Sensitive Detection of RNase A Activity and Collaborative Drug Screening Based on rGO and Fluorescence Probe

A highly sensitive nanopore platform for measuring RNase A activity

Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.

Advanced Theranostic Strategies for Viral Hepatitis Using Carbon Nanostructures

There are several treatment protocols for acute viral hepatitis, and it is critical to recognize acute hepatitis in its earliest stages. Public health measures to control these infections also rely on rapid and accurate diagnosis. The diagnosis of viral hepatitis remains expensive, and there is no adequate public health infrastructure, while the virus is not well-controlled. New methods for screening and detecting viral hepatitis through nanotechnology are being developed. Nanotechnology significantly reduces the cost of screening. In this review, the potential of three-dimensional-nanostructured carbon substances as promising materials due to fewer side effects, and the contribution of these particles to effective tissue transfer in the treatment and diagnosis of hepatitis due to the importance of rapid diagnosis for successful treatment, were extensively investigated. In recent years, three-dimensional carbon nanomaterials such as graphene oxide and nanotubes with special chemical, electrical, and optical properties have been used for the diagnosis and treatment of hepatitis due to their high potential. We expect that the future position of nanoparticles in the rapid diagnosis and treatment of viral hepatitis can be better determined.

RNA Hydrolysis at Mineral-Water Interfaces

As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe₂O₃) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.

Optical Biosensor Based on Graphene and Its Derivatives for Detecting Biomolecules

Graphene and its derivatives show great potential for biosensing due to their extraordinary optical, electrical and physical properties. In particular, graphene and its derivatives have excellent optical properties such as broadband and tunable absorption, fluorescence bursts, and strong polarization-related effects. Optical biosensors based on graphene and its derivatives make nondestructive detection of biomolecules possible. The focus of this paper is to review the preparation of graphene and its derivatives, as well as recent advances in optical biosensors based on graphene and its derivatives. The working principle of face plasmon resonance (SPR), surface-enhanced Raman spectroscopy (SERS), fluorescence resonance energy transfer (FRET) and colorimetric sensors are summarized, and the advantages and disadvantages of graphene and its derivatives applicable to various types of sensors are analyzed, and the methods of surface functionalization of graphene and its derivatives are introduced; these optical biosensors can be used for the detection of a range of biomolecules such as single cells, cellular secretions, proteins, nucleic acids, and antigen-antibodies; these new high-performance optical sensors are capable of detecting changes in surface structure and biomolecular interactions with the advantages of ultra-fast detection, high sensitivity, label-free, specific recognition, and the ability to respond in real-time. Problems in the current stage of application are discussed, as well as future prospects for graphene and its biosensors. Achieving the applicability, reusability and low cost of novel optical biosensors for a variety of complex environments and achieving scale-up production, which still faces serious challenges.

Single Molecule-Level Detection via Liposome-Based Signal Amplification Mass Spectrometry Counting Assay

Because of the low atomization and/or ionization efficiencies of many biological macromolecules, the application of mass spectrometry to the direct quantitative detection of low-abundance proteins and nucleic acids remains a significant challenge. Herein, we report mass spectrum tags (MS-tags) based upon gold nanoparticle (AuNP)-templated phosphatidylcholine phospholipid (DSPC) liposomes, which exhibit high and reliable signals via electrospray ionization (ESI). Using these MS-tags, we constructed a liposome signal amplification-based mass spectrometric (LSAMS) "digital" counting assay to enable ultrasensitive detection of target nucleic acids. The LSAMS system consists of liposomes modified with a gold nanoparticle core and surface-anchored photocleavable DNA. In the presence of target nucleic acids, the modified liposome and a magnetic bead simultaneously hybridize with the target nucleic acid. After magnetic separation and photolysis, the MS-tag is released and can be analyzed by ESI-MS. At very low target concentrations, one liposome particle corresponds to one target molecule; thus, the concentration of the target can be estimated by counting the number of liposomes. With this assay, hepatitis C (HCV) virus RNA was successfully analyzed in clinical samples.

A rGO-DNAzyme assisted fluorescence method for sensitive RNase A activity assay and natural compound screening

As a key regulator of human physiology and metabolic processes, ribonuclease (RNase) A can be used as an important biomarker for predicting human disease occurrence. Hence, establishing sensitive methods for tracking RNase A activity in vitro and in living cells is of great importance. Herein, we present a convenient fluorescence method assisted by reduced graphene oxide (rGO) and DNAzyme mediated fluorescence signal release for RNase A assay. The fluorescence change of the new method showed a positive linear relation with RNase A concentration in the range from 0.5 pg μL^-1 to 1 ng μL^-1 with a detection limit of 0.089 pg μL^-1. By using this method to screen the effector of RNase A from natural compounds, the natural compound of B6 was found to stimulate RNase A activity in vitro and in vivo, the result of which was supported by the real-time imaging of RNase A in living cells. In summary, this fluorescence method with high sensitivity and specificity provides an alternative for RNase A activity assay and effector screening.

Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery

Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.

Tailored Biosensors for Drug Screening, Efficacy Assessment, and Toxicity Evaluation

Biosensors have been flourishing in the field of drug discovery with pronounced developments in the past few years. They facilitate the screening and discovery of innovative drugs. However, there is still a lack of critical reviews that compare the merits and shortcomings of these biosensors from a pharmaceutical point of view. This contribution presents a critical and up-to-date overview on the recent progress of tailored biosensors, including surface plasmon resonance, fluorescent, photoelectrochemical, and electrochemical systems with emphasis on their mechanisms and applications in drug screening, efficacy assessment, and toxicity evaluation. Multiple functional nanomaterials have also been incorporated into the biosensors. Representative examples of each type of biosensors are discussed in terms of design strategy, response mechanism, and potential applications. In the end, we also compare the results and summarize the major insights gained from the works, demonstrating the challenges and prospects of biosensors-assisted drug discovery.

Functionalized Graphene Platforms for Anticancer Drug Delivery

Two-dimensional nanomaterials are emerging as promising candidates for a wide range of biomedical applications including tissue engineering, biosensing, pathogen incapacitation, wound healing, and gene and drug delivery. Graphene, due to its high surface area, photothermal property, high loading capacity, and efficient cellular uptake, is at the forefront of these materials and plays a key role in this multidisciplinary research field. Poor water dispersibility and low functionality of graphene, however, hamper its hybridization into new nanostructures for future nanomedicine. Functionalization of graphene, either by covalent or non-covalent methods, is the most useful strategy to improve its dispersion in water and functionality as well as processability into new materials and devices. In this review, recent advances in functionalization of graphene derivatives by different (macro)molecules for future biomedical applications are reported and explained. In particular, hydrophilic functionalization of graphene and graphene oxide (GO) to improve their water dispersibility and physicochemical properties is discussed. We have focused on the anticancer drug delivery of polyfunctional graphene sheets.

Ruthenium(II) Complex-Based G-quadruplex DNA Selective Luminescent 'Light-up' Probe for RNase H Activity Detection

A bis-heteroleptic ruthenium(II) complex, 1[PF₆ ]₂ of benzothiazole amide substituted 2,2'-bipyridine ligand (bmbbipy) has been synthesized for the selective detection of G-quadruplex (GQ) DNA and luminescence-assay-based RNase H activity monitoring. Compound 1[PF₆ ]₂ exhibited aggregation-caused quenching (ACQ) in water. Aggregate formation was supported by DLS, UV-vis, and ¹ H NMR spectroscopy results, and the morphology of aggregated particles was witnessed by SEM and TEM. 1[PF₆ ]₂ acted as an efficient GQ DNA-selective luminescent light-up probe over single-stranded and double-stranded DNA. The competency of 1[PF₆ ]₂ for selective GQ structure detection was established by PL and CD spectroscopy. For 1[PF₆ ]₂ , the PL light-up is exclusively due to the rigidification of the benzothiazole amide side arm in the presence of GQ-DNA. The interaction between the probe and GQ-DNA was analyzed by molecular docking analysis. The GQ structure detection capability of 1[PF₆ ]₂ was further applied in the luminescent 'off-on' RNase H activity detection. The assay utilized an RNA:DNA hybrid, obtained from 22AG2-RNA and 22AG2-DNA sequences. RNase H solely hydrolyzed the RNA of the RNA:DNA duplex and released G-rich 22AG2-DNA, which was detected via the PL enhancement of 1[PF₆ ]₂ . The selectivity of RNase H activity detection over various other restriction enzymes was also demonstrated.

Two-Dimensional Material-Based Biosensors for Virus Detection

Viral infections are one of the major causes of mortality and economic losses worldwide. Consequently, efficient virus detection methods are crucial to determine the infection prevalence. However, most detection methods face challenges related to false-negative or false-positive results, long response times, high costs, and/or the need for specialized equipment and staff. Such issues can be overcome by access to low-cost and fast response point-of-care detection systems, and two-dimensional materials (2DMs) can play a critical role in this regard. Indeed, the unique and tunable physicochemical properties of 2DMs provide many advantages for developing biosensors for viral infections with high sensitivity and selectivity. Fast, accurate, and reliable detection, even at early infection stages by the virus, can be potentially enabled by highly accessible surface interactions between the 2DMs and the analytes. High selectivity can be obtained by functionalization of the 2DMs with antibodies, nucleic acids, proteins, peptides, or aptamers, allowing for specific binding to a particular virus, viral fingerprints, or proteins released by the host organism. Multiplexed detection and discrimination between different virus strains are also feasible. In this Review, we present a comprehensive overview of the major advances of 2DM-based biosensors for the detection of viruses. We describe the main factors governing the efficient interactions between viruses and 2DMs, making them ideal candidates for the detection of viral infections. We also critically detail their advantages and drawbacks, providing insights for the development of future biosensors for virus detection. Lastly, we provide suggestions to stimulate research in the fast expanding field of 2DMs that could help in designing advanced systems for preventing virus-related pandemics.

RNase A activity analysis and imaging using label-free DNA-templated silver nanoclusters

A label-free, ultra-sensitive and turn-on method for detecting RNase A has been developed using enhanced DNA-templated silver nanoclusters (DNA-AgNCs) as the fluorescence probe. In this system, an RNA strand, which can perfectly hybridize with DNA template of nanocluster synthesis, was applied to lock the fluorescent signal of DNA-AgNCs by forming an RNA/DNA duplex. Meanwhile, the hybridized RNA/DNA duplex was used as the substrate of RNase A. The fluorescence signal of AgNCs was restored due to the degradation of RNA by RNase A. From the fluorescence signal change of this system caused by RNase A, it was found that the fluorescence signal showed a positive linear relation with RNase A concentration in the range from 0.2 pg/μL to 10 pg/μL with a detection limit of 0.098 pg/μL. Except for potential inhibitor screening and the kinetic study of this enzyme, this strategy was further used for monitoring dynamic change of RNase A in living cells successfully. In summary, the simple and sensitive method for RNase A assay can be hopefully used for drug screening in vitro and in vivo.

Sensitive RNase A detection and intracellular imaging using a natural compound-assisted tetrahedral DNA nanoprobe

We report an intracellular imaging and assay nanoplatform for RNase A using a DNA tetrahedron-based fluorescent probe as a substrate.

Monitoring VEGF mRNA and imaging in living cells in vitro using rGO-based dual fluorescent signal amplification platform

VEGF mRNA, as an important biomarker for disease diagnosis and therapeutics, has received extensive attention. However, how to monitor its mRNA levels rapidly and sensitively remains a challenge. Herein, a strategy was designed for facile and efficient detection of VEGF mRNA and imaging in living cells using a collaborative system of a fluorophore-labeled single-stranded probe (P), reduced graphene oxide (rGO) and double-specific nuclease (DSN). The combination of strong fluorophore-quenching ability of rGO with DSN assisted signal amplification contributes to the superior sensitivity of the assay for VEGF mRNA, which was reflected by the lower limit of mRNA detection of 100 fM obtained using dual signal amplification manner. Furthermore, the developed sensor was directly used for intracellular mRNA imaging in vitro without the assistance of transfection reagent. In summary, the simple, ultra-sensitive and cost-effective mRNA assay system, which provided a general analysis strategy for other mRNAs assay by replacing the sequence of the probe, is hopeful for applying on the clinical diagnosis and therapy.

Homogeneous Electrochemiluminescence Biosensor for the Detection of RNase A Activity and Its Inhibitor

Ribonuclease A (RNase A) is increasingly considered as a biomarker for tumor diagnosis, and it is of great significance to develop an ultrasensitive, cost-effective assay for RNase A detection. Electrochemiluminescence (ECL) technology has distinctive advantages in the development of biosensors for diverse targets. However, most of the ECL biosensors require the complex process of electrode modification, which is laborious and time consuming. In this work, an immobilization-free homogeneous ECL assay was developed for the highly sensitive detection of RNase A activity for the first time. On the basis of the fact that RNase A can specifically hydrolyze RNA at the site of ribonucleotide uracil (rU), a rU-containing chimeric DNA probe is designed and labeled with Ru(bpy)₃²⁺ (act as ECL indicator). The chimeric DNA probe hardly diffuses to the surface of negatively charged indium tin oxide (ITO) electrode due to the strong electrostatic repulsion between the negatively charged DNA and ITO electrode, resulting in a weak ECL signal detected. When the RNase A is present, the chimeric DNA probe is hydrolyzed into small fragments, which contains little negative charge and can diffuse easily to the ITO electrode surface due to the decreased electrostatic repulsion. In this case, an enhanced ECL signal can be detected. Under the optimal conditions, there is a linear relationship between the ECL signal and the concentration of RNase A in the range of 0.001-0.10 ng/mL, and the detection limit is 0.2 pg/mL. In addition, the proposed ECL sensing system is also applied to detect the RNase A inhibitor, taking As³⁺ as an example. The proposed homogeneous ECL sensing system provides a new approach for the highly sensitive and convenient detection of RNase A as well as other ribonucleases only by redesigning a responding chimeric DNA probe.

Recent advances in graphene-based nanomaterials: properties, toxicity and applications in chemistry, biology and medicine

This review (with 239 refs.) summarizes the progress that has been made in applications of graphene-based nanomaterials (such as plain graphene, graphene oxides, doped graphene oxides, graphene quantums dots) in biosensing, imaging, drug delivery and diagnosis. Following an introduction into the field, a first large section covers the toxicity of graphene and its derivatives (with subsections on bacterial toxicity and tissue toxicity). The use of graphene-based nanomaterials in sensors is reviewed next, with subsections on electrochemical, FET-based, fluorescent, chemiluminescent and colorimetric sensors and probes. The large field of imaging is treated next, with subchapters on optical, PET-based, and magnetic resonance based methods. A concluding section summarizes the current status, addresses current challenges, and gives an outlook on potential future trends. Graphical Abstract Schematic presentation of the potential applications of graphene-based materials in life science and biomedicine, emphatically reflected in some vital areas such as DNA analysis, biological monitoring, drug delivery, in vitro labelling, in vivo imaging, tumor target, etc.

A novel fluorescence method for activity assay and drug screening of T4 PNK by coupling rGO with ligase reaction

T4 polynucleotide kinase (PNK) is the primary member of the 5′-kinase family that can transfer the γ-phosphate residue of ATP to the 5′-hydroxyl group of oligonucleotides.

A review on graphene-based nanocomposites for electrochemical and fluorescent biosensors

Biosensors with high sensitivity, selectivity and a low limit of detection, reaching nano/picomolar concentrations of biomolecules, are important to the medical sciences and healthcare industry for evaluating physiological and metabolic parameters.