Paper-Based Solid-Phase Nucleic Acid Hybridization Assay Using Immobilized Quantum Dots as Donors in Fluorescence Resonance Energy Transfer

Sandwich-type aptamer-based biosensors for thrombin detection

Thrombin, a proteolytic enzyme, plays an essential role in catalyzing many blood clotting reactions. Thrombin can act as a marker for some blood-related diseases, such as leukemia, thrombosis, Alzheimer's disease and liver disease. Therefore, its diagnosis is of great importance in the fields of biological and medical research. Biosensors containing sandwich-type structures have attracted much consideration owing to their superior features such as reproducible and stable responses with easy improvement in the sensitivity of detection. Sandwich-type platforms can be designed using a pair of receptors that are able to bind to diverse locations of the same target. Herein, we investigate recent advances in the progress and applications of thrombin aptasensors containing a sandwich-type structure, in which two thrombin-binding aptamers (TBAs) identify different parts of the thrombin molecule, leading to the formation of a sandwich structure and ultimately signal detection. We also discuss the pros and cons of these approaches and outline the most logical approach in each section.

An overview of polymer surface coated synthetic quantum dots as therapeutics and sensors applications

Quantum dots (QDs) are a class of remarkable materials that have garnered significant attention since their initial discovery. It is noteworthy to mention that it took approximately a decade for these materials to be successfully implemented in practical applications. While QDs have demonstrated notable optical properties, it is important to note that these attributes alone have not rendered them a feasible substitute for traditional organic dyes. Furthermore, it is worth noting that the substance under investigation exhibited inherent toxicity and instability in its initial state, primarily due to the presence of a heavy metal core. In the initial stages of research, it was observed that the integration of nanocomposites had a positive impact on the properties of QDs. The discovery of these nanocomposites was motivated by the remarkable properties exhibited by biocomposites found in nature. Recent discoveries have shed light on the potential utilization of QDs as a viable strategy for drug delivery, offering a promising avenue to enhance the efficacy of current pharmaceuticals and pave the way for the creation of innovative therapeutic approaches. The primary objective of this review was to elucidate the distinctive characteristics that render QDs highly suitable for utilization as nanocarriers. In this study, we will delve into the multifaceted applications of QDs as sensing nanoprobes and their utilization in diverse drug delivery systems. The focus of our investigation was directed toward the utilization of QD/polymer composites in sensing applications, with particular emphasis on their potential as chemical sensors, biosensors, and physical sensors.

Viscosity-Based Flow Sensor on Paper for Quantitative and Label-Free Detection of α-Amylase and Its Inhibitor

α-Amylase (AMS) in human serum is a critical biomarker for the early diagnosis of pancreatic damage. In addition, the inhibition of α-amylase has long been thought to decrease the occurrence of diabetes. Thus, it is critical to construct a facile and convenient method for the determination of AMS and its inhibitor. In this study, we demonstrate a novel amylase sensor based on translating the viscosity change of the aqueous solution into the difference of the water diffusion length on a pH paper strip. AMS can be quantitatively detected by measuring the viscosity change of the amylopectin solution in the presence of AMS with different concentrations. The paper-based AMS sensor has a very high sensitivity with a detection limit of 0.017 U/mL and also shows excellent specificity. In addition, the inhibitory effect of acarbose on AMS is demonstrated with the IC₅₀ value determined to be 21.66 ± 1.13 μg/mL. Furthermore, it is also evaluated for the detection of AMS in human serum samples of healthy people and acute pancreatitis patients. The difference in amylase levels between the two groups is unambiguously distinguished. Overall, this study provides a very simple, cost-effective, equipment-free, high-throughput, and label-free method for rapid and quantitative detection of α-amylase and may have significant applications in the diagnosis of acute pancreatitis and the screening of AMS inhibitors.

Hydrogel-assisted paper-based lateral flow sensor for the detection of trypsin in human serum

The detection of trypsin and its inhibitor is significantly important for both clinical diagnosis and disease treatment. Herein, we demonstrate a hydrogel-assisted paper-based lateral flow sensor for the detection of trypsin and its inhibitor for the first time. The gelatin hydrogel is hydrolyzed based on the gel-to-sol transition in the presence of trypsin, which results in the release of the trapped water molecules in the gelatin hydrogel. By placing one end of a pH indicator strip onto the hydrolyzed gelatin hydrogel, water is flowing along the pH indicator strip. However, in the absence of trypsin, water cannot flow along the pH indicator strip as the water molecules are trapped in the gelatin hydrogel. The detection limit of the system reaches as low as 1.0 × 10^-6 mg/mL, and it is also applied to the quantitative detection of trypsin in human serum. In addition, the detection of a clinical drug aprotinin that is an inhibitor of trypsin is also successfully achieved. Noteworthy, only the gelatin hydrogel, pH indicator strip, and PS substrate are needed to fulfill the detection of trypsin without the need of other chemicals or reagents. Overall, we develop a particularly simple, elegant, robust, competitive, high-throughput, and low-cost approach for the rapid and label-free detection of trypsin and its inhibitor, which is very promising in the development of commercial products for sensing, diagnostic, and pharmaceutical applications. Besides, the hydrogel-assisted paper-based lateral flow sensor can also be employed to detect other analytes of interest by use of different stimuli-responsive hydrogel systems.

Nanostructures for Biosensing, with a Brief Overview on Cancer Detection, IoT, and the Role of Machine Learning in Smart Biosensors

Biosensors are essential tools which have been traditionally used to monitor environmental pollution and detect the presence of toxic elements and biohazardous bacteria or virus in organic matter and biomolecules for clinical diagnostics. In the last couple of decades, the scientific community has witnessed their widespread application in the fields of military, health care, industrial process control, environmental monitoring, food-quality control, and microbiology. Biosensor technology has greatly evolved from in vitro studies based on the biosensing ability of organic beings to the highly sophisticated world of nanofabrication-enabled miniaturized biosensors. The incorporation of nanotechnology in the vast field of biosensing has led to the development of novel sensors and sensing mechanisms, as well as an increase in the sensitivity and performance of the existing biosensors. Additionally, the nanoscale dimension further assists the development of sensors for rapid and simple detection in vivo as well as the ability to probe single biomolecules and obtain critical information for their detection and analysis. However, the major drawbacks of this include, but are not limited to, potential toxicities associated with the unavoidable release of nanoparticles into the environment, miniaturization-induced unreliability, lack of automation, and difficulty of integrating the nanostructured-based biosensors, as well as unreliable transduction signals from these devices. Although the field of biosensors is vast, we intend to explore various nanotechnology-enabled biosensors as part of this review article and provide a brief description of their fundamental working principles and potential applications. The article aims to provide the reader a holistic overview of different nanostructures which have been used for biosensing purposes along with some specific applications in the field of cancer detection and the Internet of things (IoT), as well as a brief overview of machine-learning-based biosensing.

Resonance Energy Transfer-Based Biosensors for Point-of-Need Diagnosis-Progress and Perspectives

The demand for point-of-need (PON) diagnostics for clinical and other applications is continuing to grow. Much of this demand is currently serviced by biosensors, which combine a bioanalytical sensing element with a transducing device that reports results to the user. Ideally, such devices are easy to use and do not require special skills of the end user. Application-dependent, PON devices may need to be capable of measuring low levels of analytes very rapidly, and it is often helpful if they are also portable. To date, only two transduction modalities, colorimetric lateral flow immunoassays (LFIs) and electrochemical assays, fully meet these requirements and have been widely adopted at the point-of-need. These modalities are either non-quantitative (LFIs) or highly analyte-specific (electrochemical glucose meters), therefore requiring considerable modification if they are to be co-opted for measuring other biomarkers. Förster Resonance Energy Transfer (RET)-based biosensors incorporate a quantitative and highly versatile transduction modality that has been extensively used in biomedical research laboratories. RET-biosensors have not yet been applied at the point-of-need despite its advantages over other established techniques. In this review, we explore and discuss recent developments in the translation of RET-biosensors for PON diagnoses, including their potential benefits and drawbacks.

Luminescent Nanomaterials (II)

In this review, we focus on sensing techniques and biological applications of various luminescent nanoparticles including quantum dot (QD), up-conversion nanoparticles (UCNPs) following the previous chapter. Fluorescent phenomena can be regulated or shifted by interaction between biological targets and luminescence probes depending on their distance, which is so-called Fӧrster resonance energy transfer (FRET). QD-based FRET technique, which has been widely applied as a bioanalytical tool, is described. We discuss time-resolved fluorescence (TRF) imaging and flow cytometry technique, using photoluminescent nanoparticles with unique properties for effectively improving selectivity and sensitivity. Based on these techniques, bioanalytical and biomedical application, bioimaging with QD, UCNPs, and Euripium-activated luminescent nanoprobes are covered. Combination of optical property of these luminescent nanoparticles with special functions such as drug delivery, photothermal therapy (PTT), and photodynamic therapy (PDT) is also described.

Affinity Immobilization of Semiconductor Quantum Dots and Metal Nanoparticles on Cellulose Paper Substrates

Colloidal semiconductor quantum dots (QDs), metal nanoparticles, and cellulose paper are materials with numerous applications in bioanalysis and beyond. The functional properties of QDs and metal NPs are substantially different than those of cellulose, such that their integration with cellulose paper is potentially enabling for many applications. Here, we characterize and evaluate multiple chemistries that modify cellulose paper substrates for the affinity-based immobilization of QDs, gold nanoparticles (Au NPs), and platinum nanoparticles (Pt NPs). These chemistries include grafting of cellulose fibers with imidazole and dithiol groups, as well as the aminosilanization of cellulose fibers (both with and without subsequent grafting with dithiol groups). Cellulose modifications and nanoparticle immobilization are characterized by multiple techniques, including, but not limited to, X-ray photoelectron spectroscopy, scanning electron microscopy, and optical imaging, extinction, and fluorescence measurements. We demonstrate the on-paper immobilization of color-tuned mixtures of QDs, on-paper patterning of QDs by microcontact printing, and post-immobilization enhancement of energy transfer and model assays of protease activity. The robustness of QD photoluminescence is also evaluated between immobilization chemistries. Paper-immobilized Au NPs and Pt NPs are evaluated as potential substrates for SERS and as supported catalysts for a model decolorization reaction. Our cumulative results indicate that there may not be a one-size-fits-all immobilization chemistry. Instead, the immobilization chemistry should be tailored and optimized for the downstream application.

Integrated hand-powered centrifugation and paper-based diagnosis with blood-in/answer-out capabilities

To date, 55% of inhabitants of the developing world still live in rural regions and they have a very urgent need to improve the level of disease diagnosis, especially in resource-limited settings. Herein, we present a microfluidic system that centrifuges whole blood and quantifies contained biomarkers in a rapid, feasible and integrated way. Such a device provides a blood-in/answer-out capability and is small enough to be carried by any individual in any environment. The successful integration a hand-powered centrifuge and immunoassay unit within a rotational paper-based device allows for diagnostic application by untrained users and in environments where access to electricity cannot be assumed. In addition, the low cost (~$ 0.5), light weight and small instrumental footprint make the device ideally suited for rapid on-site detection. To validate the applicability of the system in a clinical diagnostic testing, we successfully perform enzyme-linked immunosorbent assay (ELISA) analysis of carcinoembryonic antigen and alpha fetoprotein from human blood samples. We expect that this powerful platform technology will provide the opportunities for point-of-care diagnosis in resource-limited settings.

Dual-Color Plasmonic Nanosensor for Radiation Dosimetry

Radiation dosimeters are critical for accurately assessing the levels of radiation exposure of tumor sites and surrounding tissues and for optimizing therapeutic interventions as well as for monitoring environmental exposure. To fill the need for a simple, user-friendly, and inexpensive dosimeter, we designed an innovative colorimetric nanosensor-based assay for detecting ionizing radiation. We show that hydroxyl radicals generated by ionizing radiation can be used to etch gold nanorods (AuNRs) and silver nanoprisms (AgNPRs), yielding reproducible color changes for radiation dose detection in the range of 50-2000 rad, broad enough to cover doses used in hyperfractionated, conventional, and hypofractionated radiotherapy. This range of doses detected by this assay correlates with radiation-induced DNA damage response in mammalian cells. Furthermore, this AuNR- and AgNPR-based sensing platform has been established in a paper format that can be readily adopted for a wide range of applications and translation.

Multifunctional Droplet Microfluidic Platform for Rapid Immobilization of Oligonucleotides on Semiconductor Quantum Dots

Quantum dot-DNA oligonucleotide (QD-DNA) conjugates have been used in many fields such as nucleic acid bioassays, intracellular probes, and drug delivery systems. A typical solid-phase method that achieves rapid loading of oligonucleotides on surfaces of QDs involves a two-step reaction and is performed in a batch-based approach. In contrast, droplet microfluidics offers many advantages that are unavailable when using batch processing, providing rapid and dense immobilized DNA oligonucleotides on QDs. The presented droplet microfluidic approach allows high-quality QD-DNA conjugates to be produced using one single device, which is designed to have two droplet generators, one droplet merger, and one mixer. One of the droplet generators coencapsulates QDs and magnetic beads (MBs) into nanoliter-sized droplets for the production of QD-MB conjugates and the other encapsulates oligonucleotides in nanoliter-sized droplets. These two streams of droplets then merge at a one-to-one ratio in a chamber. The merged droplets travel along the mixer, which is a serpentine microchannel with 30 turns, resulting in QD-DNA conjugation structures of high quality. This multifunctional microfluidic device provides advantages such as higher degree of control over the reaction conditions, minimized cross-contamination and impurities, and reduction of reagent consumption while eliminating any need for external vortexing and pipetting. To evaluate the quality of the QD-DNA conjugates, they were used as Forster resonance energy transfer (FRET) probes to quantify oligonucleic targets.

A novel trimodal system on a paper-based microfluidic device for on-site detection of the date rape drug "ketamine"

Paper-based microfluidic device was designed with wax-printing to combine potentiometric, fluorimetric and colorimetric detection zones. This newly developed trimodal paper chip has been used for on-site determination of ketamine hydrochloride (KET) as a date rape drug in beverages. The device employed polyaniline nano-dispersion as conducting polymer in ion sensing paper electrodes designed to fit USB plug connector. Carbon dots-gold nanoparticles and cobalt thiocyanate were used in fluorescence and color detection zones, respectively. Cellular phone's camera facilitated the on-site fluorimetric and color detection. The implemented trimodal detection system exhibited specificity for KET detection in the presence of several other beverage interferences i.e., biogenic amines. This innovative sensor brings together analytical figures of merit for effective KET detection in single aliquot of spiked beverages. The proposed paper-based chip also fulfils WHO criteria for point-of-care devices posing the proposed trimodal paper device as an active part for rapid, on-site drug diagnostics and to be applied further for other similar drugs.

Ratiometric fluorescent nanoprobes for visual detection: Design principles and recent advances - A review

Signal generation techniques for visual detection of analytes have received a great deal of attention in various sensing fields. These approaches are considered to be advantageous when instrumentation cannot be employed, such as for on-site assays, point-of-care tests, and he althcare diagnostics in resource-constrained areas. Amongst various visual detection approaches explored for non-invasive quantitative measurements, ratiometric fluorescence sensing has received particular attention as a potential method to overcome the limitations of intensity-based probes. This technique relies on changes in the intensity of two or more emission bands (induced by an analyte), resulting in an effective internal referencing which improves the sensitivity of the detection. The self-calibration, together with the unique optophysical properties of nanoparticles (NPs) have made the ratiometric fluorescent nanoprobes more sensitive and reliable, which in turn, can result in more precise visual detection of the analytes. Over the past few years, a vast number of ratiometric sensing probes using nanostructured fluorophores have been designed and reported for a wide variety of sensing, imaging, and biomedical applications. In this work, a review on the NP-based ratiometric fluorescent sensors has been presented to meticulously elucidate their development, advances and challenges. With a special emphasis on visual detection, the most important steps in the design of fluorescent ratiometric nanoprobes have been given and based on different classes of analytes, recent applications of fluorescent ratiometric nanoprobes have been summarized. The challenges for the future use of the technique investigated in this review have been also discussed.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Enhanced Immunoassay Using a Rotating Paper Platform for Quantitative Determination of Low Abundance Protein Biomarkers

The changing concentrations of circulating protein biomarkers have been correlated with a variety of diseases. Quantitative bioassays capable of sensitive and specific determination of protein biomarkers at low levels can be essential for therapeutic treatments that can improve outcomes for patients. Herein, we describe the investigation of a rotating paper device (RPD) for quantitative determination of targeted proteins at the fM concentration level. The RPD consists of two circular papers each separately supported with a plastic disc. Protein detection is conducted via enhanced immunoassay using amplification in a sequential workflow, which includes a sandwich immunoassay in the upper paper and a signal amplification reaction in the lower paper. The sandwich immunoassay is conducted using biobarcode nanoparticles (BNPs) and results in the release of reporter oligonucleotides from BNPs. These oligonucleotides are transferred to the bottom paper, where they engage in a target recycling methodology that leads to the production of a colorimetric signal. The assay was evaluated for quantitation of interleukin-6 (IL-6), a cytokine biomarker in serum. A limit of detection of 63 fM and a dynamic range of 200 fM-8 pM was observed for the assay. The specificity of the assay was successfully verified against several common protein biomarkers.

Detection of cystic fibrosis transmembrane conductance regulator ΔF508 gene mutation using a paper-based nucleic acid hybridization assay and a smartphone camera

Diagnostic technology that makes use of paper platforms in conjunction with the ubiquitous availability of digital cameras in cellular telephones and personal assistive devices offers opportunities for development of bioassays that are cost effective and widely distributed. Assays that operate effectively in aqueous solution require further development for implementation in paper substrates, overcoming issues associated with surface interactions on a matrix that offers a large surface-to-volume ratio and constraints on convective mixing. This report presents and compares two related methods for determination of oligonucleotides that serve as indicators of cystic fibrosis, differentiating between the normal wild-type sequence, and a mutant-type sequence that has a 3-base replacement. The transduction strategy operates by selective hybridization of oligonucleotide probes that are conjugated to fluorescent quantum dots, where hybridization of target sequences causes a molecular fluorophore to approach the quantum dot and become emissive through fluorescence resonance energy transfer. Detection can rely on hybridization of a target that is labelled with Cy3 fluorophore, or in the presence of an unlabelled target when a sandwich assay format is implemented with a labelled reporter oligonucleotide. Selectivity to determine the presence of mismatched sequences involves appropriate selection of nucleotide sequences to set melt temperatures, in conjunction with control of stringency conditions using formamide as a chaotrope. It was determined that both direct and sandwich assays on paper substrates are able to distinguish between wild-type and mutant-type samples.

Improvement in the Reproducibility of a Paper-based Analytical Device (PAD) Using Stable Covalent Binding between Proteins and Cellulose Paper

Paper-based analytical devices (PADs) have been widely used in many fields because they are affordable and portable. For reproducible quantitative analysis, it is crucial to strongly immobilize proteins on PADs. Conventional techniques for immobilizing proteins on PADs are based on physical adsorption, but proteins can be easily removed by weak physical forces. Therefore, it is difficult to ensure the reproducibility of the analytical results of PADs using physical adsorption. To overcome this limitation, in this study, we showed a method of covalent binding of proteins to cellulose paper. This method consists of three steps, which include periodate oxidation of paper, the formation of a Schiff base, and reductive amination. We identified aldehyde and imine groups formed on paper using FT-IR analysis. This covalent bonding approach enhanced the binding force and binding capacity of proteins. We confirmed the activity of an immobilized antibody through a sandwich immunoassay. We expect that this immobilization method will contribute to the commercialization of PADs with high reproducibility and sensitivity.

Paper-based platform for detection by hybridization using intrinsically labeled fluorescent oligonucleotide probes on quantum dots

A paper-based platform was investigated in which the selective detection of oligonucleotide targets by hybridization was accomplished via the enhancement of fluorescence emission from intrinsically labeled DNA probes that were immobilized on the surface of quantum dots (QDs). Multiple copies of a derivative of thiazole orange, an intercalating dye known to form non-emissive dimers, were conjugated to single-stranded oligonucleotide probes. Dimerization resulted in the formation of H-aggregates where excitonic interactions led to the suppression of fluorescence. The hybridization of the oligonucleotide probe with a complementary target resulted in the enhancement of fluorescence emission as the dimers dissociated and the dyes preferentially intercalated with the duplex. The detection of oligonucleotide targets using this configuration eliminated the need for labeling the target strands, and fluorescence intensity was proportional to the extent of hybridization. In addition, the dye molecules were excited using Foerster Resonance Energy Transfer (FRET) from QD donors, which resulted in improved selectivity and allowed for ratiometric detection. A solution-phase hybridization assay based on similar operational principles has been previously reported, and this new work investigated the advantages offered for this transduction scheme using paper-based solid-phase substrates. QD-probe conjugates were immobilized in sufficient density on the paper matrix to provide for multiple-donor-multiple-acceptor interactions that resulted in a 20-fold enhancement of acceptor emission compared to the solution-based assay, providing a limit of detection of 0.1 pmol. The paper-based assay provided for the reduction of the time needed for sample preparation and data acquisition, demonstrated that transduction was possible in a complex matrix (goat serum) without compromising on the performance observed in buffer solution, and that oligonucleotides generated from standard PCR amplification could be detected.

Simple Way To Fabricate Novel Paper-Based Valves Using Plastic Comb Binding Spines

A novel strategy for fabricating the paper-based valves on microfluidic paper-based analytical devices (μPADs) was described to control fluid in a user-friendly way. Initial prototypes of 3D μPADs manipulate the spatial distribution of fluid within the device. The movable paper channel in a different layer could be achieved using the channel's connection or disconnection to realize the valve function using plastic comb binding spines (PCBS). The entire valve manipulation process was similar to a desk calendar that can be flipped over and turned back. It is notable that this kind of PCBS valve can control a fluid in a simple and easy way without the timing setting or any trigger, and this advantage makes it user-friendly for untrained users to carry out the complex and high throughput operations. The reusable plastic comb binding spines greatly reduce the cost of fabricating paper-based valves. To evaluate the performance, the actual samples of Fe (II) and nitrite were successfully analyzed. We hope this method will introduce a new approach to fabrication of paper-based valves on μPADs in the future.

Paper-based biodetection using luminescent nanoparticles

Point-of-care and in-field technologies for rapid, sensitive and selective detection of molecular biomarkers have attracted much interest. Rugged bioassay technology capable of fast detection of markers for pathogens and genetic diseases would in particular impact the quality of health care in the developing world, but would also make possible more extensive screening in developed countries to tackle problems such as those associated with water and food quality, and tracking of infectious organisms in hospitals and clinics. Literature trends indicate an increasing interest in the use of nanomaterials, and in particular luminescent nanoparticles, for assay development. These materials may offer attributes for development of assays and sensors that could achieve improvements in analytical figures of merit, and provide practical advantages in sensitivity and stability. There is opportunity for cost-efficiency and technical simplicity by implementation of luminescent nanomaterials as the basis for transduction technology, when combined with the use of paper substrates, and the ubiquitous availability of cell phone cameras and associated infrastructure for optical detection and transmission of results. Luminescent nanoparticles have been described for a broad range of bioanalytical targets including small molecules, oligonucleotides, peptides, proteins, saccharides and whole cells (e.g., cancer diagnostics). The luminescent nanomaterials that are described herein for paper-based bioassays include metal nanoparticles, quantum dots and lanthanide-doped nanocrystals. These nanomaterials often have broad and strong absorption and narrow emission bands that improve opportunity for multiplexed analysis, and can be designed to provide emission at wavelengths that are efficiently processed by conventional digital cameras. Luminescent nanoparticles can be embedded in paper substrates that are designed to direct fluid flow, and the resulting combination of technologies can offer competitive analytical performance at relatively low cost.

Quantum Dot-PNA Conjugates for Target-Catalyzed RNA Detection

Detection of pathogenic nucleic acids remains one of the most reliable approaches for the diagnosis of a broad range of diseases. Current PCR-based methods require experienced personnel and cannot be easily used for point-of-care diagnostics, making alternative strategies for the sensitive, reliable, and cost-efficient detection of pathogenic nucleic acids highly desirable. Here, we report an enzyme-free method for the fluorometric detection of RNA that relies on a target-induced fluorophore transfer onto a semiconductor quantum dot (QD), uses PNA probes as selective recognition elements and can be read out with simple and inexpensive equipment. For QD-PNA conjugates with optimized PNA content, limits of detection of dengue RNA in the range of 10 pM to 100 nM can be realized within 5 h in the presence of a high excess of noncomplementary RNA.

Enzymatic amplification of oligonucleotides in paper substrates

Several solution-based methods have recently been adapted for use in paper substrates for enzymatic amplification to increase the number of copies of DNA sequences. There is limited information available about the impact of a paper matrix on DNA amplification by enzymatic processes, and about how to optimize conditions to maximize yields. The work reported herein provides insights about the impact of physicochemical properties of a paper matrix, using nuclease-assisted amplification by exonuclease III and nicking endonuclease Nt. Bbv, and a quantum dot (QD) - based Forster Resonance Energy Transfer (FRET) assay to monitor the extent of amplification. The influence of several properties of paper on amplification efficiency and kinetics were investigated, such as surface adsorption of reactants, and pore size. Additional factors that impact amplification processes such as target length and the packing density of oligonucleotide probes on the nanoparticle surfaces were also studied. The work provides guidance for development of more efficient enzymatic target-recycling DNA amplification methods in paper substrates.

Fluorogenic PNA probes

Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.

Development of quantum dot-based biosensors: principles and applications

We review the recent advances in quantum dot-based biosensors and focus on quantum dot-based fluorescent, bioluminescent, chemiluminescent, and photoelectrochemical biosensors.

Inorganic Nanoparticles as Donors in Resonance Energy Transfer for Solid-Phase Bioassays and Biosensors

Bioassays for the rapid detection and quantification of specific nucleic acids, proteins, and peptides are fundamental tools in many clinical settings. Traditional optical emission methods have focused on the use of molecular dyes as labels to track selective binding interactions and as probes that are sensitive to environmental changes. Such dyes can offer good detection limits based on brightness but typically have broad emission bands and suffer from time-dependent photobleaching. Inorganic nanoparticles such as quantum dots and upconversion nanoparticles are photostable over prolonged exposure to excitation radiation and tend to offer narrow emission bands, providing a greater opportunity for multiwavelength multiplexing. Importantly, in contrast to molecular dyes, nanoparticles offer substantial surface area and can serve as platforms to carry a large number of conjugated molecules. The surface chemistry of inorganic nanoparticles offers both challenges and opportunities for the control of solubility and functionality for selective molecular interactions by the assembly of coatings through coordination chemistry. This report reviews advances in the compositional design and methods of conjugation of inorganic quantum dots and upconversion nanoparticles and the assembly of combinations of nanoparticles to achieve energy exchange. Our interest is the exploration of configurations where the modified nanoparticles can be immobilized to solid substrates for the development of bioassays and biosensors that operate by resonance energy transfer (RET).

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection

Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed.

Graphical Abstract

Bioresponsive Release System for Visual Fluorescence Detection of Carcinoembryonic Antigen from Mesoporous Silica Nanocontainers Mediated Optical Color on Quantum Dot-Enzyme-Impregnated Paper

An all-in-one paper-based analytical device (PAD) was successfully developed for visual fluorescence detection of carcinoembryonic antigen (CEA) on CdTe/CdSe quantum dot (QD)-enzyme-impregnated paper by coupling with a bioresponsive controlled-release system from DNA-gated mesoporous silica nanocontainers (MSNs). The assay was carried out in a centrifuge tube by using glucose-loaded MSNs with a CEA aptamer and a QD-enzyme-paper attached on the lid. Initially, single-strand complementary DNA to a CEA aptamer was covalently conjugated to the aminated MSN, and then glucose (enzyme substrate) molecules were gated into the pore with the help of the aptamer. Glucose oxidase (GOD) and CdTe/CdSe QDs were coimmobilized on paper for the visual fluorescence signal output. Upon target CEA introduction in the detection cell, the analyte specifically reacted with the immobilized aptamer on the MSN to open the pore, thereby resulting in the glucose release. The released glucose was oxidized by the immobilized GOD on paper to produce gluconic acid and hydrogen peroxide, and the latter quenched the fluorescence of CdTe/CdSe QDs, which could be determined by the naked eye on a portable smartphone and a commercial fluorospectrometer. Under optimal conditions, the PAD-based sensing system enabled sensitive discrimination of target CEA against other biomarkers or proteins in a linear range of 0.05-20 ng mL^-1 with a limit of detection of 6.7 pg mL^-1 (ppt). In addition, our strategy displayed high specificity, good reproducibility, and acceptable accuracy for analyzing human serum specimens with a commercial human CEA ELISA kit. Importantly, this methodology offers promise for simple analysis of biological samples and is suitable for use in the mass production of miniaturized devices, thus opening new opportunities for protein diagnostics and biosecurity.

Nanomaterials-modified cellulose paper as a platform for biosensing applications

Recently, paper substrates have attracted tremendous interest from both academia and industry. Not only is paper highly abundant and portable, it is lightweight, disposable, easy-to-use, and can be rolled or folded into 3D configurations. More importantly, with a unique porous bulk structure and rough and absorptive surface properties, the construction of nanomaterials-functionalized cellulose has enabled cellulose paper to be applied for point-of-care (POC) paper devices with reasonably good performance at low cost. In this review, the latest advances in the modification of nanomaterials on paper cellulose are summed up. To begin with, the attractive properties of paper-based analytical devices are described. Then, fabricating methods for the functionalization of cellulose with diverse materials, including noble metals, bimetals, metal oxides, carbon nanomaterials, and molecular imprinting polymer nanoparticles, as well as their applications, are introduced in detail. Finally, the current critical issues, challenges, and future prospectives for exploring a paper-based analytical system based on nanomaterials-modified cellulose are discussed. It is believed that more strategies will be developed in the future to construct nanomaterials-functionalized cellulose, paving the way for the mass production of POC paper devices with a satisfactory performance.

Resonance Energy Transfer-Based Nucleic Acid Hybridization Assays on Paper-Based Platforms Using Emissive Nanoparticles as Donors

Quantum dots (QDs) and upconverting nanoparticles (UCNPs) are luminescent nanoparticles (NPs) commonly used in bioassays and biosensors as resonance energy transfer (RET) donors. The narrow and tunable emissions of both QDs and UCNPs make them versatile RET donors that can be paired with a wide range of acceptors. Ratiometric signal processing that compares donor and acceptor emission in RET-based transduction offers improved precision, as it accounts for fluctuations in the absolute photoluminescence (PL) intensities of the donor and acceptor that can result from experimental and instrumental variations. Immobilizing NPs on a solid support avoids problems such as those that can arise with their aggregation in solution, and allows for facile layer-by-layer assembly of the interfacial chemistry. Paper is an attractive solid support for the development of point-of-care diagnostic assays given its ubiquity, low-cost, and intrinsic fluid transport by capillary action. Integration of nanomaterials with paper-based analytical devices (PADs) provides avenues to augment the analytical performance of PADs, given the unique optoelectronic properties of nanomaterials. Herein, we describe methodology for the development of PADs using QDs and UCNPs as RET donors for optical transduction of nucleic acid hybridization. Immobilization of green-emitting QDs (gQDs) on imidazole functionalized cellulose paper is described for use as RET donors with Cy3 molecular dye as acceptors for the detection of SMN1 gene fragment. We also describe the covalent immobilization of blue-emitting UCNPs on aldehyde modified cellulose paper for use as RET donors with orange-emitting QDs (oQDs) as acceptors for the detection of HPRT1 gene fragment. The data described herein is acquired using an epifluorescence microscope, and can also be collected using technology such as a typical electronic camera.

Highly sensitive turn-on fluorescence detection of thrombomodulin based on fluorescence resonance energy transfer

As an integral glycoprotein on the surface of endothelial cells, thrombomodulin (TM) has very high affinity for thrombin. TM has been regarded to be a marker of endothelial damage since it can be released during endothelial cell injury. In this work, a highly sensitive fluorescence method for the quantitative detection of TM was developed. TM antibody (Ab) and bovine serum albumin (BSA) were bound on gold nanoparticles (AuNPs) to construct BSA-AuNPs-Ab nanocomposites and they were characterized by transmission electron microscope and UV-vis spectrophotometry. The fluorescence of acridine orange (AO) was quenched by the prepared gold nanocomposites based on fluorescence resonance energy transfer (FRET). In the presence of TM, the fluorescence was turned on due to the effective separation of AO from the surface of gold nanocomposites. Under optimum conditions, the enhanced fluorescence intensity displayed a linear relationship with the logarithm of the TM concentration from 0.1pgmL^-1 to 5ngmL^-1 with a low detection limit of 12fgmL^-1. The release of soluble thrombomodulin (sTM) by the injured HUVEC-C cells in the presence of H₂O₂ was investigated using the proposed method. The released sTM content in the growth medium was found to be increased with the enhancement of contact time of the cells with H₂O₂.

A reusable and naked-eye molecular probe with aggregation-induced emission (AIE) characteristics for hydrazine detection

We report a reusable fluorogenic probe for naked-eye sensing of hydrazine in solution and in the gaseous phase.

CdTe/CdSe quantum dot-based fluorescent aptasensor with hemin/G-quadruplex DNzyme for sensitive detection of lysozyme using rolling circle amplification and strand hybridization

Lysozyme with a small monomeric globular enzymatic protein is part of the innate immune system, and its deficiency can cause the increased incidence of disease. Herein, we devise a new signal-enhanced fluorescence aptasensing platform for quantitative screening of lysozyme by coupling with rolling circle amplification (RCA) and strand hybridization reaction, accompanying the assembly of CdTe/CdSe quantum dots (QDs) and hemin/G-quadruplex DNzyme. Initially, target-triggered release of the primer was carried out from DNA duplex via the reaction of the aptamer with the analyte, and the released primer could be then utilized as the template to produce numerous repeated oligonucleotide sequences by the RCA reaction. Following that, the formed long-stranded DNA simultaneously hybridized with the CdTe/CdSe QD-labeled probe and hemin/G-quadruplex DNzyme strand in the system, thereby resulting in the quenching of QD fluorescent signal through the proximity hemin/G-quadruplex DNzyme on the basis of transferring photoexcited conduction band electrons of quantum dots to Fe(III)/Fe(II)-protoporphyrin IX (hemin) complex. Under optimal conditions, the fluorescent signal decreased with the increasing target lysozyme within the dynamic range from 5.0 to 500nM with a detection limit (LOD) of 2.6nM at the 3s_blank criterion. Intra-assay and interassay coefficients of variation (CVs) were below 8.5% and 11.5%, respectively. Finally, the system was applied to analyze spiked human serum samples, and the recoveries in all cases were 85-111.9%.

Quantum Dot-Modified Paper-Based Assay for Glucose Screening

A simple and inexpensive method to fabricate a colloidal CdSe/ZnS quantum dots-modified paper-based assay for glucose is herein reported. The circular paper sheets were uniformly loaded and displayed strong fluorescence under a conventional hand-held UV lamp (365 nm). The assay is based on the use of glucose oxidase enzyme (GOx), which impregnated the paper sheets, producing H₂O₂ upon the reaction with the glucose contained in the samples. After 20 min of exposure, the fluorescence intensity changed due to the quenching caused by H₂O₂. To obtain a reading, the paper sheets were photographed under 365 nm excitation using a digital camera. Several parameters, including the amount of QD, sample pH, and amount of GOx were optimized to maximize the response to glucose. The paper-based assay showed a sigmoidal-shaped response with respect to the glucose concentration in the 5-200 mg·dL^-1 range (limit of detection of 5 μg·dL^-1), demonstrating their potential use for biomedical applications.

A three-dimensional silver nanoparticles decorated plasmonic paper strip for SERS detection of low-abundance molecules

The fabrication of SERS substrates, which can offer the advantages of strong Raman signal enhancement with good reproducibility and low cost, is still a challenge for practical applications. In this work, a simple three-dimensional (3D) paper-based SERS substrate, which contains plasmonic silver-nanoparticles (AgNPs), has been developed by the silver mirror reaction. This paper strip was characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray diffraction (XRD), etc. Pretreatment of the paper as well as the reaction time, temperature, and reagent concentrations for the silver mirror reaction were varied for further studies. With the optimized experimental parameters, the AgNPs synthesized and distributed in-situ on the paper strip could give more favorable SERS performance. The limit of detection (LOD) as low as 10(-11)M for Rhodamine 6G (R6G) and 10(-9)M for p-aminothiophenol (p-ATP) plus wide linear range for the log-log plot of Raman intensity versus analyte concentration were achieved. The detection of R6G in rain water was also carried out successfully. The merits of this protocol include low cost, easy operation, high sensitivity and acceptable stability, which make it ideal for the detection of environmental samples in trace amounts.

Quantum dot-DNA aptamer conjugates coupled with capillary electrophoresis: A universal strategy for ratiometric detection of organophosphorus pesticides

Based on the highly sensitivity and stable-fluorescence of water-soluble CdTe/CdS core-shell quantum dots (QDs) with broad-specificity DNA aptamers, a novel ratiometric detection strategy was proposed for the sensitive detection of organophosphorus pesticides by capillary electrophoresis with laser-induced fluorescence (CE-LIF). The as-prepared QDs were first conjugated with the amino-modified oligonucleotide (AMO) by amidation reaction, which is partial complementary to the DNA aptamer of organophosphorus pesticides. Then QD-labeled AMO (QD-AMO) was incubated with the DNA aptamer to form QD-AMO-aptamer duplex. When the target organophosphorus pesticides were added, they could specifically bind the DNA aptamer, leading to the cleavage of QD-AMO-aptamer duplex, accompany with the release of QD-AMO. As a result, the ratio of peak height between QD-AMO and QD-AMO-aptamer duplex changed in the detection process of CE-LIF. This strategy was subsequently applied for the detection of phorate, profenofos, isocarbophos, and omethoate with the detection limits of 0.20, 0.10, 0.17, and 0.23μM, respectively. This is the first report about using QDs as the signal indicators for organophosphorus pesticides detection based on broad-specificity DNA aptamers by CE-LIF, thus contributing to extend the scope of application of QDs in different fields. The proposed method has great potential to be a universal strategy for rapid detection of aptamer-specific small molecule targets by simply changing the types of aptamer sequences.

Linkage inversion assembled nano-aptasensors (LIANAs) for turn-on fluorescence detection

A strategy for aptamer-based biosensing termed linkage inversion assembled nano-aptasensors (LIANAs) is shown to be a generally applicable approach to the sensitive and specific detection of a target molecule in turn-on fluorescence solution-based and paper-based tests.

Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)-probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non-ratiometric QD-FRET transduction method. The selectivity of the hybridization assays was demonstrated by the detection of single nucleotide polymorphism.

Patterned paper sensors printed with long-chain DNA aptamers

There is growing interest in developing printable paper sensors to enable rapid testing of analytes for environmental, food safety, and clinical applications. A major challenge is to find suitable bioinks that are amenable to high-speed printing and remain functional after printing. We report on a simple and effective approach wherein an aqueous ink composed of megadalton-sized tandem repeating structure-switching DNA aptamers (concatemeric aptamers) is used to rapidly create patterned paper sensors on filter paper by inkjet printing. These concatemeric aptamer reporters remain immobilized at the point of printing through strong adsorption but retain sufficient segmental mobility to undergo structure switching and fluorescence signaling to provide both qualitative and quantitative detection of small molecules and protein targets. The convenience of inkjet printing allows for the patterning of internally referenced sensors with multiplexed detection, and provides a generic platform for on-demand printing of sensors even in remote locations.

A fluorescent light-up platform with "AIE + ESIPT" characteristics for multi-target detection both in solution and on paper strip

We report a fluorescent light-up platform for multi-target detection in aqueous solution and on paper strip. The platform is based on a salicylaldazine fluorogen with aggregation-induced emission (AIE) and excited state intramolecular proton transfer (ESIPT) characteristics, which shows distinct advantages including ease of chemical modifications, free of self-quenching effect, excellent light-up ratio and large Stokes shift. To demonstrate the versatility of the platform, palladium cation and perborate anion, as well as UV light, were selected as the targets. The three representative probes, AIE-Pd, AIE-perborate and AIE-UV, light up specifically in the presence of the target both in aqueous solution and on paper strip. The immediate naked-eye response makes the probes ideal for instrument-free and power-free detection.