"Fitting" makes "sensing" simple: label-free detection strategies based on nucleic acid aptamers

The Biomedical Applications of Biomolecule Integrated Biosensors for Cell Monitoring

Cell monitoring is essential for understanding the physiological conditions and cell abnormalities induced by various stimuli, such as stress factors, microbial invasion, and diseases. Currently, various techniques for detecting cell abnormalities and metabolites originating from specific cells are employed to obtain information on cells in terms of human health. Although the states of cells have traditionally been accessed using instrument-based analysis, this has been replaced by various sensor systems equipped with new materials and technologies. Various sensor systems have been developed for monitoring cells by recognizing biological markers such as proteins on cell surfaces, components on plasma membranes, secreted metabolites, and DNA sequences. Sensor systems are classified into subclasses, such as chemical sensors and biosensors, based on the components used to recognize the targets. In this review, we aim to outline the fundamental principles of sensor systems used for monitoring cells, encompassing both biosensors and chemical sensors. Specifically, we focus on biosensing systems in terms of the types of sensing and signal-transducing elements and introduce recent advancements and applications of biosensors. Finally, we address the present challenges in biosensor systems and the prospects that should be considered to enhance biosensor performance. Although this review covers the application of biosensors for monitoring cells, we believe that it can provide valuable insights for researchers and general readers interested in the advancements of biosensing and its further applications in biomedical fields.

Excitation wavelength-dependent lanthanide-disalicylaldehyde coordination hybrid capable of distinguishing D2O from H2O

The increasing demands in fields of anti-counterfeiting, fluorescence analysis, clinical therapy and LED illumination are urgently eager for more excellent optically switchable luminescent materials with the stable and multimodal fluorescence in single-component matrix. Herein, the lanthanide-disalicylaldehyde coordination hybrid H2Qj4/TbxEuy is proposed as an efficient luminescent matrix to connect terbium sensibilization with ESIPT (excited-state intramolecular proton transfer) effects, and three multi-emission hybrids are finally designed and synthesized by regulating Tb3+ and Eu3+ ratios. Surprisingly, the H2Qj4/Tb0.91Eu0.09 shows the excitation wavelength-dependent luminescence in solution which originates from two energy transfer ways of terbium sensibilization effect. It exhibits green and red lights under the 369 and 394 nm UV lamp, respectively. Three hybrids are further used as lab-on-a-molecule fluorescent probes to perform multianalyte detection for various solvents by selected fluorescent sensing channels. By means of PCA (principal component analysis) and HCA (hierarchical cluster analysis), all of them can successfully detect and discriminate17 common solvents, especially the H2O and D2O. Moreover, the H2Qj4/Tb0.91Eu0.09 also shows the wide linear responses of H2O content in D2O, discrimination of two-component solvent mixtures, hygroscopicity evaluation of D2O and information encryption which will advance the progress of multimodal luminescent materials and multianalyte chemosensors.

Aptamer-based Upconversion Fluorescence Sensor for Doxorubicin Detection

Doxorubicin is a common chemotherapeutic drug used to treat a variety of cancers. Monitoring the concentration of doxorubicin in human biological fluids is vital for treatment. In this work, we report an aptamer-functionalized, 808 nm-excited core-shell upconversion fluorescence sensor for specific detection of doxorubicin (DOX). Upconversion nanoparticles and DOX are used as energy donors and energy acceptors respectively. Aptamers immobilized on the surface of upconversion nanoparticles act as the molecular recognition element for DOX. The binding of DOX to the immobilized aptamers results in the fluorescence quenching of the upconversion nanoparticles via a fluorescence resonance energy transfer process. The relative fluorescence intensity exhibits a good linear response to DOX concentration in the range of 0.5 μM to 55 μM with a detection limit of 0.5 μM. The aptasensor displays high specificity and anti-interference against other antibiotics, common ions, and biomolecules owing to strong and specific interactions of aptamers towards DOX. The sensor is further applied for the detection of DOX in urine with spike recoveries of nearly 100%.

Label-Free Electrochemical Methods for Disease Detection

Label-free electrochemical biosensing leverages the advantages of label-free techniques, low cost, and fewer user steps, with the sensitivity and portability of electrochemical analysis. In this review, we identify four label-free electrochemical biosensing mechanisms: (a) blocking the electrode surface, (b) allowing greater access to the electrode surface, (c) changing the intercalation or electrostatic affinity of a redox probe to a biorecognition unit, and (d) modulating ion or electron transport properties due to conformational and surface charge changes. Each mechanism is described, recent advancements are summarized, and relative advantages and disadvantages of the techniques are discussed. Furthermore, two avenues for gaining further diagnostic information from label-free electrochemical biosensors, through multiplex analysis and incorporating machine learning, are examined.

Dual targets-induced specific hemin/G-quadruplex assemblies for label-free electrochemical detection capable of distinguishing Salmonella and its common serotype in food samples

Efficient detection of pathogenic bacteria is paramount for ensuring food safety and safeguarding public health. Herein, we developed a label-free and signal-on dual-target recognition electrochemical DNA sensing platform based on the conformational formation of split G-quadruplex. This platform focused on achieving sensitive and low-cost detection of Salmonella and its most human-infecting S. typhimurium serotype. In simple terms, the dual-target recognition probe (DTR-6P) was ingeniously designed for the loop sequence on the loop-mediated isothermal amplification (LAMP) amplicons. It could recognize two different genes and release their corresponding G-rich sequences. The exfoliated G-rich sequences could be captured by the capture probes on the electrode, and then the bimolecular G-quadruplex or the tetramolecular G-quadruplex would be formed to capture hemin, thereby enabling dual-signal reporting. The minimum detection amount of target genes can be as low as 2 copies/μL. Encouragingly, the real food samples contaminated by Salmonella and the S. typhimurium serotype can be readily identified. The sensing platform with ingenious design paves a new way for label-free, multi-target simultaneous detection, whose advantage of rapidity, sensitivity, cost-effectiveness, and specificity also lay a solid foundation for practical applications.

A modular aldol approach for internal fluorescent molecular rotor chalcone surrogates for DNA biosensing applications

Fluorescent molecular rotors (FMRs) are critical tools for probing nucleic acid structure and function. Many valuable FMRs have been incorporated into oligonucleotides, although the methods of doing so can be cumbersome. Development of synthetically simple, high yielding modular methods to fine-tune dye performance is crucial to expand the biotechnological applications of oligonucleotides. Herein, we report the utility of 6-hydroxy-indanone (6HI) with a glycol backbone to serve as a handle for on-strand aldehyde capture as a modular aldol approach for site-specific insertion of internal FMR chalcones. Aldol reactions with aromatic aldehydes containing N-donors proceed in high yield to create modified DNA oligonucleotides, which in the duplex match the stability of the fully paired canonical B-form with strong stacking interactions between the planar probe and the flanking base pairs, as evidenced by molecular dynamics (MD) simulations. The FMR chalcones possess remarkable quantum yields (Φ_fl up to 76%) in duplex DNA, coupled with large Stokes shifts (Δν up to 155 nm), light-up emissions (I_rel up to 60-fold) that span the visible region (λ_em 518-680 nm) with brightness up to 17 480 cm^-1 M^-1. The library also contains a FRET pair and dual emission probes, suitable for ratiometric sensing. The ease of aldol insertion coupled with the excellent performance of the FMR chalcones permits their future wide-spread use.

A turn-on unlabeled colorimetric biosensor based on aptamer-AuNPs conjugates for amyloid-β oligomer detection

Amyloid-β oligomers (AβO) have been identified as core biomarkers for early diagnosis of Alzheimer's disease (AD). For the first time, a "turn-on" unlabeled colorimetric aptasensor based on aptamer-polythymine (polyT)-polyadenine (polyA)-gold nanoparticles (pA-pT-apt@AuNPs) was developed for highly sensitive and specific detection of amyloid-β_1-40 oligomers (Aβ40-O). In this system, polyA sequence could preferentially anchor onto AuNPs surface as well as reduce the non-specific adsorption, and the aptamer could form upright conformation for the specific recognition of Aβ40-O. The aggregation of pA-pT-apt@AuNPs was induced by MgCl₂. However, the addition of Aβ40-O enabled the aptamer fold adaptively upon recognition and aptamer-Aβ40-O complex formed surrounding AuNPs, effectively stabilizing pA-pT-apt@AuNPs against salt-induced aggregation, therefore the color of pA-pT-apt@AuNPs solution still retained red. Based on this principle, the proposed aptasensor exhibited high sensitivity with the limit of detection of 3.03 nM and a linear detectable range from 10.00 nM to 100.0 nM. The superb sensitivity was achieved via the optimization of the length of polyA and polyT spacer. This pA-pT-apt@AuNPs based colorimetric aptasensor provides a rapid, cost-effective, highly sensitive detection method for Aβ40-O, which is valuable for the early diagnosis of AD.

Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates

As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.

Activatable G-quadruplex based catalases for signal transduction in biosensing

Discovery of oxidative catalysis with G-quadruplex•hemin constructs prompted a range of exciting developments in the field of biosensor design. Thus, G-quadruplex based DNAzymes with peroxidase activity found a niche as signal transduction modules in a wide range of analytical applications. The ability of nucleic acid scaffolds to recognise a variety of practically meaningful markers and to translate the recognition events into conformational changes powers numerous sensor design possibilities. In this work, we establish a catalase activity of G-quadruplex•hemin scaffolds. Catalase activated hydrogen peroxide decomposition generates molecular oxygen that forms bubbles. Observation of bubbles is a truly equipment free signal readout platform that is highly desirable in limited resources or do-it-yourself environments. We take a preliminary insight into a G-quadruplex structure-folding topology-catalase activity correlation and establish efficient operating conditions. Further, we demonstrate the platform's potential as a signal transduction modality for reporting on biomolecular recognition using an oligonucleotide as a proof-of-concept target. Ultimately, activatable catalases based on G-quadruplex•hemin scaffolds promise to become valuable contributors towards accessible molecular diagnostics applications.

Overcoming Major Barriers to Developing Successful Sensors for Practical Applications Using Functional Nucleic Acids

For many years, numerous efforts have been focused on the development of sensitive, selective, and practical sensors for environmental monitoring, food safety, and medical diagnostic applications. However, the transition from innovative research to commercial success is relatively sparse. In this review, we identify four scientific barriers and one technical barrier to developing successful sensors for practical applications, including the lack of general methods to (a) generate receptors for a wide range of targets, (b) improve sensor selectivity to overcome interferences, (c) transduce the selective binding to different optical, electrochemical, and other signals, and (d) tune dynamic range to match thresholds of detection required for different targets; and the costly development of a new device. We then summarize solutions to overcome these barriers using sensors based on functional nucleic acids that include DNAzymes, aptamers, and aptazymes and how these sensors are coupled to widely available measurement devices to expand their capabilities and lower the barrier for their practical applications in the field and point-of-care settings.

Recent Progress on Highly Selective and Sensitive Electrochemical Aptamer-based Sensors

Highly selective, sensitive, and stable biosensors are essential for the molecular level understanding of many physiological activities and diseases. Electrochemical aptamer-based (E-AB) sensor is an appealing platform for measurement in biological system, attributing to the combined advantages of high selectivity of the aptamer and high sensitivity of electrochemical analysis. This review summarizes the latest development of E-AB sensors, focuses on the modification strategies used in the fabrication of sensors and the sensing strategies for analytes of different sizes in biological system, and then looks forward to the challenges and prospects of the future development of electrochemical aptamer-based sensors.

Magnetic Fluorescent Quantum Dots Nanocomposites in Food Contaminants Analysis: Current Challenges and Opportunities

The presence of food contaminants can cause foodborne illnesses, posing a severe threat to human health. Therefore, a rapid, sensitive, and convenient method for monitoring food contaminants is eagerly needed. The complex matrix interferences of food samples and poor performance of existing sensing probes bring significant challenges to improving detection performances. Nanocomposites with multifunctional features provide a solution to these problems. The combination of the superior characteristics of magnetic nanoparticles (MNPs) and quantum dots (QDs) to fabricate magnetic fluorescent quantum dots (MNPs@QDs) nanocomposites are regarded as an ideal multifunctional probe for food contaminants analysis. The high-efficiency pretreatment and rapid fluorescence detection are concurrently integrated into one sensing platform using MNPs@QDs nanocomposites. In this review, the contemporary synthetic strategies to fabricate MNPs@QDs, including hetero-crystalline growth, template embedding, layer-by-layer assembly, microemulsion technique, and one-pot method, are described in detail, and their advantages and limitations are discussed. The recent advances of MNPs@QDs nanocomposites in detecting metal ions, foodborne pathogens, toxins, pesticides, antibiotics, and illegal additives are comprehensively introduced from the perspectives of modes and detection performances. The review ends with current challenges and opportunities in practical applications and prospects in food contaminants analysis, aiming to promote the enthusiasm for multifunctional sensing platform research.

Construction and bioapplications of aptamer-based dual recognition strategy

Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.

Targeted extracellular vesicle delivery systems employing superparamagnetic iron oxide nanoparticles

In the past decade, the study of extracellular vesicles (EVs), especially exosomes (50-150 nm) have attracted growing interest in numerous areas of cancer and tissue regeneration due to their unique biological features. A low isolation yield and insufficient targeting abilities limit their therapeutic applicability. Recently, superparamagnetic iron oxide nanoparticles (SPIONs) with magnetic navigation have been exploited to enhance the targeting ability of EVs. To construct targeted EV delivery systems engineered by SPIONs, several groups have pioneered the use of different techniques, such as electroporation, natural incubation, and cell extrusion, to directly internalize SPIONs into EVs. Furthermore, some endogenous ligands, such as transferrins, antibodies, aptamers, and streptavidin, were shown to enable modification of SPIONs, which increases binding with EVs. In this review, we summarized recent advances in targeted EV delivery systems engineered by SPIONs and focused on the key methodological approaches and the current applications of magnetic EVs. This report aims to address the existing challenges and provide comprehensive insights into targeted EV delivery systems. STATEMENT OF SIGNIFICANCE: Targeted extracellular vesicle (EV) delivery systems engineered by superparamagnetic iron oxide nanoparticles (SPIONs) have attracted wide attention and research interest in recent years. Such strategies employ external magnet fields to manipulate SPION-functionalized EVs remotely, aiming to enhance their accumulation and penetration in vivo. Although iron oxide nanoparticle laden EVs are interesting, they are controversial at present, hampering the progress in their clinical application. A thorough integration of these studies is needed for an advanced insight and rational design of targeted EV delivery systems. In this review, we summarize the latest advances in the design strategies of targeted EV delivery systems engineered by SPIONs with a focus on their key methodological approaches, current applications, limitation and future perspectives, which may facilitate the development of natural theranostic nanoplatforms.

Sandwich electrochemical carcinoembryonic antigen aptasensor based on signal amplification of polydopamine functionalized graphene conjugate Pd-Pt nanodendrites

Carcinoembryonic antigen (CEA) is considered as a disease biomarker, which is related to various cancers and tumors in the human bodies. Sensitive detection of CEA is significant for clinical diagnosis and treatment. Herein, we proposed an electrochemical aptasensor for CEA detection based on the amplification driven by polydopamine functional graphene and Pd-Pt nanodendrites (PDA@Gr/Pd-PtNDs), conjugated hemin/G-quadruplex (hemin/G4), which possess mimicking peroxidases activity. Firstly, PDA@Gr was modified on the electrode surface for fixing CEA aptamer 1 (Apt1). Then, PDA@Gr/Pd-PtNDs with large surface area served as matrix for immobilization of hemin/G4 to obtain the secondary aptamer. In virtue of the sandwich-type specific reaction between CEA and the corresponding aptamers, the second aptamer was captured on the sensing interface, which can catalyze the oxidation of signal probe hydroquinone (HQ) with H₂O₂ and amplify current signal. Furthermore, the electrochemical signals of HQ were proportional with CEA concentrations. Under the optimal conditions, a dynamic response range from 50 pg/mL to 1.0 μg/mL and a detection limit of 6.3 pg/mL for CEA were obtained. Moreover, the proposed strategy represented satisfactory sensitivity and stability, and showed a good precision in real samples application.

Ratiometric G-Quadruplex Assay for Robust Lead Detection in Food Samples

Lead (Pb²⁺) pollution is a serious food safety issue, rapid detection of Pb²⁺ residual in food is vital to guarantee food quality and safety. Here we proposed ratiometric aptamer probes, allowing robust Pb²⁺ supervision in food samples. Pb²⁺ specific aptamer can bolster a transition of G-quadruplex structural response to Pb²⁺; this process can be monitored by N-methyl mesoporphyrin IX (NMM), which is highly specific to G-quadruplex. Particularly, the utilization of G-quadruplex specific dye and terminal-labeled fluorophore allowed to endue ratiometric signal outputs towards Pb²⁺, dramatically increase the robustness for lead detection. The ratiometric G-quadruplex assay allowed a facile and one-pot Pb²⁺ detection at room temperature using a single-stranded DNA aptamer. We demonstrated its feasibility for detecting lead pollution in fresh eggs and tap water samples. The ratiometric G-quadruplex design is expected to be used for on-site Pb²⁺ testing associated with food safety.

Aptamer-Modified Cu2+-Functionalized C-Dots: Versatile Means to Improve Nanozyme Activities-"Aptananozymes"

The covalent linkage of aptamer binding sites to nanoparticle nanozymes is introduced as a versatile method to improve the catalytic activity of nanozymes by concentrating the reaction substrates at the catalytic nanozyme core, thereby emulating the binding and catalytic active-site functions of native enzymes. The concept is exemplified with the synthesis of Cu²⁺ ion-functionalized carbon dots (C-dots), modified with the dopamine binding aptamer (DBA) or the tyrosinamide binding aptamer (TBA), for the catalyzed oxidation of dopamine to aminochrome by H₂O₂ or the oxygenation of l-tyrosinamide to the catechol product, which is subsequently oxidized to amidodopachrome, in the presence of H₂O₂/ascorbate mixture. Sets of structurally functionalized DBA-modified Cu²⁺ ion-functionalized C-dots or sets of structurally functionalized TBA-modified Cu²⁺ ion-functionalized C-dots are introduced as nanozymes of superior catalytic activities (aptananozymes) toward the oxidation of dopamine or the oxygenation of l-tyrosinamide, respectively. The aptananozymes reveal enhanced catalytic activities as compared to the separated catalyst and respective aptamer constituents. The catalytic functions of the aptananozymes are controlled by the structure of the aptamer units linked to the Cu²⁺ ion-functionalized C-dots. In addition, the aptananozyme shows chiroselective catalytic functions demonstrated by the chiroselective-catalyzed oxidation of l/d-DOPA to l/d-dopachrome. Binding studies of the substrates to the different aptananozymes and mechanistic studies associated with the catalytic transformations are discussed.

Label-Free Creatinine Optical Sensing Using Molecularly Imprinted Titanium Dioxide-Polycarboxylic Acid Hybrid Thin Films: A Preliminary Study for Urine Sample Analysis

Creatinine (CR) is a representative metabolic byproduct of muscles, and its sensitive and selective detection has become critical in the diagnosis of kidney diseases. In this study, poly(acrylic acid) (PAA)-assisted molecularly imprinted (MI) TiO2 nanothin films fabricated via liquid phase deposition (LPD) were employed for CR detection. The molecular recognition properties of the fabricated films were evaluated using fiber optic long period grating (LPG) and quartz crystal microbalance sensors. Imprinting effects were examined compared with nonimprinted (NI) pure TiO2 and PAA-assisted TiO2 films fabricated similarly without a template. In addition, the surface modification of the optical fiber section containing the LPG with a mesoporous base coating of silica nanoparticles, which was conducted before LPD-based TiO2 film deposition, contributed to the improvement of the sensitivity of the MI LPG sensor. The sensitivity and selectivity of LPGs coated with MI films were tested using CR solutions dissolved in different pH waters and artificial urine (near pH 7). The CR binding constants of the MI and NI films, which were calculated from the Benesi–Hildebrand plots of the wavelength shifts of the second LPG band recorded in water at pH 4.6, were estimated to be 67 and 7.8 M–1, respectively, showing an almost ninefold higher sensitivity in the MI film. The mechanism of the interaction between the template and the TiO2 matrix and the film composition was investigated via ultraviolet–visible and attenuated total reflectance Fourier-transform infrared spectroscopy along with X-ray photoelectron spectroscopy analysis. In addition, morphological studies using a scanning electron microscope and atomic force microscope were conducted. The proposed system has the potential for practical use to determine CR levels in urine samples. This LPG-based label-free CR biosensor is innovative and expected to be a new tool to identify complex biomolecules in terms of its easy fabrication and simplicity in methodology.

MXene and black phosphorus based 2D nanomaterials in bioimaging and biosensing: progress and perspectives

Bioimaging and biosensing have garnered interest in early cancer diagnosis due to the ability of gaining in-depth insights into cellular functions and providing a wide range of diagnostic parameters. Emerging 2D materials of multielement MXenes and monoelement black phosphorous nanosheets (BPNSs) with unique intrinsic physicochemical properties such as a tunable bandgap and layer-dependent fluorescence, high carrier mobility and transport anisotropy, efficient fluorescence quenching capability, desirable light absorption and thermoelastic properties, and excellent biocompatibility and biosafety properties provide promising nano-platforms for bioimaging and biosensing applications. In view of the growing attention on the rising stars of the post-graphene age in the progress of bioimaging and biosensing, and their common feature characteristics as well as complementarity for constructing complexes, the main objective of this review is to reveal the recent advances in the design of MXene or BPNS based nanoplatforms in the field of bioimaging and biosensing. The preparation and surface functionalization methods, biosafety, and other important aspects of bioimaging and biosensing applications of MXenes and BPNSs have been assessed systematically, along with highlighting the main challenges in further biomedical application. The review not only focuses on the advancements in 2D materials for use in bioimaging and biosensing but also assesses the possibility of their future potential in bioapplications.

A Comprehensive Study on Aptasensors For Cancer Diagnosis

Cancer is the most devastating disease in the present scenario, killing millions of people every year. Early detection, accurate diagnosis, and timely treatment are considered to be the most effective ways to control this disease. Rapid and efficient detection of cancer at their earliest stage is one of the most significant challenges in cancer detection and cure. Numerous diagnostic modules have been developed to detect cancer cells early. As nucleic acid equivalent to antibodies, aptamers emerge as a new class of molecular probes that can identify cancer-related biomarkers or circulating rare cancer/ tumor cells with very high specificity and sensitivity. The amalgamation of aptamers with the biosensing platforms gave birth to "Aptasensors." The advent of highly sensitive aptasensors has opened up many new promising point-of-care diagnostics for cancer. This comprehensive review focuses on the newly developed aptasensors for cancer diagnostics.

Photoelectrochemical detection for 3,3',4,4'-tetrachlorobiphenyl in fish based on synergistic effects by Schottky junction and sensitization

In this study, a novel signal amplification strategy on photoelectrochemical (PEC) aptasensor was designed for high-sensitivity and -selectivity detection of 3,3',4,4'-tetrachlorobiphenyl (PCB77) on the basis of Schottky junction and sensitization. First, the Schottky barrier not only provided an electron-transfer irreversible passage from CuO to Au Nanoparticles (NPs) but also generated excellent local surface plasmon resonance between CuO and Au NPs, thus improving the efficiency of charge separation and light absorption. Second, to further improve the response of the PEC aptasensor under the action of the sensitization, the complementary-DNA-functionalized CdS quantum dots were introduced onto the surface of CuO/Au NPs via hybridization of the target aptamer. The PEC aptasensor exhibited a low detection limit of 17.3 pg L^-1, and a wide linear response was shown at a range of 0.2-220 ng L^-1 depending on the variation of photocurrent before and after incubation.

A label-free fluorescent biosensor based on a catalyzed hairpin assembly for HIV DNA and lead detection

Herein, a label-free fluorescent signal amplification system based on a catalyzed hairpin assembly (CHA) is reported. In this system, two hairpin probes, H1 and H2, were well-designed in which G-quadruplex sequences were integrated into H2. The CHA reaction was triggered by target/trigger DNA and G-quadruplex sequences were released, which can bind the fluorescent amyloid dye thioflavin T (ThT) to provide fluorescence signals. At the same time, target/trigger DNA was released from the product of the CHA reaction (H1-H2), which continued to initiate the next CHA cycle, and the signal was eventually amplified. This signal amplification approach has been successfully used to develop a label-free fluorescent sensing platform for sensitive detection of human immunodeficiency virus (HIV) DNA and Pb²⁺.

Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells

RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn²⁺-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.

Recent progress in fluorescent probes for bacteria

Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.

Mimicking Functions of Native Enzymes or Photosynthetic Reaction Centers by Nucleoapzymes and Photonucleoapzymes

The covalent linkage of catalytic units to aptamer sequence-specific nucleic acids exhibiting selective binding affinities for substrates leads to functional scaffolds mimicking native enzymes, nucleoapzymes. The binding of the substrates to the aptamer and their structural orientation with respect to the catalytic units duplicate the functions of the active center of enzymes. The possibility of linking the catalytic sites directly, or through spacer units, to the 5'-end, 3'-end, and middle positions of the aptamers allows the design of nucleoapzyme libraries, revealing structure-functions diversities, and these can be modeled by molecular dynamics simulations. Catalytic sites integrated into nucleoapzymes include DNAzymes, transition metal complexes, and organic ligands. Catalytic transformations driven by nucleoapzymes are exemplified by the oxidation of dopamine or l-arginine, hydroxylation of tyrosine to l-DOPA, hydrolysis of ATP, and cholic acid-modified esters. The covalent linkage of photosensitizers to the tyrosinamide aptamer leads to a photonucleoapzyme scaffold that binds the N-methyl-N'-(3-aminopropane)-4,4'-bipyridinium-functionalized tyrosinamide to the aptamer. By linking the photosensitizer directly, or through a spacer bridge to the 5'-end or 3'-end of the aptamer, we demonstrate a library of supramolecular photosensitizer/electron acceptor photonucleoapzymes mimicking the functions of photosystem I in the photosynthetic apparatus. The photonucleoapzymes catalyze the photoinduced generation of NADPH, in the presence of ferredoxin-NADP+-reductase (FNR), or the photoinduced H2 evolution catalyzed by Pt nanoparticles. The future prospects of nucleoapzymes and photonucleoapzymes are discussed.

Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing

Light-up DNA aptamers are promising label-free signal-transducers for biosensing applications due to their high chemical stability and low synthetic cost. Herein, we demonstrate that a dapoxyl DNA aptamer DAP-10-42 can be converted into a sensor generating a fluorescence signal at different wavelengths in the range of 500-660 nm depending on the dye that is present. This results from the discovered promiscuity of DAP-10-42 in binding fluorogenic dyes including arylmethane dyes. We have designed a split DAP-10-42 aptasensor for the detection of a katG gene fragment from Mycobacterium tuberculosis with a point mutation causing isoniazid resistance. Efficient interrogation of the gene fragment after nucleic acid sequence-based amplification (NASBA) is achieved directly in a protein-containing NASBA sample. This report lays a foundation for the application of the DAP-10-42 aptamer as a versatile sensing platform.

Nanoscale Affinity Double Layer Overcomes the Poor Antimatrix Interference Capability of Aptamers

Poor antimatrix interference capability of aptamers is one of the major obstacles preventing their wide applications for real-sample detections. Here, we devise a multiple-function interface, denoted as a nanoscale affinity double layer (NADL), to overcome this bottleneck via in situ simultaneous target enrichment, purification, and detection. The NADL consists of an upper aptamer layer for target purification and sensing and a lower nanoscale solid-phase microextraction (SPME) layer for sample enrichment. The targets flowing through the NADL-functionalized surface are instantly million-fold enriched and purified by the sequential extraction of aptamer and SPME. The formation of the aptamer-target complex is greatly enhanced, enabling ultrasensitive detection of targets with minimized interference from the matrix. Taking the fiber-optic evanescent wave sensor as an example, we demonstrated the feasibility and generality of the NADL. The unprecedented detection of limits of 800, 4.8, 40, and 0.14 fM were, respectively, achieved for three representative small-molecule targets with distinct hydrophobicity (kanamycin A, sulfadimethoxine, and di-(2-ethylhexyl) phthalate) and protein target (human serum albumin), corresponding to 2500 to 3 × 10⁸-fold improvement compared to the sensors without the NADL. Our sensors also showed exceptionally high target specificity (>1000) and tunable dynamic ranges simply by manipulating the SPME layer. With these features comes the ability to directly detect targets in diluted environmental, food, and biological samples at concentrations all well below the tolerance limits.

Low-Noise Solid-State Nanopore Enhancing Direct Label-Free Analysis for Small Dimensional Assemblies Induced by Specific Molecular Binding

Solid-state nanopores show special potential as a new single-molecular characterization for nucleic acid assemblies and molecular machines. However, direct recognition of small dimensional species is still quite difficult due the lower resolution compared with biological pores. We recently reported a very efficient noise-reduction and resolution-enhancement mechanism via introducing high-dielectric additives (e.g., formamide) into conical glass nanopore (CGN) test buffer. Based on this advance, here, for the first time, we apply a bare CGN to directly recognize small dimensional assemblies induced by small molecules. Cocaine and its split aptamer (Capt assembly) are chosen as the model set. By introducing 20% formamide into CGN test buffer, high cocaine-specific distinguishing of the 113 nt Capt assembly has been realized without any covalent label or additional signaling strategies. The signal-to-background discrimination is much enhanced compared with control characterizations such as gel electrophoresis and fluorescence resonance energy transfer (FRET). As a further innovation, we verify that low-noise CGN can also enhance the resolution of small conformational/size changes happening on the side chain of large dimensional substrates. Long duplex concatamers generated from the hybridization chain reaction (HCR) are selected as the model substrates. In the presence of cocaine, low-noise CGN has sensitively captured the current changes when the 26 nt aptamer segment is assembled on the side chain of HCR duplexes. This paper proves that the introduction of the low-noise mechanism has significantly improved the resolution of the solid-state nanopore at smaller and finer scales and thus may direct extensive and deeper research in the field of CGN-based analysis at both single-molecular and statistical levels, such as molecular recognition, assembly characterization, structure identification, information storage, and target index.

Functional Aptamer-Embedded Nanomaterials for Diagnostics and Therapeutics

In the past decades, various nanomaterials with unique properties have been explored for bioapplications. Meanwhile, aptamers, generated from the systematic evolution of ligands by exponential enrichment technology, are becoming an indispensable element in the design of functional nanomaterials because of their small size, high stability, and convenient modification, especially endowing nanomaterials with recognition capability to specific targets. Therefore, the incorporation of aptamers into nanomaterials offers an unprecedented opportunity in the research fields of diagnostics and therapeutics. Here, we focus on recent advances in aptamer-embedded nanomaterials for bioapplications. First, we briefly introduce the properties of nanomaterials that can be functionalized with aptamers. Then, the applications of aptamer-embedded nanomaterials in cellular analysis, imaging, targeted drug delivery, gene editing, and cancer diagnosis/therapy are discussed. Finally, we provide some perspectives on the challenges and opportunities that have arisen from this promising area.

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

Aptamer-based approaches for the detection of waterborne pathogens

Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.

Ratiometric fluorescent sensing of the parallel G-quadruplex produced by PS2.M: implications for K+ detection

Fluorescent ligands that selectively bind to a specific G-quadruplex (GQ) topology (antiparallel, hybrid or parallel) are highly sought after for aptasensor development and nanodevice construction. The coumarin-benzothiazole hybrid (BnBtC) is an internal charge transfer (ICT) ratiometric fluorescent probe, which displays two well-resolved emission bands at ∼450 nm for the coumarin component and ∼650 nm for the ICT band. The red ICT emission of BnBtC displays turn-on responses to protic solvent polarity and upon binding GQ structures, especially those produced by the hemin binding aptamer (PS2.M). In the present work, BnBtC was found to exhibit enhanced ICT emission upon binding the parallel GQ topology of PS2.M that is selectively produced in the presence of K+. This ability to discriminate K+ from other cationic metal ions through a turn-on ratiometric fluorescent response demonstrates the potential utility of the BnBtC probe for biosensor applications.

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.

Nanomaterial-based aptamer sensors for analysis of illicit drugs and evaluation of drugs consumption for wastewater-based epidemiology

The abuse of illicit drugs usually associated with dramatic crimes may cause significant problems for the whole society. Wastewater-based epidemiology (WBE) has been demonstrated to be a novel and cost-effective way to evaluate the abuse of illicit drugs at the community level, and has been used as a routine method for monitoring and played a significant role for combating the crimes in some countries, e.g. China. The method can also provide temporal and spatial variation of drugs of abuse. The detection methods mainly remain on the conventional liquid chromatography coupled with mass spectrometry, which is extremely sensitive and selective, however needs advanced facility and well-trained personals, thus limit it in the lab. As an alternative, sensors have emerged to be a powerful analytical tool for a wide spectrum of analytes, in particular aptamer sensors (aptasensors) have attracted increasing attention and could act as an efficient tool in this field due to the excellent characteristics of selectivity, sensitivity, low cost, miniaturization, easy-to-use, and automation. In this review, we will briefly introduce the context, specific assessment process and applications of WBE and the recent progress of illicit drug aptasensors, in particular focusing on optical and electrochemical sensors. We then highlight several recent aptasensors for illicit drugs in new technology integration and discuss the feasibility of these aptasensor for WBE. We will summarize the challenges and propose our insights and opportunity on aptasensor for WBE to evaluate community-wide drug use trends and public health.

Stimuli-Responsive Biomolecule-Based Hydrogels and Their Applications

This Review presents polysaccharides, oligosaccharides, nucleic acids, peptides, and proteins as functional stimuli-responsive polymer scaffolds that yield hydrogels with controlled stiffness. Different physical or chemical triggers can be used to structurally reconfigure the crosslinking units and control the stiffness of the hydrogels. The integration of stimuli-responsive supramolecular complexes and stimuli-responsive biomolecular units as crosslinkers leads to hybrid hydrogels undergoing reversible triggered transitions across different stiffness states. Different applications of stimuli-responsive biomolecule-based hydrogels are discussed. The assembly of stimuli-responsive biomolecule-based hydrogel films on surfaces and their applications are discussed. The coating of drug-loaded nanoparticles with stimuli-responsive hydrogels for controlled drug release is also presented.

Intrinsic "Turn-On" Aptasensor Detection of Ochratoxin A Using Energy-Transfer Fluorescence

Ochratoxin A (OTA) is an intrinsically fluorescent phenolic mycotoxin that contaminates a wide range of food products and is a serious health threat to animals and humans. An OTA binding aptamer (OTABA) that folds into an antiparallel G-quadruplex (GQ) in the absence and presence of target OTA has been incorporated into a vast variety of aptasensor platforms for OTA detection. The development of a simple, aptamer-based approach would allow for detection of the toxin without the use of complex analytical instrumentation, which has been the gold standard for OTA detection thus far. However, to date, none of the aptasensor platforms have utilized the natural fluorescence of the phenolic toxin for detection. Herein, we report that OTA binding to OTABA involves π-stacking interactions that lead to GQ-to-toxin energy transfer (ET), which affords a "turn-on" fluorescence self-signaling platform in which the emission of the aptamer-target complex is enhanced in comparison to the free toxin alone. Selective excitation of the GQ-OTA complex at 256 nm leads to a 4-fold enhancement in OTA fluorescence. The GQ-OTA ET detection platform boasts a limit of detection ∼2 ng/mL, which is comparable to a previously demonstrated fluorescence resonance energy transfer immunoassay platform for OTA detection, and displays excellent OTA selectivity and recovery from red wine samples.

Nucleoapzymes: catalyst-aptamer conjugates as enzyme-mimicking structures

The conjugation of catalytic sites to sequence-specific, ligand-binding nucleic acid aptamers yields functional catalytic ensembles mimicking the catalytic/binding properties of native enzymes. These catalyst-aptamer conjugates termed 'nucleoapzymes' reveal structural diversity, and thus, vary in their catalytic activity, due to the different modes of conjugation of the catalytic units to the nucleic acid aptamer scaffold. The concept of nucleoapzymes is introduced with the assembly of a set of catalysts consisting of the hemin/G-quadruplex DNAzyme (hGQ) conjugated to the dopamine aptamer. The nucleoapzymes catalyze the oxidation of dopamine by H2O2 to yield aminochrome. The catalytic processes are controlled by the structures of the nucleoapzymes, and chiroselective oxidation of l-DOPA and d-DOPA by the nucleoapzymes is demonstrated. In addition, the conjugation of a Fe(III)-terpyridine complex to the dopamine aptamer and of a bis-Zn(II)-pyridyl-salen-type complex to the ATP-aptamer yields hybrid nucleoapzymes (conjugates where the catalytic site is not a biomolecule) that catalyze the oxidation of dopamine to aminochrome by H2O2 and the hydrolysis of ATP to ADP, respectively. Variable, structure-controlled catalytic activities of the different nucleoapzymes are demonstrated. Molecular dynamic simulations are applied to rationalize the structure-catalytic function relationships of the different nucleoapzymes. The challenges and perspectives of the research field are discussed.

Ligand-Induced G-Quadruplex Polymorphism: A DNA Nanodevice for Label-Free Aptasensor Platforms

G-Quadruplexes (GQs) serve as popular recognition elements for DNA aptasensors and are incorporated into a DNA nanodevice capable of controlled conformational changes to activate a sensing mechanism. Herein we highlight the utility of a GQ-GQ nanodevice fueled by GQ-specific ligands as a label-free aptasensor detection strategy. The concept was first illustrated utilizing the prototypical polymorphic human telomeric repeat sequence (H-Telo22, d[AG3(T2AG3)3]) that can undergo ligand-induced topology changes between antiparallel, parallel, or hybrid GQ structures. The H-Telo22-ligand interactions served as a model of the GQ-GQ nanodevice. The utility of the device in a real aptasensor platform was then highlighted utilizing the ochratoxin A (OTA) binding aptamer (OTABA) that folds into an antiparallel GQ in the absence and presence of target OTA. Three cationic fluorogenic ligands served as GQ-specific light-up probes and as potential fuel for the GQ-GQ nanodevice by producing an inactive GQ topology (parallel or hybrid) of OTABA. Our findings demonstrate efficient OTA-mediated dye displacement with excellent emission sensitivity for OTA detection when the fluorogenic dyes induce a topology change in OTABA (parallel or hybrid). However, when the fluorogenic dye fails to induce a conformational change in the antiparallel fold of OTABA, subsequent additions of OTA to the aptamer-dye complex results in poor dye displacement with weak emission response for OTA detection. These results are the first to exemplify a ligand-induced GQ-GQ nanodevice as an aptasensor mechanism and demonstrate diagnostic applications for topology-specific GQ binders.

Electrochromic, Closed-Bipolar Electrodes Employing Aptamer-Based Recognition for Direct Colorimetric Sensing Visualization

In this paper, we adapt the electrochemical, aptamer-based (E-AB) sensor platform to develop colorimetric aptamer-based sensors using a closed-bipolar electrode (C-BPE) system. The C-BPE E-AB sensors provide quantitative detection of target molecules based on the rate of color change of an electrochromic Prussian blue (PB) thin-film indicator electrode. The C-BPE cathode, or sensing electrode, is modified with a redox-labeled aptamer that binds to a specific target. More specifically, we employed sequences specific for adenosine triphosphate (ATP) and tobramycin as test-bed targets because these sequences are well vetted. The C-BPE anode, or indicator electrode, was coated with an electrochromic thin film comprising Prussian white (PW) that, when reduced to PB, is accompanied by a corresponding color change used for analytical detection. The rate of color change from PW to PB is facilitated by a potassium ferricyanide-catalyzed oxidation of leucomethylene blue (LB) to methylene blue (MB), the redox label conjugated to the aptamer on the sensing electrode. We demonstrate that the rate of color change is quantitatively related to the concentration of target analyte, which provides a means for naked eye determination. When combined with smartphone-based colorimetric detection, these C-BPE E-AB sensors present a user-friendly alternative to traditional E-AB sensors that rely on voltammetric analysis and a potentiostat, opening up the possibility of point-of-use applications.