nm. However, the addition of a label-free miRNA-191 probe caused a significant change in fluorescence intensity and absorbance, indicating the binding of single-stranded miRNAs to the MOF through van der Waals interactions and π-π stacking. The presence of the target miRNA-191 caused the probe to be released from the surface of the MOF owing to hybridization, which increased the peroxidase-like activity of Zr/Pr-MOF. Both response signals showed acceptable linear relationship and low detection limits. Fluorescence and colorimetry have an LOD of 0.69 and 8.62 pM, respectively. This study demonstrates the reliability and sensitivity of miRNA identification in human serum samples.

MOF-mediated dual energy transfer nanoprobe integrated with exonuclease III amplification strategy for highly sensitive detection of DNA

Accurate quantitative detection of DNA is an advanced strategy in various fields (such as disease diagnosis and environmental monitoring), but the classical DNA detection method usually suffers from low sensitivity, expensive thermal cyclers, or strict annealing conditions. Herein, a MOF-ERA platform for ultrasensitive HBV-DNA detection is constructed by integrating metal-organic framework (MOF)-mediated double energy transfer nanoprobe with exonuclease III (Exo III)-assisted target recycling amplification. The proposed double energy transfer containing a donor and two receptors is simply composed of MOFs (UiO-66-NH2, a well-studied MOF) modified with a signal probe formed by the hybridization of carboxyuorescein (FAM)-labeled DNA (FDNA) and black hole quencher (BHQ1)-terminated DNA (QDNA), resulting in low fluorescence signal. After the addition of HBV-DNA, Exo III degradation to FDNA is activated, leading to the liberation of the numerous FAM molecules, followed by the generation of a significant fluorescence signal owing to the negligible binding of MOFs with free FAM molecules. The results certify that the MOF-ERA platform can be successfully used to assay HBV-DNA in the range of 1.0-25.0 nM with a detection limit of 97.2 pM, which is lower than that without BHQ1 or Exo III. The proposed method with the superiorities of low background signal and high selectivity holds promise for early disease diagnosis and clinical biomedicine applications.

DNA-Directed Assembly of Hierarchical MOF-Cellulose Nanofiber Microbioreactors with "Branch-Fruit" Structures

Assembling metal-organic frameworks (MOFs) into ordered multidimensional porous superstructures promises the encapsulation of enzymes for heterogeneous biocatalysts. However, the full potential of this approach has been limited by the poor stability of enzymes and the uncontrolled assembly of MOF nanoparticles onto suitable supports. In this study, a novel and exceptionally robust Ni-imidazole-based MOF was synthesized in water at room temperature, enabling in situ enzyme encapsulation. Based on this MOF platform, we developed a DNA-directed assembly strategy to achieve the uniform placement of MOF nanoparticles onto bacterial cellulose nanofibers, resulting in a distinctive "branch-fruit" structure. The resulting hybrid materials demonstrated remarkable versatility across various catalytic systems, accommodating natural enzymes, nanoenzymes, and multienzyme cascades, thus showcasing enormous potential as universal microbioreactors. Furthermore, the hierarchical composites facilitated rapid diffusion of the bulky substrate while maintaining the enzyme stability, with ∼3.5-fold higher relative activity compared to the traditional enzyme@MOF immobilized in bacterial cellulose nanofibers.

Harmonizing Enzyme-like Cofactors to Boost Nanozyme Catalysis

Engineering isolated metal sites resembling the primary coordination sphere of metallocofactors enables atomically dispersed materials as promising nanozymes. However, most existing nanozymes primarily focus on replicating specific metallocofactors while neglecting other supporting cofactors within active pockets, leading to reduced electron transfer (ET) efficiency and thus inferior catalytic performances. Herein, we report a metal-organic framework UiO-67 nanozyme with atomically dispersed iron sites, which involves multiple tailored enzyme-like nanocofactors that synergistically drive the ET process for enhanced peroxidase-like catalysis. Among them, the linker-coupled atomic iron site plays a critical role in substrate activation, while bare linkers and zirconia nodes facilitate the ET efficiency of intermediates. The synergy of three nanocofactors results in a 4.29-fold enhancement compared with the single effort of isolated metal site-based nanocofactor, holding promise in immunoassay for sensitive detection of chlorpyrifos. This finding opens a new way for designing high-performance nanozymes by harmonizing various nanocofactors at the atomic and molecular scale.

Real-time intelligent detection of ethephon based on a high-throughput ratiometric fluorescent probe

Ethephon (ETH) is a common pesticide, and its overuse has resulted in a variety of health problems for humans. However, the existing ETH detection methods are tedious and time-consuming, and real-time ETH identification remains a significant difficulty. To mitigate this concern, a dual-emission ratiometric fluorescent probe Ru@ZrMOF was rationally synthesized for the detection of ETH. In the presence of ETH, the emission peak at 435 nm gradually increased, while the peak at 600 nm remained constant, accompanied by the fluorescence color change from red, pink, blue-violet to blue. The fluorescence intensity ratio (F435/F600) demonstrated two linear relations with the ETH concentration ranges at 3 - 50 μM and 50 - 500 μM, with a lowest detection limit at 1 μM. This was attributed to the formation of Zr-O-P bonds which attenuated the ligand-metal charge transfer (LMCT) process, resulting in the recovery of blue fluorescence of the ligand 2-Aminoterephthalic acid (2-APDC). To validate the practical application of the developed platform, a YOLO v5x-based WeChat applet "96 Speckles" was developed, and a 96-well plate and smartphone-embedded 3D-printed portable toolbox was designed for the real-time intelligent detection of ETH. This smart platform allows for real-time and efficient ETH analysis in various real samples including apples, pears and tomatoes.

Metal-organic framework integrated hydrogel bioreactor for smart detection of metal ions

Bioreactors with environment responsiveness for smart detection has attracted widespread interest. Bioreactors that operate in liquid have excellent reaction speed and sensitivity, and those that operate at a solid interface have unique portability and stability. However, bioreactors that can simultaneously take advantage of both properties are still limited. Here, we developed a metal-organic framework (MOF) integrated hydrogel bioreactor that can accommodate both solid and liquid properties by using a hydrogel as a quasi-liquid medium. To enhance the stability and intelligence of the hydrogel bioreactor, we have opted for the utilization of europium metal-organic framework (Eu-MOF) as the optical output to withstand long-term storage challenges, and DNA as the highly programmable substance for intelligent target response. On this basis, smart detection of metal ions and biological micro-molecules have been achieved. Notably, this quasi-liquid hydrogel bioreactor has effectively tackled the intrinsic issues of inadequate dispersion stability of Eu-MOF in liquid systems and poor stability of DNA against environmental interference. Moreover, this MOF integrated hydrogel bioreactor has been applied to the construction of a portable hydrogel bioreactor, which enables platform-free and arrayed target detection via a smartphone, providing a new perspective for further promoting the application of quasi-liquid hydrogel bioreactors and intelligent nanobiological sensors.

DNAzyme-driven bipedal DNA walker and catalytic hairpin assembly multistage signal amplified electrochemical biosensor based on porous AuNPs@Zr-MOF for detection of Pb2

As a highly toxic and refractory heavy metal contaminant, Pb2+ seriously endangers human health. The problems of low sensitivity and high cost of signal labeling widely exist in common electrochemical biosensors. Herein, a Pb2+ electrochemical biosensor was constructed using a DNAzyme-driven bipedal DNA Walker and catalytic hairpin assembly as the multistage signal amplification strategy. Compared with Zr-MOF, AuNPs@Zr-MOF has a larger porosity and specific surface area, which can effectively load MB to amplify the current signal. Pb2+ can trigger a dual signal amplification reaction to gradually accumulate the signal of methylene blue/gold nanoparticle @ zirconium-based metal organic frameworks (MB/AuNPs@Zr-MOF) on the electrode. The ingeniously designed sensing strategy realized the analysis of Pb2+ with a wide linear range from 0.05 to 1000 nmol/L and a lower limit of detection (LOD) of 4.65 pmol/L. In addition, the sensor has strong anti-interference ability and can accurately detect Pb2+ in various food samples.

Recombinant streptococcal protein G-modified metal-organic framework ZIF-8 for the highly selective purification of immunoglobulin G from human serum

A novel solid phase extractant His-rSPG@ZIF-8 was prepared by covalently coupling recombinant streptococcal protein G (His-rSPG) with ZIF-8. The His-rSPG@ZIF-8 composite was characterized by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy (Raman), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Due to the specific binding between the immunoglobulin binding region of His-rSPG and the Fc region of immunoglobulin G (IgG), the His-rSPG@ZIF-8 composite demonstrated exceptional selectivity in adsorbing IgG. In Britton-Robinson buffer (BR buffer) with a salt concentration of 500 mmol L-1 (0.04 mol L-1, pH 8.0), the His-rSPG@ZIF-8 composite exhibited a remarkable adsorption efficiency of 99.8 % for 0.05 mg of the composite on 200 μL of IgG solution (100 μg mL-1). The adsorption behavior of the His-rSPG@ZIF-8 composite aligns with the Langmuir adsorption model, and the theoretical maximum adsorption capacity is 1428.6 mg g-1. The adsorbed IgG molecules were successfully eluted using a SDS solution (0.5 %, m/m), resulting in a recovery rate of 91.2 %. Indeed, the His-rSPG@ZIF-8 composite was successfully utilized for the isolation and purification of IgG from human serum samples. The obtained IgG exhibited high purity, as confirmed by SDS-PAGE analysis. Additionally, LC-MS/MS analysis was employed to identify the human serum proteins following the adsorption and elution process using the His-rSPG@ZIF-8 composite material. The results revealed that the recovered solution contained an impressive content of immunoglobulin, accounting for 62.4 % of the total protein content. Furthermore, this process also led to the significant enrichment of low abundance proteins such as Serpin B4 and Cofilin-1. Consequently, the His-rSPG@ZIF-8 composite holds great promise for applications such as IgG purification and immunoassays. At the same time, it expands the application of metal-organic frameworks in the field of proteomics.

Ratiometric fluorescence aptasensor for the detection of patulin in apple juice based on the octahedral UiO-66-TCPP metal-organic framework and aptamer systems

Patulin (PAT) is a potentially harmful mycotoxin to human health and is known to contaminate apple juice. In this work, we developed a ratiometric fluorescence aptasensor using tetrakis(4-carboxyphenyl)porphyrin (H2TCPP)-treated octahedral UiO-66-NH2 (defined as UiO-66-TCPP) to detect PAT. This 2-aminoterephthalic acid and H2TCPP functionalized metal-organic framework showed multiple adsorption effects (hydrogen bonding and π-π stacking) on the aptamer (Apt) and served as a quenching material. When the target PAT bound specifically to the Apt, the fluorescence of the 6-carboxyfluorescein-labeled Apt would recover, and the fluorescence of the H2TCPP ligand remained unchanged. This ratiometric fluorescence property improved the accuracy of PAT detection. Moreover, the introduction of the H2TCPP ligand enhanced the quenching efficiency of UiO-66-NH2, thus improving the sensitivity of the fluorescent aptasensor (UiO-66-TCPP vs. UiO-66-NH2: 0.0162 ng/mL vs. 1.8 ng/mL). In addition, we used UiO-66-TCPP to detect PAT in apple juice samples. This work provides a good paradigm for the construction of ratiometric fluorescence aptasensors with high sensitivity and accuracy.

A smartphone-based electrochemical POCT for CEA based on signal amplification of Zr6MOFs

Carcinoembryonic antigen (CEA) is a biomarker of high expression in cancer cells. Highly sensitive and selective detection of CEA holds significant clinical value in the diagnosis, monitoring and efficacy evaluation of malignant tumors. In this work, a smartphone-based electrochemical point-of-care testing (POCT) platform for the detection of CEA was developed based on a Zr6MOF signal amplification strategy. Ferrocene labeled DNA strands (Fc-DNA) were immobilized on Zr6MOFs to form a Fc-DNA/Zr6MOF signal probe. Double-stranded DNA (dsDNA) formed by complementary DNA (cDNA) and CEA aptamer was assembled on a screen-printed electrode via an Au-S bond. When CEA was added, the aptamer specifically bound with CEA, resulting in the exposure of cDNA. Then, Fc-DNA/Zr6MOF signal probes were introduced on the electrode surface through hybridization between Fc-DNA and cDNA. The detection of CEA was realized by measuring the electrochemical response of Fc. The POCT device was made by connecting a modified electrode with a smartphone through a Sensit Smart USB flash disk. Due to the signal amplification of Zr6MOFs, this POCT platform exhibited high sensitivity, wide linear range, and low detection limit for CEA detection. The developed POCT platform has been used for the detection of CEA in actual human serum samples with satisfactory results.

Reactivity of metal-oxo clusters towards biomolecules: from discrete polyoxometalates to metal-organic frameworks

Metal-oxo clusters hold great potential in several fields such as catalysis, materials science, energy storage, medicine, and biotechnology. These nanoclusters of transition metals with oxygen-based ligands have also shown promising reactivity towards several classes of biomolecules, including proteins, nucleic acids, nucleotides, sugars, and lipids. This reactivity can be leveraged to address some of the most pressing challenges we face today, from fighting various diseases, such as cancer and viral infections, to the development of sustainable and environmentally friendly energy sources. For instance, metal-oxo clusters and related materials have been shown to be effective catalysts for biomass conversion into renewable fuels and platform chemicals. Furthermore, their reactivity towards biomolecules has also attracted interest in the development of inorganic drugs and bioanalytical tools. Additionally, the structural versatility of metal-oxo clusters allows for the efficiency and selectivity of the biomolecular reactions they promote to be readily tuned, thereby providing a pathway towards reaction optimization. The properties of the catalyst can also be improved through incorporation into solid supports or by linking metal-oxo clusters together to form Metal-Organic Frameworks (MOFs), which have been demonstrated to be powerful heterogeneous catalysts. Therefore, this review aims to provide a comprehensive and critical analysis of the state of the art on biomolecular transformations promoted by metal-oxo clusters and their applications, with a particular focus on structure-activity relationships.

A label-free ratiometric fluorescent aptasensor based on a peroxidase-mimetic multifunctional ZrFe-MOF for the determination of tetrodotoxin

A Fe/Zr bimetal-organic framework (ZrFe-MOF) is utilized to establish a ratiometric fluorescent aptasensor for the determination of tetrodotoxin (TTX). The multifunctional ZrFe-MOF possesses inherent fluorescence at 445 nm wavelength, peroxidase-mimetic activity, and specific recognition and adsorption capabilities for aptamers, owing to its organic ligand, and Fe and Zr nodes. The peroxidation of o-phenylenediamine (OPD) substrate generates fluorescent 2,3-diaminophenazine (OPDox) at 555 nm wavelength, thus quenching the inherent fluorescence of ZrFe-MOF because of the fluorescence resonance energy transfer (FRET) effect. TTX aptamers, which are absorbed on the material surface without immobilization or fluorescent labeling, inhibit the peroxidase-mimetic activity of ZrFe-MOF. It causes the decreased OPDox fluorescence at 555 nm wavelength and the inverse restoration of ZrFe-MOF fluorescence at 445 nm wavelength. With TTX, the aptamers specifically bind to TTX, triggering rigid complex release from ZrFe-MOF surface and reactivating its peroxidase-mimetic activity. Consequently, the two fluorescence signals exhibit opposite changes. Employing this ratiometric strategy, the determination of TTX is achieved with a detection limit of 0.027 ng/mL and a linear range of 0.05-500 ng/mL. This aptasensor also successfully determines TTX concentrations in puffer fish and clam samples, demonstrating its promising application for monitoring trace TTX in food safety.

Aptamer-based kinetically controlled DNA reactions coupled with metal-organic framework nanoprobes for sensitive detection of SARS-CoV-2 spike protein

Since the outbreak in 2019, COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the deadliest infectious disease worldwide for people of all ages, from children to older adults. As a main structural protein of SARS-CoV-2, spike protein is reported to play a key role in the entry of the virus into host cells and is considered as an effective antigenic marker for COVID-19 diagnosis. Herein, we develop a new aptamer-based fluorescence method for SARS-CoV-2 spike protein detection based on using kinetically controlled DNA reactions and metal-organic framework nanoprobes. Specifically, the binding of SARS-CoV-2 spike protein to its aptamer is designed to precisely control the kinetics of a DNA displacement reaction, leading to the release of free signaling probes. By reasonable integration of magnetic enrichment and exonuclease-fuelled recycling, the released probes efficiently disrupt the interaction within metal-organic framework nanoprobes, thereby generating a remarkable fluorescent response. Experimental results show that the method not only exhibits a wide linear range and a low detection limit of 7.8 fg mL-1 for SARS-CoV-2 spike protein detection but also demonstrates desirable specificity and utility in complex samples. Therefore, the method may provide a valuable tool for the detection of SARS-CoV-2 spike protein, and has bright prospects in the rapid diagnosis of COVID-19, which is of great significance for guiding rational treatment during a pandemic of respiratory infectious diseases and reducing the occurrence of severe disease in children.

A Versatile G-Quadruplex (G4)-Coated Upconverted Metal-Organic Framework for Hypoxic Tumor Therapy

Given the complexity of the tumor microenvironment, multiple strategies are being explored to tackle hypoxic tumors. The most efficient strategies combine several therapeutic modalities and typically requires the development of multifunctional nanocomposites through sophisticated synthetic procedures. Herein, the G-quadruplex (G4)-forming sequence AS1411-A (d[(G2 T)4 TG(TG2 )4 A]) is used for both its anti-tumor and biocatalytic properties when combined with hemin, increasing the production of O2 ca. two-fold as compared to the parent AS1411 sequence. The AS1411-A/hemin complex (GH) is grafted on the surface and pores of a core-shell upconverted metal-organic framework (UMOF) to generate a UMGH nanoplatform. Compared with UMOF, UMGH exhibits enhanced colloidal stability, increased tumor cell targeting and improved O2 production (8.5-fold) in situ. When irradiated by near-infrared (NIR) light, the UMGH antitumor properties are bolstered by photodynamic therapy (PDT), thanks to its ability to convert O2 into singlet oxygen (1 O2 ). Combined with the antiproliferative activity of AS1411-A, this novel approach lays the foundation for a new type of G4-based nanomedicine.

Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications

Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.

A Direct-Contact Photocurrent-Direction-Switching Biosensing Platform Based on In Situ Formation of CN QDs/TiO2 Nanodiscs and Double-Supported 3D DNA Walking Amplification

Herein, a direct-contact photocurrent-direction-switching photoelectrochemical (PEC) biosensing platform for the ultrasensitive and selective detection of soluble CD146 (sCD146) is reported for the first time via in situ formation of carbon nitride quantum dots (CN QDs)/titanium dioxide (TiO2 ) nanodiscs with the double-supported 3D DNA walking amplification. In this platform, metal organic frameworks (MOFs)-derived porous TiO2 nanodiscs exhibit excellent anodic photocurrent, whereas a single-stranded auxiliary DNA (ssDNA) as biogate is absorbed onto the TiO2 nanodiscs to block active sites. Subsequently, with the help of intermediate DNAs from target sCD146-induced double-supported 3D DNA walking signal amplification, the ssDNA can leave away from the surface of TiO2 nanodiscs due to the specific hybridization with intermediate DNAs. Afterward, the successful direct contact of CN QDs on TiO2 nanodiscs by porosity and electrostatic adsorption, leads to the effective photocurrent-direction switching from anodic to cathodic photocurrent. Based on direct-contact photocurrent-direction-switching CN QDs/TiO2 nanodiscs system and double-supported 3D DNA walking signal amplification, sCD146 is detected sensitively with a wide linear range (10 fg mL-1 to 5 ng mL-1 ) and a low limit of detection (2.1 fg mL-1 ). Also, the environmentally friendly and direct-contact photocurrent-direction-switching PEC biosensor has an application prospect for cancer biomarker detection.

Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids

Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.

DNA-directed assembly of nanomaterials and their biomedical applications

In the past decades, DNA has been widely used in the field of nanostructures due to its unique programmable properties. Besides being used to form its own diverse structures such as the assembly of DNA origami, DNA can also be used for the assembly of nanostructures with other materials. In this review, different strategies for the functionalization of DNA on nanoparticle surfaces are listed, and the roles of DNA in the assembly of nanostructures as well as the influencing factors are discussed. Finally, the biomedical applications of DNA-assembled nanostructures were summarized. This review provided new insight into the application of DNA in nanostructure assembly.

Allosteric probe-triggered isothermal amplification to activate CRISPR/Cas12a for sensitive electrochemiluminescence detection of Salmonella

We report an electrochemiluminescence (ECL) sensor for Salmonella detection based on allosteric probe as a bio-recognition element and CRISPR/Cas12a as a signal amplification strategy. In the presence of Salmonella, the structure switching occurs on allosteric probes, resulting in their hybridization with primers to trigger isothermal amplification. Salmonella is then released to initiate the next reaction cycle accompanying by generating a large amount of dsDNA, which are subsequently recognized by CRISPR-gRNA for activating the trans-cleavage activity of Cas12a. Furthermore, the activated Cas12a can indiscriminately cut the ssDNA which is bound to the electrode, enabling the release of the ECL emitter porphyrinic Zr metal - organic framework (MOF, PCN-224) and exhibiting a decreased ECL signal accordingly. The linear range is 50 CFU·mL^-1-5 × 10⁶ CFU·mL^-1 and the detection limit is calculated to be 37 CFU·mL^-1. This method sensitively detects Salmonella in different types of real samples, indicating it is a promising strategy for Salmonella detection.

A MOF/DNA luminescent sensing platform for detection of potential COVID-19 biomarkers and drugs

COVID-19 has afflicted people's lives worldwide. Interleukin-6 (IL-6) is an important COVID-19 biomarker in human body fluids that can be used as a reference to monitor COVID-19 in real-time and therefore to reduce the risk of virus transmission. On the other hand, oseltamivir is a potential COVID-19 curing drug, but its overuse easily leads to hazardous side effects, calling for its real time monitoring in body fluids. For these purposes, a new yttrium metal-organic framework (Y-MOF) has been synthesized, in which the 5-(4-(imidazole-1-yl)phenyl)isophthalic linker contains a large aromatic backbone capable of strongly interacting with DNA sequences through π-π stacking interactions, which makes it appealing to build a unique sensor based on DNA functionalized MOFs. The MOF/DNA sequence hybrid luminescent sensing platform presents excellent optical properties associated with a high Förster resonance energy transfer (FRET) efficiency. Furthermore, to construct a dual emission sensing platform, a 5'-carboxylfluorescein (FAM) labeled DNA sequence (S2) with a stem-loop structure that can specifically interact with IL-6 has been associated with the Y-MOF. The resulting Y-MOF@S2 exhibits an efficient ratiometric detection of IL-6 in human body fluids with an extremely high K_sv value 4.3 × 10⁸ M^-1 and a low detection limit (LOD) of 70 pM. Finally, the Y-MOF@S2@IL-6 hybrid platform allows the detection of oseltamivir with high sensitivity (K_sv value is as high as 5.6 × 10⁵ M^-1 and LOD is 54 nM), due to the fact that oseltamivir can disconnect the loop stem structure constructed by S2, leading to a strong quenching effect towards Y-MOF@S2@IL-6. The nature of the interactions between oseltamivir and Y-MOF has been elucidated using density functional theory calculations while the sensing mechanism for the dual detection of IL-6 and oseltamivir has been deciphered based on luminescence lifetime tests and confocal laser scanning microscopy.

Photoexcited Ru single-atomic sites for efficient biomimetic redox catalysis

The unsatisfactory catalytic activity of nanozymes owing to their inefficient electron transfer (ET) is the major challenge in biomimetic catalysis-related biomedical applications. Inspired by the photoelectron transfers in natural photoenzymes, we herein report a photonanozyme of single-atom Ru anchored on metal-organic frameworks (UiO-67-Ru) for achieving photoenhanced peroxidase (POD)-like activity. We demonstrate that the atomically dispersed Ru sites can realize high photoelectric conversion efficiency, superior POD-like activity (7.0-fold photoactivity enhancement relative to that of UiO-67), and good catalytic specificity. Both in situ experiments and theoretical calculations reveal that photoelectrons follow the cofactor-mediated ET process of enzymes to promote the production of active intermediates and the release of products, demonstrating more favorable thermodynamics and kinetics in H2O2 reduction. Taking advantage of the unique interaction of the Zr-O-P bond, we establish a UiO-67-Ru-based immunoassay platform for the photoenhanced detection of organophosphorus pesticides.

Chromium hydroxide nanoparticles-based fluorescent aptameric sensing for sensitive patulin detection: The significance of nanocrystal and morphology modulation

The widespread of patulin (PAT) and its potential hazards to human health call for alternative rapid assays to monitor it in food and the environment. Herein, we prepared chromium hydroxide [Cr(OH)₃] nanoparticles via a one-pot chemical precipitation strategy and used them to fabricate a turn-on fluorescent aptasensor employing a morphological effect for sensitive PAT detection. Three Cr(OH)₃ nanoparticle structures were synthesized by changing the solvent, and their structures and physicochemical properties were investigated. Then, we evaluated the effects of morphological structures on the fluorescence quenching-recovery capability of Cr(OH)₃ nanoparticles before and after incubation with PAT. We found that the Cr(OH)₃-3 nanoparticles efficiently absorbed the fluorescence dye 6-carboxyfluorescein labeled aptamer (FAM-Apt) and quenched the fluorophore through photoinduced electron transfer. Under optimal experimental conditions, the turn-on fluorescent aptasensor for PAT determination displayed two linear ranges (0.01-10 ng/mL and 1-200 ng/mL) with a low detection limit of 7.3 pg/mL. Moreover, the proposed aptasensor had no cross-reactivity with interferents that usually coexist with PAT and can be used to detect PAT in apple juices accurately. The results of the as-fabricated method were not significantly different from the high-performance liquid chromatography. Hence, we demonstrated that different Cr(OH)₃ nanoparticles can be prepared by changing reaction conditions, and provided a novel strategy to improve the detection performance of fluorescent aptasensor by changing the morphological structure and crystalline properties of nano-quenchers.

A novel CRISPR/Cas14a-based electrochemical biosensor for ultrasensitive detection of Burkholderia pseudomallei with PtPd@PCN-224 nanoenzymes for signal amplification

In this work, PtPd nanoparticles functionalized porphyrin metal-organic framework nanoenzymes (PtPd@PCN-224 nanoenzymes) are exploited as signal amplification tags to fabricate a rapid and ultrasensitive sensitive CRISPR/Cas14a-based electrochemical biosensor for Burkholderia pseudomallei (B. pseudomallei) specific DNA sequences detection. The prepared PtPd@PCN-224 nanoenzymes not only catalyze the reduction peak current of H₂O₂ to obtain a strong electrochemical signal output, but also provide massive active sites for the assembly of nucleic acids by Zr-O-P bonds. Besides, the designed target-activated CRISPR/Cas14a is able to recognize the target DNA sequences and further trigger the trans-cleavage of ssDNA for signal amplification. Benefiting from the target-activated CRISPR/Cas14a and PtPd@PCN-224 nanoenzymes, the developed electrochemical biosensor for B. pseudomallei DNA detection exhibits high sensitivity with detection of limit down to 12.8 aM and excellent specificity for distinguishing non-targeted bacteria. Moreover, the CRISPR/Cas14a-based electrochemical detection platform can also apply for other pathogenic bacteria diagnostic by well-designing sgRNA for target sequence recognition, possessing high flexibility and versatility in clinical diagnosis.

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

Adsorption of DNA probes onto nanomaterials is a promising strategy for bioassay establishment typically using fluorescence or catalytic activities to generate signals. Albeit important, there is currently a lack of systematic understanding of the sensing behaviors building on nanomaterial-DNA interactions, which greatly limits the rational method design and their subsequent applications. Herein, the issue was investigated by employing multifunctional metal-organic frameworks (MOFs) (FeTCPP⊂UiO-66) as a model that was synthesized via integrating heme-like ligand FeTCPP into commonly used MOFs (UiO-66). Our results demonstrated that the fluorescently labeled DNA adsorbed onto FeTCPP⊂UiO-66 was quenched through photoinduced electron transfer, fluorescence resonance energy transfer, and the internal filtration effect. Among different DNA structures, double-stranded DNA and hybridization chain reaction products largely retained their fluorescence due to desorption and conformational variation, respectively. In addition, ssDNA could maximally inhibit the peroxidase activity of FeTCPP⊂UiO-66, and this inhibition was strongly dependent on the strand length but independent of base composition. On the basis of these discoveries, a fluorescence/colorimetric dual-modal detection was designed against aflatoxin B1 with satisfactory performances obtained to further verify our results. This study provided some new insights into the sensing behaviors based on MOF-DNA interactions, indicating promising applications for rational bioassay design and its performance improvement.

Ultrarapid Microwave-Assisted Synthesis of Fluorescent Silver Coordination Polymer Nanoparticles and Its Application in Detecting Alkaline Phosphatase Activity

Fluorescent silver coordination polymer nanoparticles (Ag-TPA CPNs) were synthesized using a combination of terephthalic acid (TPA) and silver nitrate via an ultrarapid microwave-assisted strategy within 15 min. The Ag-TPA CPNs displayed a high fluorescent quantum yield (QY = 20.19%) and large Stokes shift (~200 nm), with two emission peaks at 490 nm and 520 nm under an excitation wavelength of 320 nm. A fluorescent "turn-off" method using fluorescent Ag-TPA CPNs was applied to detect the alkaline phosphatase (ALP) activity on the basis of the ALP-catalyzed hydrolysis of ascorbic acid 2-phosphate (AA2P) to ascorbic acid (AA), and the AA product triggered the reduction of Ag⁺ ions into silver nanoparticles. The fluorescent lifetime of Ag-TPA CPNs decreased from 3.93 ms to 3.80 ms after the addition of ALP, which suggests that this fluorescent "turn-off" detection of ALP activity is a dynamic quenching process. The fluorescent intensity had a linear relationship with the concentration of ALP in the range of 0.2-12 mU/mL (r = 0.991) and with a limit of detection (LOD) of 0.07 mU/mL. It showed high selectivity in ALP detection towards metal ions and amino acids, as well as other enzymes such as horseradish peroxidase, glucose oxidase, tyrosinase, trypsin, lysozyme, and superoxides. When it was applied for the fluorescent "turn-off" detection of ALP activity in serum samples, mean recovery levels ranging from 99.5% to 101.2% were obtained, with relative standard deviations (RSDs) lower than 4% accuracy. Therefore, it is an efficient and accurate tool for analyzing ALP levels in biosamples.

Dual-Modal Apoptosis Assay Enabling Dynamic Visualization of ATP and Reactive Oxygen Species in Living Cells

ATP and reactive oxygen species (ROS) are considered significant indicators of cell apoptosis. However, visualizing the interplay between apoptosis-related ATP and ROS is challenging. Herein, we developed a metal-organic framework (MOF)-based nanoprobe for an apoptosis assay using duplex imaging of cellular ATP and ROS. The nanoprobe was fabricated through controlled encapsulation of gold nanorods with a thin zirconium-based MOF layer, followed by modification of the ROS-responsive molecules 2-mercaptohydroquinone and 6-carboxyfluorescein-labeled ATP aptamer. The nanoprobe enables ATP and ROS visualization via fluorescence and surface-enhanced Raman spectroscopy, respectively, avoiding the mutual interference that often occurs in single-mode methods. Moreover, the dual-modal assay effectively showed dynamic imaging of ATP and ROS in cancer cells treated with various drugs, revealing their apoptosis-related pathways and interactions that differ from those under normal conditions. This study provides a method for studying the relationship between energy metabolism and redox homeostasis in cell apoptosis processes.

A Versatile Design-Enabled Analysis of Circulating Extracellular Vesicles in Disease Diagnosis

Circulating extracellular vesicles (EVs) are considered as potential biomarkers for treatment and diagnosis of many diseases. Most of the existing methods for the EV analysis only have a single function and thus reveal limited information carried by EVs. Herein, a phosphatidylserine-targeting peptide-facilitated design that enables the versatile analysis of circulating EVs for varying requirement is proposed. In the design, DNA probes are inserted into the EV membrane through hydrophobic interactions, and accelerate the removal of protective shielding from DNA-gated metal-organic framework, thereby releasing a large number of methylene blue molecules to amplify the electrochemical signal. Electrochemical results demonstrate equally high sensitivities toward the quantification of EVs derived from different cell sources using an indiscriminative DNA probe. More importantly, the probe can be endowed with extended function for more accurate classification of cell-specific features through the identification of specific EV biomarkers, and demonstrates the potential use in the diagnosis of cardiovascular in a principle-of-proof study for clinical application. Therefore, the method provides a versatile design for the identification of EV features, and may address the needs of clinical diagnosis in the future.

Metal-Organic Framework-DNA Bio-Barcodes Amplified CRISPR/Cas12a Assay for Ultrasensitive Detection of Protein Biomarkers

CRISPR/Cas12a shows excellent potential in disease diagnostics. However, insensitive signal conversion strategies hindered its application in detecting protein biomarkers. Here, we report a metal-organic framework (MOF)-based DNA bio-barcode integrated with the CRISPR/Cas12a system for ultrasensitive detection of protein biomarkers. In this work, zirconium-based MOF nanoparticles were comodified with antibodies and bio-barcode phosphorylated DNA as an efficient signal converter, which not only recognized the protein biomarker to form the sandwich complex but also released the bio-barcode DNA activators after MOF dissociation to activate the trans-cleavage activity of Cas12a. Due to the obvious advantages, including numerous loaded oligonucleotides, a convenient release process, and the nontoxic release reagent, this MOF-DNA bio-barcode strategy could amplify the CRISPR/Cas12a system to achieve simple and highly sensitive detection of tumor protein biomarkers with detection limits of 0.03 pg/mL (PSA) and 0.1 pg/mL (CEA), respectively. Furthermore, this platform could detect PSA directly in clinical serum samples, offering a powerful tool for early disease diagnosis.

Nonsteroidal anti-inflammatory drug monitoring in serum: a Tb-MOF-based luminescent mixed matrix membrane detector with high sensitivity and reliability

The identification of drugs or biomolecules for public health monitoring requires facile analytical technologies with excellent sensitivity, portability and reliability. In the past decades, different sensing materials have inspired the development of various bioanalytical strategies. However, sensing platforms based on powder materials are not suitable for medical diagnosis, which limits further exploration and application of biosensors. Herein, a point-of-care testing (POCT) membrane was designed from an energy competition mechanism and achieved the detection of the nonsteroidal antiphlogistic diclofenac, and exhibited remarkable testing efficacy at the ppb level. The mixed matrix membrane (MMM) sensor consists of electrospun polyacrylonitrile nanofibers and luminescent Tb-MOFs and possess the advantages of high stability, outstanding anti-interference ability, efficient detection (LOD = 98.5 ppb) and easy visual recognition. Furthermore, this MMM sensor exhibits excellent recyclability in serum, which is beneficial for developing a portable and convenient device to distinguish diclofenac in practical sensing applications. Meanwhile, the feasibility and mechanism of this recyclable sensor were verified by theory and experiments, indicating that it is a promising device for diclofenac detection in biological environments to evaluate the toxic effect caused by the accumulation of nonsteroidal drugs.

Metal Organic Framework-Based Bio-Barcode CRISPR/Cas12a Assay for Ultrasensitive Detection of MicroRNAs

CRISPR/Cas12a has shown great potential in molecular diagnostics, but its application in sensing of microRNAs (miRNAs) was limited by sensitivity and complexity. Here, we have sensitively and conveniently detected microRNAs by reasonably integrating metal-organic frameworks (MOFs) based biobarcodes with CRISPR/Cas12a assay (designated as MBCA). In this work, DNA-functionalized Zr-MOFs were designed as the converter to convert and amplify each miRNA target into activators that can initiate the trans-cleavage activity of CRISPR/Cas12a to further amplify the signal. Such integration provides a universal strategy for sensitive detection of miRNAs. By tuning the complementary sequences modified on nanoprobes, this assay achieves subattomolar sensitivity for different miRNAs and was selective to single-based mismatches. With the proposed method, the expression of miR-21 in different cancer cells can be assessed, and breast cancer patients and healthy individuals can be differentiated by analyzing the target miRNAs extracted from serum samples, holding great potential in clinical diagnosis.

CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin

Overexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression of ssDNA and the related antigens in the population and brisk activity in gene-editing technologies in the treatment/detection may lead to the presence of pCRISPR in the blood. Therefore, the detection and evaluation of their trace concentrations are of critical importance. CaZnO-based nanoghosts (NGs) were synthesized with the assistance of a high-gravity technique at a 1,800 MHz field, capitalizing on the use of Rosmarinus officinalis leaf extract as the templating agent. A complete chemical, physical and biological investigation revealed that the synthesized NGs presented similar morphological features to the mesenchymal stem cells (MSCs), resulting in excellent biocompatibility, interaction with ssDNA- and/or pCRISPR-surface, through various chemical and physical mechanisms. This comprise the unprecedented synthesis of a fully inorganic nanostructure with behavior that is similar to MSCs. Furthermore, the endowed exceptional ability of inorganic NGs for detective sensing/folding of ssDNA and pCRISPR and recombinant SARS-CoV-2 spike antigen (RSCSA), along with in-situ hydrogen peroxide detection on the HEK-293 and HeLa cell lines, was discerned. On average, they displayed a high drug loading capacity of 55%, and the acceptable internalizations inside the HT-29 cell lines affirmed the anticipated MSCs-like behavior of these inorganic-NGs.