Translating molecular detections into a simple temperature test using a target-responsive smart thermometer

Functional DNA Regulated CRISPR-Cas12a Sensors for Point-of-Care Diagnostics of Non-Nucleic-Acid Targets

Beyond its extraordinary genome editing ability, the CRISPR-Cas systems have opened a new era of biosensing applications due to its high base resolution and isothermal signal amplification. However, the reported CRISPR-Cas sensors are largely only used for the detection of nucleic acids with limited application for non-nucleic-acid targets. To realize the full potential of the CRISPR-Cas sensors and broaden their applications for detection and quantitation of non-nucleic-acid targets, we herein report CRISPR-Cas12a sensors that are regulated by functional DNA (fDNA) molecules such as aptamers and DNAzymes that are selective for small organic molecule and metal ion detection. The sensors are based on the Cas12a-dependent reporter system consisting of Cas12a, CRISPR RNA (crRNA), and its single-stranded DNA substrate labeled with a fluorophore and quencher at each end (ssDNA-FQ), and fDNA molecules that can lock a DNA activator for Cas12a-crRNA, preventing the ssDNA cleavage function of Cas12a in the absence of the fDNA targets. The presence of fDNA targets can trigger the unlocking of the DNA activator, which can then activate the cleavage of ssDNA-FQ by Cas12a, resulting in an increase of the fluorescent signal detectable by commercially available portable fluorimeters. Using this method, ATP and Na⁺ have been detected quantitatively under ambient temperature (25 °C) using a simple and fast detection workflow (two steps and <15 min), making the fDNA-regulated CRISPR system suitable for field tests or point-of-care diagnostics. Since fDNAs can be obtained to recognize a wide range of targets, the methods demonstrated here can expand this powerful CRISPR-Cas sensor system significantly to many other targets and thus provide a new toolbox to significantly expand the CRISPR-Cas system into many areas of bioanalytical and biomedical applications.

DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions

Metal ions can be beneficial or toxic depending on their identity, oxidation state, and concentration. Therefore, the ability to detect and quantify different types of metal ions using portable sensors or in situ imaging agents is important for better environmental monitoring, in vitro medical diagnostics, and imaging of biological systems. While numerous metal ions in different oxidation states are present in the environment and biological systems, only a limited number of them can be detected effectively using current methods. In this Account, we summarize research results from our group that overcome this limitation by the development of a novel class of activity-based sensors based on metal-dependent DNAzymes, which are DNA molecules with enzymatic activity. First, we have developed an in vitro selection method to obtain DNAzymes from a large DNA library of up to 1015 sequences that can carry out cleavage of an oligonucleotide substrate only in the presence of a specific metal ion with high selectivity. Negative selection steps can further be used to improve the selectivity against potentially competing targets by removing sequences that recognize the competing metal ions. Second, we have developed a patented catalytic beacon method to transform the metal-dependent DNAzyme cleavage reaction into a turn-on fluorescent signal by attaching a fluorophore and quenchers to the DNAzyme complex. Because of the difference in the melting temperatures of DNA hybridization before and after metal-ion-dependent cleavage of the DNAzyme substrate, the fluorophore on the DNA cleavage product can be released from its quenchers to create a turn-on fluorescent signal. Because DNAzymes are easy to conjugate with other signaling moieties, such as gold nanoparticles, lanthanide-doped upconversion nanoparticles, electrochemical agents, and gadolinium complexes, these DNAzymes can also readily be converted into colorimetric sensors, upconversion luminescence sensors, electrochemical sensors, or magnetic resonance contrast agents. In addition to describing recent progress in developing and applying these metal ion sensors for environmental monitoring, point-of-care diagnostics, cellular imaging, and in vivo imaging in zebrafish, we summarize major advantages of this class of activity-based sensors. In addition to advantages common to most activity-based sensors, such as enzymatic turnovers that allow for signal amplification and the use of initial rates instead of absolute signals for quantification to avoid interferences from sample matrices, the DNAzyme-based sensors allow for in vitro selection to expand the method to almost any metal ion under a variety of conditions, negative selection to improve the selectivity against competing targets, and reselection of DNAzymes and combination of active and inactive variants to fine-tune the dynamic range of detection. The use of melting temperature differences to separate target binding from signaling moieties in the catalytic beacon method allows the use of different fluorophores and nanomaterials to extend the versatility and modularity of this sensing platform. Furthermore, sensing and imaging artifacts can be minimized by using an inactive mutant DNAzyme as a negative control, while spatiotemporal control of sensing/imaging can be achieved using optical, photothermal, and endogenous orthogonal caging methods. Finally, current challenges, opportunities, and future perspectives for DNAzymes as activity-based sensors are also discussed.

A miniaturized photoacoustic device with laptop readout for point-of-care testing of blood glucose

Photoacoustic (PA) effect has been widely applied in many fields, e.g., physics, chemistry and biomedicine. Herein, a miniaturized PA device is developed by integrating laser source, photo chopper, PA cell, microphone, and laptop for point-of-care testing in bioassay. With glucose assay as model, a piece of paper strip preloading chitosan, starch-potassium iodide (KI) and glucose oxidase (GOD) as lab-on-paper is employed for loading sample prior to PA detection. In the presence of glucose, the product generated on the paper strip would give rise to a strong PA signal in the PA cell under the irradiation of frequency-modulated laser at 520 nm via laptop readout. With a sample volume of 20 μL, a detection limit of 0.03 mM is obtained for glucose assay, along with a linear range of 0.08-1 mM. The accuracy and practicability of the present PA device is well demonstrated by detecting glucose in whole blood. Differing from the conventional PA instrument, the present PA device is really small in bulk with competitive sensitivity and excellent stability, offering a promising tool for point-of-care testing in bioassay.

Development of an Immunosensor Based on the Exothermic Reaction between H2O and CaO Using a Common Thermometer as Readout

Thermometers, one of the most commonly used instruments at home, are normally adapted to measure temperature directly with high accuracy but rarely adopted to act as readout in the biosensors. It is necessary to find some ways to establish a relationship between the concentration of the target and the temperature change. In this study, a common thermometer was used as readout to develop a convenient immunosensor. The designed immunosensor comprises three components, including target recognition area, water flow system, and exothermic reaction bottle. The capture antibody for the target [carcinoembryonic antigen (CEA) was selected as a model target] was preloaded on the bottom of the recognition area. In the presence of CEA, a sandwich-type structure was formed between the capture antibody, CEA, and biotinylated detection antibody. Then, the streptavidin-functionalized platinum nanoparticles were labeled on the detection antibody due to biotin-avidin interaction. The captured platinum nanoparticles can effectively catalyze the decomposition of H₂O₂ into O₂. The continuous production of gas resulted in pressure increment inside the reaction bottle and further pushed the water flow into the exothermic reaction bottle. Finally, the water reacted with calcium oxide to generate a large amount of heat in the exothermic reaction bottle; thereby the temperature inside the bottle was enhanced and recorded by a common thermometer easily. The temperature enhancement has a linear relationship with the CEA concentration in the range of 7.81-500 pg/mL with a detection limit of 0.6 pg/mL. Furthermore, by taking advantage of simplicity, compatibility, stability, and high sensitivity, our temperature-based immunoassay has been applied to detect CEA in human serum samples with satisfactory results.

Functional DNA Molecules Enable Selective and Stimuli-Responsive Nanoparticles for Biomedical Applications

Nanoparticles (NPs) have enormous potential to improve disease diagnosis and treatment due to their intrinsic electronic, optical, magnetic, mechanical, and physiological properties. To realize their full potential for nanomedicine, NPs must be biocompatible and targetable toward specific biomolecules to ensure selective sensing, imaging, and drug delivery in complex environments such as living cells, tissues, animals, and human bodies. In this Account, we summarize our efforts to impart specific biocompatibility and biorecognition functionality to NPs by developing strategies to integrate inorganic and organic NPs with functional DNA (fDNA), including aptamers, DNAzymes, and aptazymes to create fDNA-NPs. These hybrid NPs take advantage of fDNA's ability to either bind targets or catalyze reactions in the presence of targets selectively and utilize their unique physicochemical properties including small size, low immunogenicity, and ease of synthesis and chemical modification in comparison with other molecules such as antibodies. By integrating inorganic NPs such as gold NPs, quantum dots, and iron oxide nanoparticles with fDNA, we designed stimuli-responsive fDNA-NPs that exhibit target induced assembly and disassembly of NPs, resulting in a variety of colorimetric, fluorescent, and magnetic resonance imaging (MRI)-based sensors for diagnostic of a broad range of analytes. To impart both biocompatibility and selectivity on inorganic NPs for targeted bioimaging, we have demonstrated DNA-mediated surface functionalization, shape-controlled synthesis, and coordinative assembly of such NPs as specific bioprobes. A highlight is provided on the construction of fDNA-based nanoprobes with light-activatable sensing and imaging functions, which provides precise control of recognition properties of fDNA with high spatiotemporal resolution. To explore the potential of organic NPs for biosensing applications, we have developed an enzyme-responsive fDNA-liposome as a universal sensing platform compatible with diverse biological targets as well as different detection methods including fluorescence, MRI, or temperature, making possible point-of-care diagnostics. To expand the application regime of organic NPs, we collaborated with the Zimmerman group to prepare single-chain block copolymer-based NPs and incorporated it with a variety of functions, including monovalent DNA for assembly, tunable surface chemistry for cellular imaging, and coordinative Cu(II) sites for catalyzing intracellular click reactions, demonstrating the potential of using organic NPs to create promising fDNA-NP systems with programmable functionalities. Furthermore, we survey our recent endeavor in integration of cell-specific aptamers with different NPs for targeted drug delivery, showing that introducing stimuli-responsive properties into NPs that target tumor microenvironments would enable safer and more effective therapy for cancers. Finally, current challenges and future perspectives in fDNA-mediated engineering of NPs for biomedical applications are discussed.

Catalase-linked immunosorbent pressure assay for portable quantitative analysis

In this study, catalase-linked immunosorbent pressure assay with a gas-generation reaction was established for quantitative detection of disease biomarker C-reactive protein (CRP) by a portable pressuremeter. The pressure-based detection system recognizes, transduces, and amplifies the target signal to a convenient target-correlated pressure signal reading in a closed chamber. Biotin molecules were modified on the surface of catalase in order to incorporate catalase into the pressure immunoassay by the streptavidin-biotin interaction. To improve the assay performance, the modification ratios of biotin molecules to catalase, and the concentrations of capture and detection antibodies were further optimized. The catalase-linked immunosorbent pressure assay allows portable and quantitation analysis of CRP with a limit of detection of 1.8 nM, which can satisfy the clinical needs for determining the risk of cardiovascular disease. The catalase-linked immunosorbent pressure assay also shows superior specificity and good accuracy. Compared to the previously reported assay catalyzed by PtNP nanozyme, catalase is not easily deactivated during storage and operation. With the merits of enzymatic efficiency, biocompatibility, low non-specific adsorption and facile modification, catalase can be reasonably used for reproducible, stable, simple quantitative detection of disease markers using a portable pressure-based assay in resource-limited settings.

Immunoassay for pathogenic bacteria using platinum nanoparticles and a hand-held hydrogen detector as transducer. Application to the detection of Escherichia coli O157:H7

An innovative approach is presented for portable and sensitive detection of pathogenic bacteria. A novel synthetic hybrid nanocomposite encapsulating platinum nanoparticles, as a highly efficient catalyst, catalyzes the hydrolysis of the ammonia-borane complex to generate hydrogen gas. The nanocomposites are used as a label for immunoassays. A portable hand-held hydrogen detector combined with nanocomposite-induced signal conversion was applied for point-of-care testing of pathogenic bacteria. A hand-held hydrogen detector was used as the transducer. Escherichia coli O157:H7 (E. coli O157: H7), as detection target, formed a sandwich structure with magnetic beads and hybrid nanocomposites. Magnetic beads were used for separation of the sandwich structure, and hybrid nanocomposites as catalysts to catalyze the generation of hydrogen from ammonia-borane. The generated hydrogen was detected by a hydrogen detector using an electrochemical method. E. coli O157:H7 has a detection limit of 10 CFU·mL^-1. The immunosensor made the hand-held hydrogen detector a point-of-care meter to be used outdoors for the detection and quantification of targets beyond hydrogen. Graphical abstract Schematic presentation of one-pot synthetic peptide-Cu₃(PO₄)₂ hybrid nanocomposites embedded PtNPs (PPNs), encapsulating many Pt particles. The PPNs acts as an ideal immunoprobe for hand-held H₂ detector signal readouts, by transforming pathogenic bacteria recognition events into H₂ signals.

Photothermal Soft Nanoballs Developed by Loading Plasmonic Cu2- xSe Nanocrystals into Liposomes for Photothermal Immunoassay of Aflatoxin B1

Photothermal effects (PTEs) have been greatly concerned with the fast development of new photothermal nanomaterials. Herein we propose a photothermal immunoassay (PTIA) by taking mycotoxins (AFB1) as an example based on the PTEs of plasmonic Cu2- xSe nanocrystals (NCs). By loading plasmonic Cu2- xSe NCs into liposomes to form photothermal soft nanoballs (ptSNBs), on which aptamer of AFB1 previously assembled, a sandwich structure of AFB1 could be formed with the aptamer on ptSNBs and capture antibody. The heat released from the ptSNBs under NIR irradiation, owing to the plasmonic photothermal light-to-heat conversion through photon-electron-phonon coupling, makes the temperature of substrate solution increased, and the increased temperature has a linear relationship with the AFB1 content. Owing to the large amounts of plasmonic Cu2- xSe NCs in the ptSNBs, the PTEs get amplified, making AFB1 higher than 1 ng/mL detectable in food even if with a rough homemade immunothermometer. The proposal of PTIA opens a new field of immunoassay including developing photothermal nanostructures, new thermometers, PTIA theory, and so on.

Ultrasensitive detection of prostate specific antigen using a personal glucose meter based on DNA-mediated immunoreaction

We report a point-of-care immunosensor coupled with a rolling circle reaction and a personal glucose meter for sensitive detection of PSA.

A sensitive and low background fluorescent sensing strategy based on g-C3N4-MnO2 sandwich nanocomposite and liposome amplification for ricin detection

Ricin is an extremely potent ribosome-inactivating protein and serves as a likely food biocontaminant or biological weapon. Thus, simple, sensitive and accurate analytical assays capable of detecting ricin are urgently needed to be established. Herein, we present a novel method for ricin B-chain (RTB) detection by using two materials: (a) a highly efficient hybrid probe that was formed by linking a glucose oxidase (GOD)-encapsulated liposome (GOD-L) to magnetic beads (MBs) through hybridization between an aptamer and a blocker and (b) a new low-background g-C3N4-MnO2 sandwich nanocomposite that exhibits fluorescence resonance energy transfer (FRET) between the g-C3N4 nanosheet and MnO2. In the presence of RTB, the strong binding between RTB and the aptamer can release the blocker-linked liposome from the surface of the MBs. After magnetic separation, the decomposed liposome can release GOD to catalyze the oxidation of glucose, generating a certain amount of H2O2. Then, H2O2 can reduce MnO2 of the g-C3N4-MnO2 nanocomposite to Mn2+, which leads to the elimination of FRET. Thus, the fluorescence of the g-C3N4 nanosheet will be turned on. Because of the excellent signal amplification ability of liposome and the characteristic highly sensitive response of the g-C3N4-MnO2 nanocomposite toward H2O2, RTB could be detected sensitively based on the significantly enhanced fluorescent intensity. The linear range of detection was from 0.25 μg mL-1 to 50 μg mL-1 and the limit of detection (LOD) was 190 ng mL-1. Moreover, the proposed assay was successfully applied in the detection of the entire ricin toxin content in a castor seed.

RNA-Cleaving DNAzymes: Old Catalysts with New Tricks for Intracellular and In Vivo Applications

DNAzymes are catalytically active DNA molecules that are normally isolated through in vitro selection methods, among which RNA-cleaving DNAzymes that catalyze the cleavage of a single RNA linkage embedded within a DNA strand are the most studied group of this DNA enzyme family. Recent advances in DNA nanotechnology and engineering have generated many RNA-cleaving DNAzymes with unique recognition and catalytic properties. Over the past decade, numerous RNA-cleaving, DNAzymes-based functional probes have been introduced into many research areas, such as in vitro diagnostics, intracellular imaging, and in vivo therapeutics. This review focus on the fundamental insight into RNA-Cleaving DNAzymes and technical tricks for their intracellular and in vivo applications, highlighting the recent progress in the clinical trial of RNA-Cleaving DNAzymes with selected examples. The challenges and opportunities for the future translation of RNA-cleaving DNAzymes for biomedicine are also discussed.