Aptamer beacons for the direct detection of proteins

Dual structure-switching aptamer-mediated signal amplification cascade for SARS-CoV-2 detection

Since the outbreak of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) at the end of 2019, the spread of the virus has posed a significant threat to public health and the global economy. This work proposed a one-step, dual-structure-switching aptamer-mediated signal amplification cascade for rapid and sensitive detection of the SARS-CoV-2 nucleocapsid protein. This system consisted of two DNA aptamers with structure-switching functionality and fuel DNA, where a cascade of strand hybridization and displacement triggered fluorescence generation and signal amplification. This aptamer-based amplification cascade required neither an amplification stage using enzymes nor pre-processing steps such as washing, viral isolation, and gene extraction. The assay could distinguish SARS-CoV-2 from other respiratory viruses and detect up to 1.0 PFU/assay of SARS-CoV-2 within 30 min at room temperature. In 35 nasopharyngeal clinical samples, the assay accurately assessed 25 positive and 10 negative clinical swab samples, which were confirmed using quantitative polymerase chain reaction. The strategy reported herein can help detect newly emerging pathogens and biomarkers of various diseases in liquid samples. In addition, the developed detection system consisting of only DNA and fluorophores can be widely integrated into liquid biopsy platforms for disease diagnosis.

Aptamer-Antibody Chimera Sensors for Sensitive, Rapid, and Reversible Molecular Detection in Complex Samples

The development of receptors suitable for the continuous detection of analytes in complex, interferent-rich samples remains challenging. Antibodies are highly sensitive but difficult to engineer in order to introduce signaling functionality, while aptamer switches are easy to construct but often yield only a modest target sensitivity. We present here a programmable antibody and DNA aptamer switch (PANDAS), which combines the desirable properties of both receptors by using a nucleic acid tether to link an analyte-specific antibody to an internal strand-displacement (ISD)-based aptamer switch that recognizes the same target through different epitopes. The antibody increases PANDAS analyte binding due to its high affinity, and the effective concentration between the two receptors further enhances two-epitope binding and fluorescent aptamer signaling. We developed a PANDAS sensor for the clotting protein thrombin and show that a tuned design achieves a greater than 300-fold enhanced sensitivity compared to that of using an aptamer alone. This design also exhibits reversible binding, enabling repeated measurements with a temporal resolution of ∼10 min, and retains excellent sensitivity even in interferent-rich samples. With future development, this PANDAS approach could enable the adaptation of existing protein-binding aptamers with modest affinity to sensors that deliver excellent sensitivity and minute-scale resolution in minimally prepared biological specimens.

Intramolecular aptamer switches

Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.

Dual Nanoparticle Conjugates for Highly Sensitive and Versatile Sensing Using 19 F Magnetic Resonance Imaging

Fluorine magnetic resonance imaging (19 F MRI) has emerged as an attractive alternative to conventional 1 H MRI due to enhanced specificity deriving from negligible background signal in this modality. We report a dual nanoparticle conjugate (DNC) platform as an aptamer-based sensor for use in 19 F MRI. DNC consists of core-shell nanoparticles with a liquid perfluorocarbon core and a mesoporous silica shell (19 F-MSNs), which give a robust 19 F MR signal, and superparamagnetic iron oxide nanoparticles (SPIONs) as magnetic quenchers. Due to the strong magnetic quenching effects of SPIONs, this platform is uniquely sensitive and functions with a low concentration of SPIONs (4 equivalents) relative to 19 F-MSNs. The probe functions as a "turn-on" sensor using target-induced dissociation of DNA aptamers. The thrombin binding aptamer was incorporated as a proof-of-concept (DNCThr ), and we demonstrate a significant increase in 19 F MR signal intensity when DNCThr is incubated with human α-thrombin. This proof-of-concept probe is highly versatile and can be adapted to sense ATP and kanamycin as well. Importantly, DNCThr generates a robust 19 F MRI "hot-spot" signal in response to thrombin in live mice, establishing this platform as a practical, versatile, and biologically relevant molecular imaging probe.

Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing

The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.

Modular Aptamer Switches for the Continuous Optical Detection of Small-Molecule Analytes in Complex Media

Aptamers are a promising class of affinity reagents because signal transduction mechanisms can be built into the reagent, so that they can directly produce a physically measurable output signal upon target binding. However, endowing the signal transduction functionality into an aptamer remains a trial-and-error process that can compromise its affinity or specificity and typically requires knowledge of the ligand binding domain or its structure. In this work, a design architecture that can convert an existing aptamer into a "reversible aptamer switch" whose kinetic and thermodynamic properties can be tuned without a priori knowledge of the ligand binding domain or its structure is described. Finally, by combining these aptamer switches with evanescent-field-based optical detection hardware that minimizes sample autofluorescence, this study demonstrates the first optical biosensor system that can continuously measure multiple biomarkers (dopamine and cortisol) in complex samples (artificial cerebrospinal fluid and undiluted plasma) with second and subsecond-scale time responses at physiologically relevant concentration ranges.

Recent advances in aptamer-based biosensors for potassium detection

Maintaining a stable level of potassium is crucial for proper bodily function because even a slight imbalance can result in serious disorders like hyperkalemia and hypokalemia. Therefore, detecting and monitoring potassium ion (K+) levels are of utmost importance. Various biosensors have been developed for rapid K+ detection, with aptamer-based biosensors garnering significant attention due to their high sensitivity and specificity. This review focuses on aptamer-based biosensors for K+ detection, providing an overview of their signal generation strategies, including electrochemical, field-effect transistor, nanopore, colorimetric, and fluorescent systems. The analytical performance of these biosensors is evaluated comprehensively. In addition, factors that affect their efficiency, such as their physicochemical properties, regeneration for reusability, and linkers/spacers, are listed. Lastly, this review examines the major challenges faced by aptamer-based biosensors in K+ detection and discusses potential future developments.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions

Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.

DNA-based customized functional modules for signal transformation

Information on the temporal and spatial scale of cellular molecules in biological systems is crucial for estimating life processes and may be conducive to an improved understanding of disease progression. This intracellular and extracellular information is often difficult to obtain at the same time due to the limitations of accessibility and sensing throughput. DNA is an excellent material for in vivo and in vitro applications, and can be used to build functional modules that can transform bio-information (input) into ATCG sequence information (output). Due to their small volume and highly amenable programming, DNA-based functional modules provide an opportunity to monitor a range of information, from transient molecular events to dynamic biological processes. Over the past two decades, with the advent of customized strategies, a series of functional modules based on DNA networks have been designed to gather different information about molecules, including the identity, concentration, order, duration, location, and potential interactions; the action of these modules are based on the principle of kinetics or thermodynamics. This paper summarizes the available DNA-based functional modules that can be used for biomolecular signal sensing and transformation, reviews the available designs and applications of these modules, and assesses current challenges and prospects.

Complementary DNA Significantly Enhancing Signal Response and Sensitivity of a Molecular Beacon Probe to Aflatoxin B1

This paper reported an improved molecular beacon method for the rapid detection of aflatoxin B1 (AFB1), a natural mycotoxin with severe carcinogenicity. With the assistance of a complementary DNA (cDNA) chain, the molecular beacon which consists of a DNA aptamer flanked by FAM and BHQ1 displayed a larger fluorescent response to AFB1, contributing to the sensitive detection of AFB1. Upon optimization of some key experimental factors, rapid detection of AFB1 ranging from 1 nM to 3 μM, within 20 min, was realized by using this method. A limit of detection (LoD) of 1 nM was obtained, which was lower than the LoD (8 nM) obtained without cDNA assistance. This aptamer-based molecular beacon detection method showed advantages in easy operation, rapid analysis and larger signal response. Good specificity and anti-interference ability were demonstrated. This method showed potential in real-sample analysis.

Switchable DNA Photocatalysts for Radical Polymerization Controlled by Chemical Stimuli

Polymerization catalysts that activate in response to specific chemical triggers offer spatial and temporal control over polymer synthesis, facilitating the development of responsive materials and custom polymer coatings. However, existing catalysts switch their activity through mechanisms that are not generalizable to chemically diverse stimuli. To approach the level of control exhibited in biological polymer synthesis, switchable polymerization catalysts need to be configurable for activation in response to diverse chemical stimuli. Here, we combine synthetic photocatalysts with conformation-switching DNA aptamers to create polymerization catalysts that respond to diverse chemical stimuli. We use the secondary structure of DNA to bring a photocatalyst and quencher dye into proximity, turning off photocatalysis. The DNA structure can be precisely designed to change conformation in response to a molecular trigger, moving the photocatalyst far from the quencher and activating photocatalysis. We show these photocatalysts can initiate free-radical polymerization to form bulk hydrogels in response to complementary DNA, a metal ion (Zn2+), or small molecules (glucose and hydrocortisone). We demonstrate the biocompatibility of these switchable photocatalysts by triggering their activation on the surface of yeast cells. Finally, we perform reversible-deactivation radical polymerization through photoinduced electron/energy transfer reversible addition-fragmentation chain-transfer in a dual-stimulus manner, in which catalytic activity is regulated reversibly by photoirradiation and the conformational state of the DNA catalyst. These results demonstrate that DNA conformational changes triggered by chemically diverse stimuli can regulate the activity of radical polymerization photocatalysts. This platform offers new capabilities in spatially and temporally controlled polymer synthesis, with potential applications in diagnostics, sensing, and environmentally responsive materials.

Identification and structural analysis of novel malathion-specific DNA aptameric sensors designed for food testing

Malathion is an organophosphate chemical (OPC) and a toxic contaminant that adversely impacts food quality, human health, biodiversity, and the environment. Due to its small size and unavailability of sensitive sensors, detection of malathion remains a challenging task. Often chromatographic methods employed to analyze OPCs suffer from several shortcomings, including cost, immobility, laboriousness, and unsuitability for point-of-care settings. Hence, developing a specific and sensitive diagnostic sensor for quick and inexpensive food testing is essential. We discovered four unique malathion-specific ssDNA aptamers; designed two independent sensing strategies using fluorescence labeling and Thioflavin T (ThT) displacement. Selected aptamers formed the G4-quadruplex-like (G4Q) structure, which helped develop a label-free detection approach with a 2.01 ppb limit of detection. Additionally, 3D structures of aptamers were generated and validated using a series of computational modeling programs. Furthermore, we explored structural features using CD spectroscopy and molecular docking, probing ligands' binding mode, and revealed vital intermolecular interactions with aptamers. Subsequently, the novel sensors were optimized to detect malathion from food samples. The novel sensors could be further developed to meet the demands of sensing and quantifying toxic contaminants from real food samples in field conditions.

Coacervate Formed by an ATP-Binding Aptamer and Its Dynamic Behavior under Nonequilibrium Conditions

Although numerous protocell models have been developed to explore the possible pathway of the origin of life on the early earth, few truly fulfill the roles of the DNA/RNA sequence and ATP molecules, which are keys to cell replication and evolution. The ATP-binding aptamer offers an opportunity to combine sequence and energy molecules. In this work, we choose the coacervate droplet as the protocell model and investigate the interaction of the DNA aptamer, poly(l-lysine)(PLL), and ATP under varying conditions. PLL and aptamers form solid precipitates, which spontaneously transform to coacervate droplets as ATP is introduced. The selective uptake and sequestration of exogenous molecules is achieved by the ATP-containing coacervates. As an electric field is applied to expel ATP, the portion of the droplet deficient in ATP becomes solid. The solid/liquid phase ratio is tunable by varying the electric field strength and excitation time. Together with the vacuolization process, a solid head with a soft mouth periodically opening and closing is created. Moreover, the composite coacervate droplet gradually grows as it is treated with an electric field and cannot recover to the original liquid phase after the power is turned off and replenished with ATP. Our work highlights that the proper integration of the DNA sequence, ATP, and energy input could be a powerful strategy for creating a protocell with certain living features.

Recent advances in aptamer applications for analytical biochemistry

Aptamers are typically defined as relatively short (20-60 nucleotides) single-stranded DNA or RNA molecules that bind with high affinity and specificity to various types of targets. Aptamers are frequently referred to as "synthetic antibodies" but are easier to obtain, less expensive to produce, and in several ways more versatile than antibodies. The beginnings of aptamers date back to 1990, and since then there has been a continual increase in aptamer publications. The intent of the present account was to focus on recent original research publications, i.e., those appearing in 2019 through April 2020, when this account was written. A Google Scholar search of this recent literature was performed for relevance-ranking of articles. New methods for selection of aptamers were not included. Nine categories of applications were organized and representative examples of each are given. Finally, an outlook is offered focusing on "faster, better, cheaper" application performance factors as key drivers for future innovations in aptamer applications.

Therapeutic Applications of Programmable DNA Nanostructures

Deoxyribonucleic acid (DNA) nanotechnology, a frontier in biomedical engineering, is an emerging field that has enabled the engineering of molecular-scale DNA materials with applications in biomedicine such as bioimaging, biodetection, and drug delivery over the past decades. The programmability of DNA nanostructures allows the precise engineering of DNA nanocarriers with controllable shapes, sizes, surface chemistries, and functions to deliver therapeutic and functional payloads to target cells with higher efficiency and enhanced specificity. Programmability and control over design also allow the creation of dynamic devices, such as DNA nanorobots, that can react to external stimuli and execute programmed tasks. This review focuses on the current findings and progress in the field, mainly on the employment of DNA nanostructures such as DNA origami nanorobots, DNA nanotubes, DNA tetrahedra, DNA boxes, and DNA nanoflowers in the biomedical field for therapeutic purposes. We will also discuss the fate of DNA nanostructures in living cells, the major obstacles to overcome, that is, the stability of DNA nanostructures in biomedical applications, and the opportunities for DNA nanostructure-based drug delivery in the future.

Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms

Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.

Antigen-Triggered Logic-Gating of DNA Nanodevices

Synthetic nanoscale devices that reconfigure dynamically in response to physiological stimuli could offer new avenues for diagnostics and therapy. Here, we report a strategy for controlling the state of DNA nanodevices based on sensing antigens with IgG antibodies. To this end, we use IgG antibodies as structural elements to kinetically trap reconfigurable DNA origami structures in metastable states. Addition of soluble antigens displace the IgGs from the objects and triggers reconfiguration. We demonstrate this mechanism by antigen-triggered disassembly of DNA origami shells for two different IgGs and their cognate antigens, and we determined the corresponding dose response curves. We also describe the logic-gated actuation of DNA objects with combinations of antigens, as demonstrated with AND-type shells that disassemble only when two different antigens are detected simultaneously. We apply our system for the antigen-triggered release of molecular payload as exemplified by the release of virus particles that we loaded into the DNA origami shells. We expect our approach to be applicable in many types of DNA nanostructures and with many other IgG-antigen combinations.

Aptamer Applications in Neuroscience

Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges.

Precise Microfluidic Luminescent Sensor Platform with Controlled Injection System

Efforts have been devoted to screening various prevalent diseases, such as severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19). Real-time polymerase chain reaction (RT-PCR), which is currently the most widely used, has high accuracy, but it requires several facilities and takes a relatively long time to check; so, new testing technology is necessary for a higher test efficiency. A chemiluminescence (CL) sensor is a relatively simple device and suitable as an alternative because it can detect very precise specimens. However, in measurements via CL, the quantitative formulation of reagents that cause color development is important. In the case of mixing using micropipettes, precise analysis is possible, but this technique is limited by uncontrollable errors or deviations in detection amounts. In addition, in using a microfluidic chip to increase field applicability, a syringe pump or other quantification injection tools are required, so problems must be overcome for practical use. Therefore, in this study, a microchip was designed and manufactured to supply a sample of a certain volume by simply blowing air and injecting a sample into the chamber. By utilizing the luminescence reaction of luminol, CuSO4 and H2O2 the performance of the prepared chip was confirmed, and the desired amount of the sample could be injected with a simple device with an error rate of 2% or less. For feasible applications, an experiment was performed to quantitatively analyze thrombin, a biomarker of heart disease. Results demonstrated that biomarkers could be more precisely detected using the proposed microchips than using micropipettes.

Obtaining Precise Molecular Information via DNA Nanotechnology

Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein-protein interactions, and molecular force.

Construction of Aptamer-Based Molecular Beacons with Varied Blocked Structures and Targeted Detection of Thrombin

A kind of blocked aptamer-functionalized molecular beacon (MB) was designed as fluorescence sensors to detect thrombins by binding-induced "turn on" structural transformation. Three MBs named MB(8 + 8), MB(15 + 8), and MB(15 + 6) consisted of two single-stranded oligonucleotides. One long single-stranded oligonucleotide (abbreviated as SS) contained a thrombin aptamer sequence and was modified with a fluorescence group and quenching group on each end side. Another short single-stranded oligonucleotide (written as cDNA) was partially complementary to the long SS. It was interesting to find that the complementary sequence length of cDNA greatly influenced the structure of the MBs. The construction of MB experiments proved that MB(8 + 8) and MB(15 + 8) could form the quenching MBs but MB(15 + 6) could not. MB(8 + 8) was composed of a SS strand paired with a complementary cDNA(8 + 8), which was called one-to-one combination, while MB(15 + 8) was two-to-two combination and MB(15 + 6) was one-to-two combination. When the ratio of SS and cDNA (15 + 8) was 1:1, the quenching efficiency reached maximum. But with the molar ratio of SS and cDNA(8 + 8) increasing, the quenching efficiency increased continuously. Under the optimal conditions that we studied, the detection limit of thrombin by MB(8 + 8) and MB(15 + 8) was 0.19 and 1.2 nM, respectively. In addition, the assay proved to be selective, and the average recovery of thrombin detected by MB(8 + 8) and MB(15 + 8) in diluted serum was 95.4 and 94.5%, respectively.

Recent Achievements in Electrochemical and Surface Plasmon Resonance Aptasensors for Mycotoxins Detection

Mycotoxins are secondary metabolites of fungi that contaminate agriculture products. Their release in the environment can cause severe damage to human health. Aptasensors are compact analytical devices that are intended for the fast and reliable detection of various species able to specifically interact with aptamers attached to the transducer surface. In this review, assembly of electrochemical and surface plasmon resonance (SPR) aptasensors are considered with emphasis on the mechanism of signal generation. Moreover, the properties of mycotoxins and the aptamers selected for their recognition are briefly considered. The analytical performance of biosensors developed within last three years makes it possible to determine mycotoxin residues in water and agriculture/food products on the levels below their maximal admissible concentrations. Requirements for the development of sample treatment and future trends in aptasensors are also discussed.

Recognition of nucleolin through interaction with RNA G-quadruplex

The development of novel biomarkers for early-stage diagnosis of prostate cancer (PCa) has attracted the attention of researchers in the last decade. Nucleolin (NCL) has emerged as a possible biomarker of PCa due to its high expression levels in the surface of PCa cells and affinity towards parallel G4s since it contains four RNA-binding domains (RBDs). Herein, we developed a novel strategy based on a microfluidic platform for the detection of NCL in biological samples, such as human plasma. The RNA G4 (rG4) sequence found in human precursor microRNA 92b (pre-miR-92b) was used as a molecular recognition probe since it forms a single dominant parallel rG4 conformation in the presence of 0.1 mM K+ as confirmed by NMR spectroscopy. The additional stability of the rG4 structure was provided by the acridine orange derivative ligand C8, which stabilizes the pre-miR-92b rG4 structure, as denoted by an increase in more than 30 °C of its melting temperature. FRET-melting assay revealed a remarkable synergistic effect of NCL RBD1,2 and C8 on the stabilization of the pre-miR-92b rG4. The binding of pre-miR-92b to NCL RBD1,2 was determined by in silico studies, which revealed a binding pocket formed by a 12-residue linker between RBD1 and RBD2. Both, pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex demonstrated high affinity towards NCL RBD1,2, as proved by fluorimetric titrations (KD range between 10-12 and 10-9 M). The stability and nuclease resistance of pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex were evaluated as molecular recognition probes to capture and detect NCL. Finally, the microfluidic platform detects NCL in complex biological samples, such as human plasma. Overall, this work demonstrates the usefulness of the microfluidic platform based on the pre-miR-92b to detect NCL and the possibility to be used as a valuable biomedical tool in PCa diagnosis.

Smart Nucleic Acids as Future Therapeutics

Nucleic acid therapeutics (NATs) hold promise in treating undruggable diseases and are recognized as the third major category of therapeutics in addition to small molecules and antibodies. Despite the milestones that NATs have made in clinical translation over the past decade, one important challenge pertains to increasing the specificity of this class of drugs. Activating NATs exclusively in disease-causing cells is highly desirable because it will safely broaden the application of NATs to a wider range of clinical indications. Smart NATs are triggered through a photo-uncaging reaction or a specific molecular input such as a transcript, protein, or small molecule, thus complementing the current strategy of targeting cells and tissues with receptor-specific ligands to enhance specificity. This review summarizes the programmable modalities that have been incorporated into NATs to build in responsive behaviors. We discuss the various inputs, transduction mechanisms, and output response functions that have been demonstrated to date.

Aptamer-based approaches to detect nucleolin in prostate cancer

We have investigated the expression of nucleolin (NCL) in liquid biopsies of prostate cancer (PCa) patients and healthy controls to determine its correlation with tumor prognosis. To detect NCL we used a modified AS1411 aptamer designated by AS1411-N5. In presence of NCL, AS1411-N5 increases the fluorescence by assuming a G-quadruplex (G4) structure, while in the absence of NCL the fluorescence signal remains quenched. The structural characterization of AS1411-N5 was performed by biophysical studies, which demonstrated the formation of G4 parallel conformation in the presence of 100 mM K+ and the ability to recognize NCL with high affinity (KD = 138.1 ± 5.5 nM). Furthermore, the clinical relevance of NCL in PCa liquid biopsies was assessed by using an NCL-based ELISA assay. The protein was measured in the peripheral blood mononuclear cells (PBMCs) cell lysate of 158 individuals, including PCa patients and healthy individuals. The results depicted a remarkable increase of NCL levels in the PBMC's lysate of PCa patients (mean of 626.1 pg/mL whole blood) when compared to healthy individuals (mean of 198.5 pg/mL whole blood). The ELISA results also provided evidence for the usefulness of determining NCL levels in advanced PCa stages. Furthermore, a microfluidic assay showed the ability of AS1411-N5 in recognizing NCL in spiked human plasma samples.

Aptamer-Based Detection of Circulating Targets for Precision Medicine

The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

Paper-Based Microfluidic Sensors for Onsite Environmental Detection: A Critical Review

A newly developed research topic, fabricated paper-based microfluidic sensors, was discussed in the field of low-cost environmental detection. Distinguished with the traditional dipstick or lateral-flow setups, these paper-based microfluidic sensors can serve as a tool for onsite quantitative and semi-quantitative measurements, without risks to cause environmental pollution. They have attracted increasing interest since the first easy-fabricated paper-based setup reported by Whitesides group in 2007. Most of the publications utilized paper-based sensors in clinical detection. In recent years, some groups started to use these sensors in environmental measurement, leading to precise, easy operation, low-cost, and eco-friendly methods for onsite detection. In this review, paper-based microfluidic sensors were briefly introduced, followed by literatures review and discussion for future perspectives.

Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K⁺ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.

Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems

Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based "smart materials". Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching

Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin-TBA complex. In the free GQ, T3 is solvent-exposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (K_d) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQ-folding aptamers in the absence of DNA topology switching.

Development of Specific Inhibitors for Oncogenic Phosphatase PPM1D by Using Ion-Responsive DNA Aptamer Library

(1) Background: Ser/Thr protein phosphatase PPM1D is an oncogenic protein. In normal cells, however, PPM1D plays essential roles in spermatogenesis and immune response. Hence, it is necessary to develop novel PPM1D inhibitors without side effects on normal cells. Stimuli-responsive molecules are suitable for the spatiotemporal regulation of inhibitory activity. (2) Methods: In this study, we designed an ion-responsive DNA aptamer library based on G-quadruplex DNA that can change its conformation and function in response to monovalent cations. (3) Results: Using this library, we identified the PPM1D specific inhibitor M1D-Q5F aptamer. The M1D-Q5F aptamer showed anti-cancer activity against breast cancer MCF7 cells. Interestingly, the induction of the structural change resulting in the formation of G-quadruplex upon stimulation by monovalent cations led to the enhancement of the inhibitory activity and binding affinity of M1D-Q5F. (4) Conclusions: These data suggest that the M1D-Q5F aptamer may act as a novel stimuli-responsive anti-cancer agent.

Flexible Multiplexed In2O3 Nanoribbon Aptamer-Field-Effect Transistors for Biosensing

Flexible sensors are essential for advancing implantable and wearable bioelectronics toward monitoring chemical signals within and on the body. Developing biosensors for monitoring multiple neurotransmitters in real time represents a key in vivo application that will increase understanding of information encoded in brain neurochemical fluxes. Here, arrays of devices having multiple In₂O₃ nanoribbon field-effect transistors (FETs) were fabricated on 1.4-μm-thick polyethylene terephthalate (PET) substrates using shadow mask patterning techniques. Thin PET-FET devices withstood crumpling and bending such that stable transistor performance with high mobility was maintained over >100 bending cycles. Real-time detection of the small-molecule neurotransmitters serotonin and dopamine was achieved by immobilizing recently identified high-affinity nucleic-acid aptamers on individual In₂O₃ nanoribbon devices. Limits of detection were 10 fM for serotonin and dopamine with detection ranges spanning eight orders of magnitude. Simultaneous sensing of temperature, pH, serotonin, and dopamine enabled integration of physiological and neurochemical data from individual bioelectronic devices.

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We fabricated flexible In₂O₃ nanoribbon transistors using cleanroom-free processes

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Flexible In₂O₃ transistors withstood crumpling and bending with stable performance

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Flexible aptamer biosensors detect neurotransmitters in real time

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Multiplexed sensors monitor temperature, pH, serotonin, and dopamine simultaneously

Aptamers in Diagnostic and Molecular Imaging Applications

The origin of the term diagnostic comes from the Greek word gnosis, meaning "to know." In medicine, a diagnostic can predict the pathology risk, disease status, treatment, and prognosis, even following therapy. An early and correct diagnosis is necessary for an efficient treatment. Moreover, it is possible to predict if and why a therapy will be successful or fail, enabling the timely application of alternative therapeutic strategies. Available diagnostics are due to the advances in biotechnology; however, more sensitive, low-cost, and noninvasive methodologies are still a challenge. Knowledge about molecular characteristics provide personalized information, which is the goal of future medicine. Today, multiple diagnostic techniques have emerged, with which it is possible to distinguish molecular patterns.In this way, aptamers are the perfect tools to recognize molecular targets and can be easily modified to confer additional functions. Their versatile characteristics and low cost make aptamers ideal for diagnostic applications.This chapter is a review of aptamer-based diagnostics in biomedicine, with a special focus on probe design and molecular imaging. Graphical Abstract.

Aptamer-integrated nucleic acid circuits for biosensing: Classification, challenges and perspectives

Owing to their high programmability and modularity, autonomous enzyme-free nucleic acid circuits are attracting ever-growing interest as signal amplifiers with potential applications in developing highly sensitive biosensing techniques. Besides nucleic acid input, the biosensing scope of aptamer-integrated nucleic acids could be further expanded to non-nucleic targets by integrating nucleic acid circuits with aptamers-a class of functional oligonucleotides with binding capabilities toward specific targets. By coupling upstream target recognition with downstream signal amplification, aptamer-integrated nucleic acid circuits enable aptasensors with increased sensitivity and enhanced performances, which may act as powerful tools in various fields including environment monitoring, personal care, clinical diagnosis, etc. In designing aptamer-integrated nucleic acid circuits, smart integration between aptamer and nucleic acid circuits plays a crucial role in developing reliable circuits with good performances. To date, although there are plenty of published researches adopting aptamer-integrated nucleic acid circuits as amplifiers in biosensing systems, deep discussion or systematic review on rational design strategies for aptamer-integrated nucleic acid circuits is still lacking. To fill this gap, rational aptamer-nucleic acid circuits integration modes were classified and summarized for the first time based on reviewing the state of art of existing aptamer-integrated nucleic acid circuits. Moreover, theoretical updates in nucleic acid circuits designs and major challenges to be overcome in developing highly sensitive aptamer-integrated nucleic acids based biosensing systems are discussed in this review.

Aptamers as Versatile Molecular Tools for Antibody Production Monitoring and Quality Control

Antibody drugs have been used to treat many diseases, and to date, this has been the most rapidly growing drug class. However, the lack of suitable methods for real-time and high-throughput monitoring of antibody production and quality control has been a hindrance to the further advancement of antibody drugs or biosimilars. Therefore, we herein report a versatile tool for one-step fluorescence monitoring of antibody production by using aptamer probes selected through the in vitro SELEX method. In this case, DNA aptamers were selected against the humanized IgG1 antibody drug trastuzumab with high specificity and affinity with a K_d value of aptamer CH1S-3 of 10.3 nM. More importantly, the obtained aptamers were able to distinguish native from heat-treated, whereas antibodies failed this test. On the basis of the advantages of rapid detection for aptamers, we designed aptamer molecular beacons for direct and sensitive detection of trastuzumab in complex samples. Unlike traditional antibody-based ELISA, the signal was observed directly upon interaction with the target without the need for time-consuming binding and multiple washing steps. To further highlight biomedical applications, the use of aptamers as potential tools for quality control and traceless purification of antibody drugs was also demonstrated. Thus, aptamers are shown to be promising alternatives for antibody production monitoring, quality control, and purification, providing technical support to accelerate antibody drug development.

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.

Engineering Light-Up Aptamers for the Detection of RNA Hairpins through Kissing Interaction

Aptasensors are biosensors that include aptamers for detecting a target of interest. We engineered signaling aptasensors for the detection of RNA hairpins from the previously described malachite green (MG) RNA aptamer. The top part of this imperfect hairpin aptamer was modified in such a way that it can engage loop-loop (so-called kissing) interactions with RNA hairpins displaying partly complementary apical loops. These newly derived oligonucleotides named malaswitches bind their cognate fluorogenic ligand (MG) exclusively when RNA-RNA kissing complexes are formed, whereas MG does not bind to malaswitches alone. Consequently, the formation of the ternary target RNA-malaswitch RNA-MG complex results in fluorescence emission, and malaswitches constitute sensors for detecting RNA hairpins. Malaswitches were designed that specifically detect precursors of microRNAs let7b and miR-206.

A Fluorescence Resonance Energy Transfer Probe Based on DNA-Modified Upconversion and Gold Nanoparticles for Detection of Lead Ions

We report a new sensor for the specific detection of lead ions (Pb²⁺) in contaminated water based on fluorescence resonance energy transfer (FRET) between upconversion nanoparticles (UCNPs) as donors and gold nanoparticles (Au NPs) as receptors. The UCNPs modified with Pb²⁺ aptamers could bind to Au NPs, which were functionalized with complementary DNA through hybridization. The green fluorescence of UCNPs was quenched to a maximum rate of 80% due to the close proximity between the energy donor and the acceptor. In the presence of Pb²⁺, the FRET process was broken because Pb²⁺ induced the formation of G-quadruplexes from aptamers, resulting in unwound DNA duplexes and separated acceptors from donors. The fluorescence of UCNPs was restored, and the relative intensity had a significant linear correlation with Pb²⁺ concentration from 0 to 50 nM. The sensor had a detection limit as low as 4.1 nM in a buffer solution. More importantly, the sensor exhibited specific detection of Pb²⁺ in complex metal ions, demonstrating high selectivity in practical application. The developed FRET prober may open up a new insight into the specific detection of environmental pollution.

Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors

In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.

Highly sensitive detection for cocaine using an aptamer-modified molybdenum disulfide/gold nanoparticle microarray

The detection of cocaine based on an aptamer-modified molybdenum disulfide@gold nanoparticle (MoS₂@AuNP) nanosheet array immobilized on aminated slides was achieved.

Anything You Can Do, I Can Do Better: Can Aptamers Replace Antibodies in Clinical Diagnostic Applications?

The mainstay of clinical diagnostics is the use of specialised ligands that can recognise specific biomarkers relating to pathological changes. While protein antibodies have been utilised in these assays for the last 40 years, they have proven to be unreliable due to a number of reasons. The search for the 'perfect' targeting ligand or molecular probe has been slow, though the description of chemical antibodies, also known as aptamers, nearly 30 years ago suggested a replacement reagent. However, uptake has been slow to progress into the clinical environment. In this review, we discuss the issues associated with antibodies and describe some of the applications of aptamers that have relevancy to the clinical diagnostic environment.