Retention of function in the DNA homolog of the RNA dopamine aptamer

Nanoplasmonic aptasensor for sensitive, selective, and real-time detection of dopamine from unprocessed whole blood

Neurotransmitters are crucial for the proper functioning of neural systems, with dopamine playing a pivotal role in cognition, emotions, and motor control. Dysregulated dopamine levels are linked to various disorders, underscoring the need for accurate detection in research and diagnostics. Single-stranded DNA (ssDNA) aptamers are promising bioreceptors for dopamine detection due to their selectivity, improved stability, and synthesis feasibility. However, discrepancies in dopamine specificity have presented challenges. Here, we surface-functionalized a nano-plasmonic biosensing platform with a dopamine-specific ssDNA aptamer for selective detection. The biosensor, featuring narrowband hybrid plasmonic resonances, achieves high specificity through functionalization with aptamers and passivation processes. Sensitivity and selectivity for dopamine detection are demonstrated across a wide range of concentrations, including in diverse biological samples like protein solutions, cerebrospinal fluid, and whole blood. These results highlight the potential of plasmonic "aptasensors" for developing rapid and accurate diagnostic tools for disease monitoring, medical diagnostics, and targeted therapies.

Sensitive and selective electrochemical aptasensing method for the voltammetric determination of dopamine based on AuNPs/PEDOT-ERGO nanocomposites

In this study, the effects of phosphate buffered saline (PBS) and graphene oxide (GO) as supporting electrolytes and dopants on the electropolymerization process of 3,4-ethylenedioxythiophene (EDOT) on glassy carbon electrode (GCE) were investigated. It was found that the PEDOT-ERGO nanocomposites obtained by a simple one-step electrochemical redox polymerization method using GO as the only supporting electrolyte and dopant possess excellent electrochemical properties. Then, the PEDOT-ERGO nanocomposites were used as electrode substrate to further modify with AuNPs, and an electrochemical aptasensor based on AuNPs/PEDOT-ERGO nanocomposites was successfully constructed for the sensitive and selective determination of dopamine (DA). Comparison of the cyclic voltammetric response of different neurotransmitters before and after aptamer assembly showed that the aptamer significantly improved the selectivity of the sensor for DA. The low detection limit of 1.0 μM (S/N = 3) indicated the good electrochemical performance of the PEDOT-ERGO nanocomposite film. Moreover, the aptasensor showed good recoveries in 50-fold diluted fetal bovine serum with RSD values all less than 5 % (n = 5), indicating that the PEDOT-ERGO nanocomposites and the electrochemical aptasensor have promising applications in other neurochemicals assay and biomedical analysis.

Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications

Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.

AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders

BACKGROUND

Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evolution of ligands by exponential enrichment (SELEX) method is a critical in vitro technique employed to identify aptamers that bind specifically to target proteins. While advanced SELEX-based methods such as Cell- and HT-SELEX are available, they often encounter issues such as extended time consumption and suboptimal accuracy. Several In silico aptamer discovery methods have been proposed to address these challenges. These methods are specifically designed to predict aptamer-protein interaction (API) using benchmark datasets. However, these methods often fail to consider the physicochemical interactions between aptamers and proteins within tertiary structures.

RESULTS

In this study, we propose AptaTrans, a pipeline for predicting API using deep learning techniques. AptaTrans uses transformer-based encoders to handle aptamer and protein sequences at the monomer level. Furthermore, pretrained encoders are utilized for the structural representation. After validation with a benchmark dataset, AptaTrans has been integrated into a comprehensive toolset. This pipeline synergistically combines with Apta-MCTS, a generative algorithm for recommending aptamer candidates.

CONCLUSION

The results show that AptaTrans outperforms existing models for predicting API, and the efficacy of the AptaTrans pipeline has been confirmed through various experimental tools. We expect AptaTrans will enhance the cost-effectiveness and efficiency of SELEX in drug discovery. The source code and benchmark dataset for AptaTrans are available at https://github.com/pnumlb/AptaTrans .

Homogeneous immunoassay utilizing fluorescence resonance energy transfer from quantum dots to tyramide dyes deposited on full immunocomplexes

There is an urgent need for homogeneous immunoassays that offer sufficient sensitivity for routine clinical practice. In this study, we have developed a highly sensitive, fluorescence resonance energy transfer (FRET)-based homogeneous immunoassay. Unlike previous FRET-based homogeneous immunoassays, where acceptors were attached to antibody molecules located far from the donor, we employed acceptors to label the entire sandwich-structured immunocomplex, including two antibodies and one antigen. As a result, the FRET signal was amplified by a factor of 10, owing to the reduced distance between the donor and acceptors. We validated our method by quantifying carcinoembryonic antigen (CEA) and α-fetoprotein (AFP) in PBS buffer and blank plasma. The limits of detection (LOD) for CEA and AFP in both PBS buffer and blank plasma were comparable, reaching sub-femtomolar levels. Furthermore, we successfully quantified CEA and AFP in three human plasma samples, thereby confirming the reliability of our method for clinical applications.

Plasmonic Coupling on an Optical Microfiber Surface: Enabling Single-Molecule and Noninvasive Dopamine Detection

Optical fibers can be effective biosensors when employed in early-stage diagnostic point-of-care devices as they can avoid interference from molecules with similar redox potentials. Nevertheless, their sensitivity needs to be improved for real-world applications, especially for small-molecule detection. This work demonstrates an optical microfiber biosensor for dopamine (DA) detection based on the DA-binding-induced aptamer conformational transitions that occur at plasmonic coupling sites on a double-amplified nanointerface. The sensor exhibits ultrahigh sensitivity when detecting DA molecules at the single-molecule level; additionally, this work provides an approach for overcoming optical device sensitivity limits, further extending optical fiber single-molecule detection to a small molecule range (e.g., DA and metal ions). The selective energy enhancement and signal amplification at the binding sites effectively avoid nonspecific amplification of the whole fiber surface which may lead to false-positive results. The sensor can detect single-molecule DA signals in body-fluids. It can detect the released extracellular DA levels and monitor the DA oxidation process. An appropriate aptamer replacement allows the sensor to be used for the detection of other target small molecules and ions at the single-molecule level. This technology offers alternative opportunities for developing noninvasive early-stage diagnostic point-of-care devices and flexible single-molecule detection techniques in theoretical research.

Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor

Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.

Zwitterionic Polymer Coated and Aptamer Functionalized Flexible Micro-Electrode Arrays for In Vivo Cocaine Sensing and Electrophysiology

The number of people aged 12 years and older using illicit drugs reached 59.3 million in 2020, among which 5.2 million are cocaine users based on the national data. In order to fully understand cocaine addiction and develop effective therapies, a tool is needed to reliably measure real-time cocaine concentration and neural activity in different regions of the brain with high spatial and temporal resolution. Integrated biochemical sensing devices based upon flexible microelectrode arrays (MEA) have emerged as a powerful tool for such purposes; however, MEAs suffer from undesired biofouling and inflammatory reactions, while those with immobilized biologic sensing elements experience additional failures due to biomolecule degradation. Aptasensors are powerful tools for building highly selective sensors for analytes that have been difficult to detect. In this work, DNA aptamer-based electrochemical cocaine sensors were integrated on flexible MEAs and protected with an antifouling zwitterionic poly (sulfobetaine methacrylate) (PSB) coating, in order to prevent sensors from biofouling and degradation by the host tissue. In vitro experiments showed that without the PSB coating, both adsorption of plasma protein albumin and exposure to DNase-1 enzyme have detrimental effects on sensor performance, decreasing signal amplitude and the sensitivity of the sensors. Albumin adsorption caused a 44.4% sensitivity loss, and DNase-1 exposure for 24 hr resulted in a 57.2% sensitivity reduction. The PSB coating successfully protected sensors from albumin fouling and DNase-1 enzyme digestion. In vivo tests showed that the PSB coated MEA aptasensors can detect repeated cocaine infusions in the brain for 3 hrs after implantation without sensitivity degradation. Additionally, the same MEAs can record electrophysiological signals at different tissue depths simultaneously. This novel flexible MEA with integrated cocaine sensors can serve as a valuable tool for understanding the mechanisms of cocaine addiction, while the PSB coating technology can be generalized to improve all implantable devices suffering from biofouling and inflammatory host responses.

A Review on Bio- and Chemosensors for the Detection of Biogenic Amines in Food Safety Applications: The Status in 2022

This article provides an overview on the broad topic of biogenic amines (BAs) that are a persistent concern in the context of food quality and safety. They emerge mainly from the decomposition of amino acids in protein-rich food due to enzymes excreted by pathogenic bacteria that infect food under inappropriate storage conditions. While there are food authority regulations on the maximum allowed amounts of, e.g., histamine in fish, sensitive individuals can still suffer from medical conditions triggered by biogenic amines, and mass outbreaks of scombroid poisoning are reported regularly. We review first the classical techniques used for selective BA detection and quantification in analytical laboratories and focus then on sensor-based solutions aiming at on-site BA detection throughout the food chain. There are receptor-free chemosensors for BA detection and a vastly growing range of bio- and biomimetic sensors that employ receptors to enable selective molecular recognition. Regarding the receptors, we address enzymes, antibodies, molecularly imprinted polymers (MIPs), and aptamers as the most recent class of BA receptors. Furthermore, we address the underlying transducer technologies, including optical, electrochemical, mass-sensitive, and thermal-based sensing principles. The review concludes with an assessment on the persistent limitations of BA sensors, a technological forecast, and thoughts on short-term solutions.

A Nucleic Acid Sequence That is Catalytically Active in Both RNA and TNA Backbones

Threose nucleic acid (TNA) is considered a potential RNA progenitor due to its chemical simplicity, base pairing property, and capability of folding into a functional tertiary structure. However, it is unknown whether the functional property can be maintained during transition from TNA to RNA. Here, we use a toggle in vitro selection to identify nucleic acid catalyst sequences that are active in both TNA and RNA backbones. One such nucleic acid enzyme with exchangeable backbone (CAMELEON) catalyzes an RNA cleavage reaction when prepared as TNA (T) and RNA (R). Further biochemical characterization reveals that CAMELEON R and T exhibit different catalytic behaviors such as rate enhancement and magnesium dependence. Structural probing and mutagenesis experiments suggest that they likely fold into distinct tertiary structures. This work demonstrates that the catalytic activity can be preserved during backbone transition from TNA to RNA and provides further experimental support for TNA as an RNA precursor in evolution.

Aptamer-Based Biosensors for the Colorimetric Detection of Blood Biomarkers: Paving the Way to Clinical Laboratory Testing

Clinical diagnostics for human diseases rely largely on enzyme immunoassays for the detection of blood biomarkers. Nevertheless, antibody-based test systems have a number of shortcomings that have stimulated a search for alternative diagnostic assays. Oligonucleotide aptamers are now considered as promising molecular recognizing elements for biosensors (aptasensors) due to their high affinity and specificity of target binding. At the moment, a huge variety of aptasensors have been engineered for the detection of various analytes, especially disease biomarkers. However, despite their great potential and excellent characteristics in model systems, only a few of these aptamer-based assays have been translated into practice as diagnostic kits. Here, we will review the current progress in the engineering of aptamer-based colorimetric assays as the most suitable format for clinical lab diagnostics. In particular, we will focus on aptasensors for the detection of blood biomarkers of cardiovascular, malignant, and neurodegenerative diseases along with common inflammation biomarkers. We will also analyze the main obstacles that have to be overcome before aptamer test systems can become tantamount to ELISA for clinical diagnosis purposes.

Confined electrochemiluminescence imaging microarray for high-throughput biosensing of single cell-released dopamine

The quantitative detection of single cell secretions is always limited by their accurate collection and the heterogeneity of different cells. In this work, a confined electrochemiluminescence (ECL) imaging microarray (CEIM) chip was designed to capture single or a few cells in each cylindrical microwell for high-throughput quantitation of cell-secreted dopamine (DA). The ITO surface at the bottom of microwells was functionalized with the film of DA aptamer modified coreactant-embedded polymer dots (Pdots), which endowed the chip with the abilities to both in situ recognize the target DA secreted from the cells and emit the ECL signal for responding the secreted target without need of any additional coreactant. At the applied potential of +1.4 V, the Pdots in the film emitted strong ECL signal, which could be quenched by the electrochemical oxidation product of DA in individual microwell for sensitive detection of single cell-released DA. The practicability of the proposed CEIM chip along with the ECL imaging and biosensing strategy was demonstrated by evaluating the amounts of single cell-released DA in different microwells under hypoxia stimulation. This protocol revealed the heterogeneity of cell secretion, and could be extended for quantitation of other secretions from different kinds of single cells.

Aptamer-modified biosensors to visualize neurotransmitter flux

Chemical biosensors with the capacity to continuously monitor various neurotransmitter dynamics can be powerful tools to understand complex signaling pathways in the brain. However, in vivo detection of neurochemicals is challenging for many reasons such as the rapid release and clearance of neurotransmitters in the extracellular space, or the low target analyte concentrations in a sea of interfering biomolecules. Biosensing platforms with adequate spatiotemporal resolution coupled to specific and selective receptors termed aptamers, demonstrate high potential to tackle such challenges. Herein, we review existing literature in this field. We first discuss nanoparticle-based systems, which have a simple in vitro implementation and easily interpretable results. We then examine methods employing near-infrared detection for deeper tissue imaging, hence easier translation to in vivo implementation. We conclude by reviewing live cell imaging of neurotransmitter release via aptamer-modified platforms. For each of these sensors, we discuss the associated challenges for translation to real-time in vivo neurochemical imaging. Realization of in vivo biosensors for neurotransmitters will drive future development of early prevention strategies, treatments, and therapeutics for psychiatric and neurodegenerative diseases.

Transliteration of synthetic genetic enzymes

Functional nucleic acids lose activity when their sequence is prepared in the backbone architecture of a different genetic polymer. The only known exception to this rule is a subset of aptamers whose binding mechanism involves G-quadruplex formation. We refer to such examples as transliteration-a synthetic biology concept describing cases in which the phenotype of a nucleic acid molecule is retained when the genotype is written in a different genetic language. Here, we extend the concept of transliteration to include nucleic acid enzymes (XNAzymes) that mediate site-specific cleavage of an RNA substrate. We show that an in vitro selected 2'-fluoroarabino nucleic acid (FANA) enzyme retains catalytic activity when its sequence is prepared as α-l-threofuranosyl nucleic acid (TNA), and vice versa, a TNA enzyme that remains functional when its sequence is prepared as FANA. Structure probing with DMS supports the hypothesis that FANA and TNA enzymes having the same primary sequence can adopt similarly folded tertiary structures. These findings provide new insight into the sequence-structure-function paradigm governing biopolymer folding.

Using Graphene-Based Biosensors to Detect Dopamine for Efficient Parkinson's Disease Diagnostics

Parkinson's disease (PD) is a neurodegenerative disease in which the neurotransmitter dopamine (DA) depletes due to the progressive loss of nigrostriatal neurons. Therefore, DA measurement might be a useful diagnostic tool for targeting the early stages of PD, as well as helping to optimize DA replacement therapy. Moreover, DA sensing appears to be a useful analytical tool in complex biological systems in PD studies. To support the feasibility of this concept, this mini-review explores the currently developed graphene-based biosensors dedicated to DA detection. We discuss various graphene modifications designed for high-performance DA sensing electrodes alongside their analytical performances and interference studies, which we listed based on their limit of detection in biological samples. Moreover, graphene-based biosensors for optical DA detection are also presented herein. Regarding clinical relevance, we explored the development trends of graphene-based electrochemical sensing of DA as they relate to point-of-care testing suitable for the site-of-location diagnostics needed for personalized PD management. In this field, the biosensors are developed into smartphone-connected systems for intelligent disease management. However, we highlighted that the focus should be on the clinical utility rather than analytical and technical performance.

In Vitro Selection of Short DNA Aptamers that Can Inhibit or Alleviate Cocaine and MK-801 Inhibition of Muscle-Type Nicotinic Acetylcholine Receptors

Ligands of high specificity and selectivity have been selected for biological molecules of interest including nicotinic acetylcholine receptor (nAChR) using combinatorial libraries of nucleic acids. The nAChR belongs to a group of structurally related proteins that regulate signal transmission between ~ 10¹² cells of the mammalian nervous system. It is inhibited by both therapeutic agents and abused drugs, including cocaine. A mechanism-based approach to alleviating noncompetitive inhibition of the mucle-type nAChR, including Torpedo, resulted in the selection of very short DNA aptamers only seven nucleotides long. By transient kinetic measurements, these DNA aptamers, which displaced cocaine from its binding site on the muscle-type nAChR, were classified into two groups based on their effects on the nAChR: Class I aptamers inhibit agonist-induced current in the muscle-type nAChR and Class II molecules alleviate inhibition by MK-801 [(+)-dizocilpine] without affecting the receptor function. The most potent Class I DNA aptamer, which inhibits the muscle-type nAChR, has an apparent dissociation constant (K_Iapt) of 5 μM, while the most efficient Class II DNA aptamer, which alleviates MK-801-induced inhibition, has an apparent dissociation constant (K_Apt) of 1.8 μM. An innovative aspect of the work is the identification of very short DNA aptamers with these properties that makes them attractive for therapeutic and diagnostic applications.

A review of biosensors for the detection of B-type natriuretic peptide as an important cardiovascular biomarker

Heart disease, as the most serious threat to human health globally, is responsible for rising mortality rates, largely due to lifestyle and diet. Unfortunately, the main problem for patients at high risk of heart disease is the validation of prognostic tests. To this end, the detection of cardiovascular biomarkers has been employed to obtain pathological and physiological information in order to improve prognosis and early-stage diagnosis of chronic heart failure. Short-term changes in B-type natriuretic peptide are known as a standard and important biomarker for diagnosis of heart failure. The most important problem for detection is low concentration and short half-life in the blood. The normal concentration of BNP in blood is less than 7 nM (25 pg/mL), which increases significantly to more than 80 pg/mL. Therefore, the development of new biosensors with better sensitivity, detection limit, and dynamic range than current commercial kits is urgently needed. This review classifies the biosensors designed for detection of BNP into electrochemical, optical, microfluidic, and lateral-flow immunoassay techniques. The review clearly demonstrates that a variety of immunoassay, aptasensor, enzymatic and catalytic nanomaterials, and fluorophores have been successfully employed for detection of BNP at low attomolar ranges. Dtection of B-type natriuretic peptide with biosensors.

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Dopamine is an essential neurotransmitter and its detection is important for bioanalytical chemistry. Two very different DNA aptamers have been reported for dopamine, one derived from an RNA aptamer (named Apt1) and other obtained via direct aptamer selection (named Apt2). In this study, we used four homogeneous binding assays to compare these two DNA dopamine aptamers. Thiazole orange (TO) fluorescence assay indicated that the Apt2 specifically bound with dopamine with a K_d of 2.37 μM, which was consistent with that from the isothermal titration calorimetry (ITC) assay. However, Apt1 had much less TO fluorescence change and also no signal from ITC. By labeling the two ends of the two aptamers by a fluorophore and a quencher, the aptamer beacons showed binding of dopamine only for Apt2. Finally, the label-free AuNP-based colorimetric assay showed no difference between these two aptamer sequences, and even non-binding random DNA showed the same response, indicating that AuNPs were not a good probe for detecting dopamine. According to the data, Apt1 does not appear to be able to bind dopamine specifically, while Apt2 showed specific binding and could be used for developing related biosensors.

Selection of DNA Aptamers for Root Exudate l-Serine Using Multiple Selection Strategies

Agricultural biosensing can aid decisions about crop health and maintenance, because crops release root exudates that can inform about their status. l-Serine has been found to be indicative of nitrogen uptake in wheat and canola. The development of a biosensor for l-serine could allow farmers to monitor crop nutrient demands more precisely. The development of robust l-serine-binding DNA aptamers is described. Because small molecules can be challenging targets for Systematic Evolution of Ligands by EXponential enrichment (SELEX), three separate DNA libraries were used for SELEX experiments. A l-homocysteine aptamer was randomized to create a starting library for a l-serine selection (randomized SELEX). The final selection rounds of the l-homocysteine selection were also used as a starting library for l-serine (redirected SELEX). Finally, an original DNA library was used (original SELEX). All three SELEX experiments produced l-serine-binding aptamers with micromolar affinity, with Red.1 aptamer having a K_d of 7.9 ± 3.6 μM. Truncation improved the binding affinity to 5.2 ± 2.7 μM, and from this sequence, a Spiegelmer with improved nuclease resistance was created with a K_d of 2.0 ± 0.8 μM. This l-serine-binding Spiegelmer has the affinity and stability to be incorporated into aptamer-based biosensors for agricultural applications.

Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing

Oligonucleotide receptors (aptamers), which change conformation upon target recognition, enable electronic biosensing under high ionic-strength conditions when coupled to field-effect transistors (FETs). Because highly negatively charged aptamer backbones are influenced by ion content and concentration, biosensor performance and target sensitivities were evaluated under application conditions. For a recently identified dopamine aptamer, physiological concentrations of Mg²⁺ and Ca²⁺ in artificial cerebrospinal fluid produced marked potentiation of dopamine FET-sensor responses. By comparison, divalent cation-associated signal amplification was not observed for FET sensors functionalized with a recently identified serotonin aptamer or a previously reported dopamine aptamer. Circular dichroism spectroscopy revealed Mg²⁺- and Ca²⁺-induced changes in target-associated secondary structure for the new dopamine aptamer, but not the serotonin aptamer nor the old dopamine aptamer. Thioflavin T displacement corroborated the Mg²⁺ dependence of the new dopamine aptamer for target detection. These findings imply allosteric binding interactions between divalent cations and dopamine for the new dopamine aptamer. Developing and testing sensors in ionic environments that reflect intended applications are best practices for identifying aptamer candidates with favorable attributes and elucidating sensing mechanisms.

Translational control of enzyme scavenger expression with toxin-induced micro RNA switches

Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. Here we present the construction of a synthetic network to implement detoxification functionality. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. Our miRNA switch results show moderate synthetic expression control over a biologically active detoxification enzyme molecule, using an established design protocol. However, following a new design approach, we demonstrated an evolutionarily designed miRNA switch to more effectively activate enzyme activity than synthetically designed versions, allowing markedly improved extrinsic user-defined control with a toxin as inducer. Our straightforward new design approach is simple to implement and uses easily accessible web-based databases and prediction tools. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic and biocomputing applications.

Controlling dopamine binding by the new aptamer for a FRET-based biosensor

Dopamine is one of the most important neurotransmitters. A high-quality DNA aptamer for dopamine was reported in 2018. However, fundamental understanding of its binding and folding is lacking, which is critical for related biosensor design. Herein, we performed careful assays using a label-free technique called isothermal titration calorimetry (ITC) to study its secondary structure. We divided this aptamer into four regions and individually examined each of them. We confirmed two stems, but the third stem is believed to be part of a loop. The aptamer was then truncated. The original aptamer had a Kd of 2.2 ± 0.3 μM at 25 °C. Shortening the structure by one or two base pairs increased the Kd to 6.9 and 44.4 μM, respectively. Dopamine binding was promoted by both increasing the Mg2+ concentration and decreasing the temperature. At 5 °C, a Kd of 0.4 μM was achieved. Based on this understanding, we designed two fluorescence resonance energy transfer (FRET) quenching biosensors that differ only by a base pair. The shorter sensor had 3-fold higher sensitivity and a detection limit of 0.9 μM. In 1% fetal bovine serum, the sensor retained a similar limit of detection of 1.14 μM. A two-fluorophore ratiometric FRET sensor was also demonstrated with a low detection limit of 0.12 μM. This work indicated the feasibility of designing folding-based sensors for dopamine, and this design can be extended to other sensing modalities such as electrochemistry and colorimetry.

Dopamine and Melamine Binding to Gold Nanoparticles Dominates Their Aptamer-Based Label-Free Colorimetric Sensing

Target-directed aptamer adsorption by gold nanoparticles (AuNPs) has been widely used to develop label-free colorimetric biosensors. However, the potential interactions between target molecules and AuNPs have not been considered, which may lead to misinterpretation of analytical results. In this work, the detection of dopamine, melamine, and K⁺ was studied as model systems to address this problem. First, dopamine and two control molecules all induced the aggregation of citrate-capped AuNPs with apparent K_d's of 5.8 μM dopamine, 51.6 μM norepinephrine, and 142 μM tyramine. Isothermal titration calorimetry measured the aptamer K_d to be 1.9 μM dopamine and 16.8 μM norepinephrine, whereas tyramine cannot bind. Surface enhanced Raman spectroscopy confirmed direct adsorption of dopamine, and the adsorbed dopamine inhibited the adsorption of DNA. Using a typical salt-induced colorimetric detection protocol, a similar color response was observed regardless of the sequence of DNA, indicating the observed color change reflected the adsorption of dopamine by the AuNPs instead of the binding of dopamine by the aptamer. For this label-free sensor to work, the interaction between the target molecule and AuNPs should be very weak, while dopamine represents an example of strong interactions. For the other two systems, the melamine detection did not reflect aptamer binding either but the K⁺ detection did, suggesting melamine also strongly interacted with AuNPs, whereas K⁺ had very weak interactions with AuNPs. Since each target molecule is different, such target/AuNP interactions need to be studied case-by-case to ensure the sensing mechanism.

Label-free liquid crystal-based biosensor for detection of dopamine using DNA aptamer as a recognition probe

We present a label-free liquid crystal-based biosensor for the detection of dopamine (DA) in aqueous solutions using dopamine-binding aptamers (DBA) as recognition elements. In this system, the dimethyloctadecyl [3-(trimethoxysilyl) propyl] ammonium chloride (DMOAP) self-assembled monolayers immobilized on glass slides support the long alkyl chains that keep the liquid crystal (LC) molecules in a homeotropic orientation. Glutaraldehyde (GA) is used as a cross-linker to immobilize DBA onto the surface of glass slides. The specific binding of DA and DBA disrupts the homeotropic orientation of LCs, thereby inducing a change in the orientation from homeotropic to a random alignment. This orientation change can be converted and visualized simply as a transition from a dark optical LC image to a brighter image under a polarized optical microscope (POM), enabling the detection of DA. The developed LC-based aptasensor shows a good linear optical response towards DA in the very wide range of 1 pM-10 μM (0.19 pg/mL to 1.9 μg/mL) and has a very low detection limit of 10 pM (∼1.9 pg/mL). The biosensor also exhibited satisfactory selectivity and could be successfully applied to detect DA in human urine. The proposed LC-based aptamer sensing method offers a simple, rapid, highly sensitive and selective, and a label-free method for the analysis of DA in real clinical samples.

In Vitro Selection of New DNA Aptamers for Human Vascular Endothelial Growth Factor 165

Two DNA aptamers that bind the heparin-binding domain (HBD) of the human vascular endothelial growth factor 165 (VEGF-165) have been previously reported. Although VEGF-165 is a homodimeric protein and the two aptamers have different sequences and secondary structures, the aptamers appear to occupy the same binding site and cannot form a 2 : 1 aptamer/protein complex, thus making them unsuitable for creating a higher-affinity dimeric DNA aptamer. This has motivated us to conduct a new in vitro selection experiment to search for new VEGF-165-binding DNA aptamers with different properties. We undertook a multistream selection strategy in which the concentration of VEGF-165 was varied significantly. We carried out 11 rounds of selection, and next-generation sequencing was conducted for every round in each stream. From comprehensive sequence analysis, we identified four classes of DNA aptamers, of which two were reported before, but two are new DNA aptamers. One of the new aptamers exhibits a unique property that has never been observed before: it is capable of forming the 2 : 1 aptamer/protein complex with VEGF-165. This work has expanded the repertoire of VEGF-165-binding DNA aptamers and creates a possibility to engineer a higher affinity homodimeric aptamer for VEGF-165.

Aptamer-Based Sensing of Small Organic Molecules by Measuring Levitation Coordinate of Single Microsphere in Combined Acoustic-Gravitational Field

We present aptamer-based sensing using a coupled acoustic-gravitational (CAG) field, which transduces a change in the density of a microparticle (MP) to a change in the levitation coordinate. A large density of the MP is initially induced by the binding of gold nanoparticles (AuNPs) on the MP through sandwich hybridization with aptamer DNA molecules. Targets added to the system interact with the aptamer DNA molecules to form complexes, and the duplex between the aptamer and the probe DNA molecules is dissociated. This leads to the release of AuNPs from the MP and a decrease in its density. As the target concentration increases, the levitation coordinate of the MP increases. From the levitation coordinate shift, we can determine the target concentration. The detection limits for adenosine triphosphate, dopamine, and ampicillin as test targets are 9.8 nM, 17 nM, and 160 pM, respectively. The dissociation constants for the aptamer-target complexes are quantitatively determined from the dependence of the levitation coordinate on the target concentration. This scheme is a useful analytical tool not only for the trace analyses of targets but also for the evaluation of aptamer-target interactions.

Post-SELEX Optimization and Characterization of a Prostate Cancer Cell-Specific Aptamer for Diagnosis

The RNA aptamer A4 binds specifically to tumor prostate cells. A4 was modified (mA4) by adding deoxyribonucleotides to its ends to remove the reactive 2' hydroxyl groups of RNA's sugar at the ends of the aptamer and to make it more stable to widespread RNase contamination in laboratories. Thus, mA4 would be more suitable to use in the clinical settings of prostate cancer (PCa). We aimed to characterize this optimized oligonucleotide to verify its potential as a diagnostic tool. The sequences and structures of A4 and mA4 were compared through in silico approaches to corroborate their similarity. Then, the degradation of mA4 was measured in appropriate media and human plasma for in vitro tests. In addition, the binding abilities of A4 to prostate cells were contrasted with those of mA4. The effects of mA4 were assessed on the viability, proliferation, and migration of human prostate cell lines RWPE-1 and PC-3 in three-dimensional (3D) cell cultures. mA4 showed configurational motifs similar to those of A4, displayed a half-life in plasma substantially higher than A4, and exhibited a comparable binding capacity to that of A4 and unaltered viability, proliferation, and migration of prostatic cells. Therefore, mA4 maintains the crucial 3D structures of A4 that would allow binding to its target, as suggested by in silico and binding analyses. mA4 may be a good PCa reporter as it does not change cellular parameters of prostate cells when incubated with it. Its additional deoxyribonucleotides make mA4 inherently more chemically stable than A4, avoiding its degradation and favoring its storage and handling for clinical applications. These characteristics support the potential of mA4 to be used in diagnostic systems for PCa.

Unraveling Determinants of Affinity Enhancement in Dimeric Aptamers for a Dimeric Protein

High-affinity aptamers can be derived de novo by using stringent conditions in SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments or can be engineered post SELEX via dimerization of selected aptamers. Using electrophoretic mobility shift assays, we studied a series of heterodimeric and homodimeric aptamers, constructed from two DNA aptamers with distinct primary sequences and secondary structures, previously isolated for VEGF-165, a homodimeric protein. We investigated four factors envisaged to impact the affinity of a dimeric aptamer to a dimeric protein: (1) length of the linker between two aptamer domains, (2) linking orientation, (3) binding-site compatibility of two component aptamers in a heterodimeric aptamer, and (4) steric acceptability of the two identical aptamers in a homodimeric aptamer. All heterodimeric aptamers for VEGF-165 were found to exhibit monomeric aptamer-like affinity and the lack of affinity enhancement was attributed to binding-site overlap by the constituent aptamers. The best homodimeric aptamer showed 2.8-fold better affinity than its monomeric unit (K_d = 13.6 ± 2.7 nM compared to 37.9 ± 14 nM), however the barrier to further affinity enhancement was ascribed to steric interference of the constituent aptamers. Our findings point to the need to consider the issues of binding-site compatibility and spatial requirement of aptamers for the development of dimeric aptamers capable of bivalent recognition. Thus, determinants highlighted herein should be assessed in future multimerization efforts.

Perspective on the Future Role of Aptamers in Analytical Chemistry

It has been almost 30 years since the invention of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology and the description of the first aptamers. In retrospect over the past 30 years, advances in aptamer development and application have demonstrated that aptamers are potentially useful reagents that can be employed in diverse areas within analytical chemistry, biotechnology, biomedicine, and molecular biology. While often touted as artificial antibodies with an ability to be selected for any target, aptamer development, unfortunately, lags behind development of analytical methodologies that employ aptamers, hindering deeper integration into the application of analytical tool development. This perspective covers recent advances in SELEX methodology for improving efficiency of the SELEX procedure and enhancing affinity and specificity of the selected aptamers, what we view as a critical barrier in the future role of aptamers in analytical chemistry. We discuss postselection modifications that can be used for enhancing performance of the selected aptamers in an analytical device by including understanding intermolecular interaction forces in the binding domain. While highlighting promising properties of aptamers that enable several analytical advances, we provide discussion on the challenges of penetration of aptamers in the analytical field.

A Review of Neurotransmitters Sensing Methods for Neuro-Engineering Research

Neurotransmitters as electrochemical signaling molecules are essential for proper brain function and their dysfunction is involved in several mental disorders. Therefore, the accurate detection and monitoring of these substances are crucial in brain studies. Neurotransmitters are present in the nervous system at very low concentrations, and they mixed with many other biochemical molecules and minerals, thus making their selective detection and measurement difficult. Although numerous techniques to do so have been proposed in the literature, neurotransmitter monitoring in the brain is still a challenge and the subject of ongoing research. This article reviews the current advances and trends in neurotransmitters detection techniques, including in vivo sampling and imaging techniques, electrochemical and nano-object sensing techniques for in vitro and in vivo detection, as well as spectrometric, analytical and derivatization-based methods mainly used for in vitro research. The document analyzes the strengths and weaknesses of each method, with the aim to offer selection guidelines for neuro-engineering research.

NIR Biosensing of Neurotransmitters in Stem Cell-Derived Neural Interface Using Advanced Core-Shell Upconversion Nanoparticles

Nondestructive neurotransmitter detection and real-time monitoring of stem cell differentiation are both of great significance in the field of neurodegenerative disease and regenerative medicine. Although luminescent biosensing nanoprobes have been developed to address this need, they have intrinsic limitations such as autofluorescence, scattering, and phototoxicity. Upconversion nanoparticles (UCNPs) have gained increasing attention for various biomedical applications due to their high photostability, low auto-fluorescent background, and deep tissue penetration; however, UCNPs also suffer from low emission intensities due to undesirable energy migration pathways. To address the aforementioned issue, a single-crystal core-shell-shell "sandwich" structured UCNP is developed that is designed to minimize deleterious energy back-transfer to yield bright visible emissions using low power density excitations. These UCNPs show a remarkable enhancement of luminescent output relative to conventional β-NaYF4:Yb,Er codoped UCNPs and β-NaYF4:Yb,Er@NaYF4:Yb "active shell" alike. Moreover, this advanced core-shell-shell UCNP is subsequently used to develop a highly sensitive biosensor for the ultrasensitive detection of dopamine released from stem cell-derived dopaminergic-neurons. Given the challenges of in situ detection of neurotransmitters, the developed NIR-based biosensing of neurotransmitters in stem cell-derived neural interfaces present a unique tool for investigating single-cell mechanisms associated with dopamine, or other neurotransmitters, and their roles in neurological processes.

In Vivo Use of a Multi-DNA Aptamer-Based Payload/Targeting System To Study Dopamine Dysregulation in the Central Nervous System

The delivery of therapeutics across the blood-brain barrier remains a considerable challenge in investigating central nervous system related processes. In this work, a liposome vehicle was surface-modified with an aptamer that binds to the transferrin receptor and was loaded with two different dopamine-binding aptamer payloads. This system was effectively used to promote the delivery of the aptamer cargo from the peripheral injection site into the brain. The effect of these delivered aptamers on behavior was investigated in vivo in a locomotor task. The first dopamine binding aptamer assessed was a DNA aptamer, the binding of which had been previously validated through the aptamer-based biosensor development reported by several independent research groups. The second aptamer investigated was the result of a novel in vitro selection experiment described herein. Our data suggest that systemic administration of the modified liposomes led to delivery of the dopamine aptamers into the brain. Fluorescence microscopy revealed differential distribution of fluorescence based on the presence or absence of the transferrin receptor aptamer on the surface of fluorescently modified liposomes. In a behavioral experiment using cocaine administration to induce elevated concentrations of neural dopamine, systemic pretreatment with the dopamine aptamer-loaded liposomes reduced cocaine-induced hyperlocomotion. Multiple controls including a transferrin-negative liposome control and transferrin-positive liposomes loaded with either a nonbinding, base-substituted dopamine aptamer or a random oligonucleotide were investigated. None of these controls altered cocaine-induced hyperlocomotion. Chronic systemic administration of the modified liposomes produced no deleterious neurobehavioral or neural degenerative effects. Importantly, this work is one example of an application for this versatile multiaptamer payload/targeting system. Its general application is limited only by the availability of aptamers for specific neural targets.

Molecular Fitness Landscapes from High-Coverage Sequence Profiling

The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The accessibility of high-throughput sequencing (HTS) has transformed this study, enabling large-scale enumeration of fitness for many mutants and even complete sequence spaces in some cases. We review the progress of high-throughput studies in mapping molecular fitness landscapes, both in vitro and in vivo, as well as opportunities for future research. Such studies are rapidly growing in number. HTS is expected to have a profound effect on the understanding of real molecular fitness landscapes.

Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing

Detection of analytes by means of field-effect transistors bearing ligand-specific receptors is fundamentally limited by the shielding created by the electrical double layer (the "Debye length" limitation). We detected small molecules under physiological high-ionic strength conditions by modifying printed ultrathin metal-oxide field-effect transistor arrays with deoxyribonucleotide aptamers selected to bind their targets adaptively. Target-induced conformational changes of negatively charged aptamer phosphodiester backbones in close proximity to semiconductor channels gated conductance in physiological buffers, resulting in highly sensitive detection. Sensing of charged and electroneutral targets (serotonin, dopamine, glucose, and sphingosine-1-phosphate) was enabled by specifically isolated aptameric stem-loop receptors.

Critical Review: DNA Aptasensors, Are They Ready for Monitoring Organic Pollutants in Natural and Treated Water Sources?

There is a growing need to monitor anthropogenic organic contaminants detected in water sources. DNA aptamers are synthetic single-stranded oligonucleotides, selected to bind to target contaminants with favorable selectivity and sensitivity. These aptamers can be functionalized and are used with a variety of sensing platforms to develop sensors, or aptasensors. In this critical review, we (1) identify the state-of-the-art in DNA aptamer selection, (2) evaluate target and aptamer properties that make for sensitive and selective binding and sensing, (3) determine strengths and weaknesses of alternative sensing platforms, and (4) assess the potential for aptasensors to quantify environmentally relevant concentrations of organic contaminants in water. Among a suite of target and aptamer properties, binding affinity is either directly (e.g., organic carbon partition coefficient) or inversely (e.g., polar surface area) correlated to properties that indicate greater target hydrophobicity results in the strongest binding aptamers, and binding affinity is correlated to aptasensor limits of detection. Electrochemical-based aptasensors show the greatest sensitivity, which is similar to ELISA-based methods. Only a handful of aptasensors can detect organic pollutants at environmentally relevant concentrations, and interference from structurally similar analogs commonly present in natural waters is a yet-to-be overcome challenge. These findings lead to recommendations to improve aptasensor performance.

Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates

Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or   l-tryptophan were selectively recognized by previously identified dopamine or l-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though, slightly greater than the previously determined solution dissociation constant. Using prefunctionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with l-3,4-dihydroxyphenylalanine, l- threo-dihydroxyphenylserine, and l-5-hydroxytryptophan enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons and future identification and characterization of novel aptamers targeting neurotransmitters or other important small molecules.

Inhibition of Human Papillomavirus Type 16 Infection Using an RNA Aptamer

Human papillomavirus type 16 (HPV16) DNA has been found in ∼50% of cervical tumors worldwide. HPV infection starts with the binding of the virus capsid to heparan sulfate (HS) receptors exposed on the surface of epithelial basal layer keratinocytes. Previously, our group isolated a high-affinity RNA aptamer (Sc5c3) specific for HPV16 L1 virus-like particles (VLPs). In this study, we report the inhibition of HPV16 infection by Sc5c3 in a pseudovirus (PsVs) model. 293TT cells were infected by HPV16 PsVs containing the yellow fluorescent protein (YFP) as reporter gene. Incubation of HPV16 PsVs with Sc5c3 before infection resulted in a dose-dependent decrease in YFP fluorescence, suggesting infection inhibition. Aptamer degradation by RNase A restored PsVs infectivity, supporting the previous observation that Sc5c3 aptamer can inhibit infection. VLP mutants with removed HS binding sites were used in binding assays to elucidate the Sc5c3 blocking mechanism; however, no binding difference was observed between wild-type and mutant VLPs, suggesting that pseudoinfection inhibition relies on mechanisms additional to electrostatic HS binding site interaction. A DNA/RNA Sc5c3 version also inhibited HPV PsVs infection, suggesting that a modified, nuclease-resistant Sc5c3 may be used to inhibit HPV16 infection in vivo.

In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target

Aptamers, synthetic oligonucleotide-based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets. However, the inherent challenges associated with the selection and characterization of aptamers for small molecule targets have resulted in their underrepresentation, despite the need for small molecule detection in fields such as medicine, the environment, and agriculture. This protocol describes the steps in the selection, sequencing, affinity characterization, and truncation of DNA aptamers that are specific for small molecule targets. © 2017 by John Wiley & Sons, Inc.

A fluorescent sensor for detecting dopamine and tyrosinase activity by dual-emission carbon dots and gold nanoparticles

In this work, we report a fluorescence strategy for detecting dopamine (DA) and sensing tyrosinase (TYR) activity on the basis of the dual-emission carbon dots (DECDs), which contain two emitters: the blue emitters (BE, maximum emission at 385nm) and yellow emitters (YE, maximum emission at 530nm). Gold nanoparticles (AuNPs) can effectively quench the two emissions of DECDs. The addition of DA aggregates AuNPs effectively, leading to the fluorescence recovery of dual emitters gradually. This strategy exhibits a high selectivity toward DA and shows good linear ranges, such as 0.5-3μM for BE and 0.1-3μM for YE. Additionally, the proposed method is successfully applied to the determination of DA in real samples with satisfactory recoveries. Subsequently, this DECDs-AuNPs platform is further taken advantage to assess TYR activity by the aid of TYR's capability for oxidation of DA into dopaquinone, which will not induce the agglomeration of AuNPs, so the fluorescence quenching of DECDs is associated with TYR activity. Finally, the mechanism of the reaction is discussed in detail, and the results suggest that both amine and phenolic hydroxyl groups of DA bring the aggregation of AuNPs.

Nucleic acid aptamers for neurodegenerative diseases

The increased incidence of neurodegenerative diseases represents a huge challenge for societies. These diseases are characterized by neuronal death and include several different pathologies, such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, Huntington's disease and transmissible spongiform encephalopathies. Most of these pathologies are often associated with the aggregation of misfolded proteins, such as amyloid-ß, tau, α-synuclein, huntingtin and prion proteins. However, the precise mechanisms that lead to neuronal dysfunction and death in these diseases remain poorly understood. Nucleic acid aptamers represent a new class of ligands that could be useful to better understand these diseases and develop better diagnosis and therapy. In this review, several of these aptamers are presented as well as their applications for neurodegenerative diseases.

Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery

Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.