Rapid Slow Off-Rate Modified Aptamer (SOMAmer)-Based Detection of C-Reactive Protein Using Isotachophoresis and an Ionic Spacer

Isotachophoresis with Oscillating Sample Zones to Control the Spatial Overlap of Co-focused Species

Microfluidic isotachophoresis (ITP) is a powerful technique that can significantly increase the reaction rate of homogeneous chemical reactions by cofocusing reactants in a narrow sample zone. Correspondingly, ITP has been utilized to reduce the reaction time in various bioanalytical assays. However, in conventional ITP, it is hardly possible to control the reaction rate in real time, i.e., speeding up or slowing down a reaction on demand. Here, we experimentally demonstrate a new mode of ITP that allows the spatial overlap of two ITP zones to be precisely controlled over time, which is a crucial first step toward controlling reaction rates. Two nonreactive samples are initially focused and separated by a spacer using a DC electric field. By superimposing an oscillating field component with sufficiently high amplitude on the DC field, the spatial overlap of their concentration profiles is temporarily increased due to electromigration dispersion. The time-average of this overlap can be precisely controlled by varying the frequency and amplitude of the oscillation. We suggest that this scheme can be transferred to chemical reactions between ionic species with sufficiently different electrophoretic mobilities. Tuning the parameters of the oscillatory electric field should allow direct control of the corresponding reaction rate.

Magnetically Detected Protein Binding Using Spin-Labeled Slow Off-Rate Modified Aptamers

Recent developments in aptamer chemistry open up opportunities for new tools for protein biosensing. In this work, we present an approach to use immobilized slow off-rate modified aptamers (SOMAmers) site-specifically labeled with a nitroxide radical via azide-alkyne click chemistry as a means for detecting protein binding. Protein binding induces a change in rotational mobility of the spin label, which is detected via solution-state electron paramagnetic resonance (EPR) spectroscopy. We demonstrate the workflow and test the protocol using the SOMAmer SL5 and its protein target, platelet-derived growth factor B (PDGF-BB). In a complete site scan of the nitroxide over the SOMAmer, we determine the rotational mobility of the spin label in the absence and presence of target protein. Several sites with sufficiently tight affinity and large rotational mobility change upon protein binding are identified. We then model a system where the spin-labeled SOMAmer assay is combined with fluorescence detection via diamond nitrogen-vacancy (NV) center relaxometry. The NV center spin-lattice relaxation time is modulated by the rotational mobility of a proximal spin label and thus responsive to SOMAmer-protein binding. The spin label-mediated assay provides a general approach for transducing protein binding events into magnetically detectable signals.

Electrophoresis-Assisted Multilayer Assembly of Nanoparticles for Sensitive Lateral Flow Immunoassay

Lateral flow immunoassay (LFIA) is a rapid, simple, and inexpensive point-of-need method. A major limitation of LFIA is a high limit of detection (LOD), which impacts its diagnostic sensitivity. To overcome this limitation, we introduce a signal-enhancement procedure that is performed after completing LFIA and involves controllably moving biotin- and streptavidin-functionalized gold nanoparticles by electrophoresis. The nanoparticles link to immunocomplexes forming multilayer aggregates on the test strip, thus, enhancing the signal. Here, we demonstrate lowering the LOD of hepatitis B surface antigen from approximately 8 to 0.12 ng mL^-1 , making it clinically acceptable. Testing 118 clinical samples for hepatitis B showed that signal enhancement increased the diagnostic sensitivity of LFIA from 73 % to 98 % while not affecting its 95 % specificity. Electrophoresis-driven enhancement of LFIA is universal (antigen-independent), takes two minutes, and can be performed by an untrained person.

Isotachophoresis: Theory and Microfluidic Applications

Isotachophoresis (ITP) is a versatile electrophoretic technique that can be used for sample preconcentration, separation, purification, and mixing, and to control and accelerate chemical reactions. Although the basic technique is nearly a century old and widely used, there is a persistent need for an easily approachable, succinct, and rigorous review of ITP theory and analysis. This is important because the interest and adoption of the technique has grown over the last two decades, especially with its implementation in microfluidics and integration with on-chip chemical and biochemical assays. We here provide a review of ITP theory starting from physicochemical first-principles, including conservation of species, conservation of current, approximation of charge neutrality, pH equilibrium of weak electrolytes, and so-called regulating functions that govern transport dynamics, with a strong emphasis on steady and unsteady transport. We combine these generally applicable (to all types of ITP) theoretical discussions with applications of ITP in the field of microfluidic systems, particularly on-chip biochemical analyses. Our discussion includes principles that govern the ITP focusing of weak and strong electrolytes; ITP dynamics in peak and plateau modes; a review of simulation tools, experimental tools, and detection methods; applications of ITP for on-chip separations and trace analyte manipulation; and design considerations and challenges for microfluidic ITP systems. We conclude with remarks on possible future research directions. The intent of this review is to help make ITP analysis and design principles more accessible to the scientific and engineering communities and to provide a rigorous basis for the increased adoption of ITP in microfluidics.

Aptamers Targeting Cardiac Biomarkers as an Analytical Tool for the Diagnostics of Cardiovascular Diseases: A Review

The detection of cardiac biomarkers is used for diagnostics, prognostics, and the risk assessment of cardiovascular diseases. The analysis of cardiac biomarkers is routinely performed with high-sensitivity immunological assays. Aptamers offer an attractive alternative to antibodies for analytical applications but, to date, are not widely practically implemented in diagnostics and medicinal research. This review summarizes the information on the most common cardiac biomarkers and the current state of aptamer research regarding these biomarkers. Aptamers as an analytical tool are well established for troponin I, troponin T, myoglobin, and C-reactive protein. For the rest of the considered cardiac biomarkers, the isolation of novel aptamers or more detailed characterization of the known aptamers are required. More attention should be addressed to the development of dual-aptamer sandwich detection assays and to the studies of aptamer sensing in alternative biological fluids. The universalization of aptamer-based biomarker detection platforms and the integration of aptamer-based sensing to clinical studies are demanded for the practical implementation of aptamers to routine diagnostics. Nevertheless, the wide usage of aptamers for the diagnostics of cardiovascular diseases is promising for the future, with respect to both point-of-care and laboratory testing.

Aptasensors for the detection of infectious pathogens: design strategies and point-of-care testing

The epidemic of infectious diseases caused by contagious pathogens is a life-threatening hazard to the entire human population worldwide. A timely and accurate diagnosis is the critical link in the fight against infectious diseases. Aptamer-based biosensors, the so-called aptasensors, employ nucleic acid aptamers as bio-receptors for the recognition of target pathogens of interest. This review focuses on the design strategies as well as state-of-the-art technologies of aptasensor-based diagnostics for infectious pathogens (mainly bacteria and viruses), covering the utilization of three major signal transducers, the employment of aptamers as recognition moieties, the construction of versatile biosensing platforms (mostly micro and nanomaterial-based), innovated reporting mechanisms, and signal enhancement approaches. Advanced point-of-care testing (POCT) for infectious disease diagnostics are also discussed highlighting some representative ready-to-use devices to address the urgent needs of currently prevalent coronavirus disease 2019 (COVID-19). Pressing issues in aptamer-based technology and some future perspectives of aptasensors are provided for the implementation of aptasensor-based diagnostics into practical application.

Advances in aptamer-based sensing assays for C-reactive protein

C-reactive protein (CRP), a non-specific acute-phase indicator of inflammation, has been widely recognized for its value in clinical diagnostic applications. With the advancement of testing technologies, there have been many reports on fast, simple, and reliable methods for CRP testing. Among these, the aptamer-based biosensors are the focus and hotspot of research for achieving high-sensitivity analysis of CRP. This review summarizes the progress of in vitro aptamer screening for CRP and the recent advances in aptamer-based CRP sensor applications, thus developing insight for the new CRP aptasensor design strategy.

Species Abundance and Reaction Off-Rate Regulate Product Formation in Reactions Accelerated Using Isotachophoresis

We present a model for second-order and pseudo-first-order reversible chemical reactions accelerated using peak-mode isotachophoresis (ITP). In such systems, ITP preconcentrates and co-locates the reactants between the leading and trailing electrolyte zones, and this significantly accelerates chemical reactions. Our model quantifies the effects of reaction rate constants and species abundance on product formation rate. We identify two key non-dimensional parameters, which are specific groupings of reaction rate constants, species concentrations, and influx rates. We then use a regular perturbation to study the effects of reverse reaction rate and relative species abundance (and relative rates of species accumulation) on production rate. We also use this perturbation method to derive an analytical expression for the quasi-steady-state production rate achievable by ITP. Our analytical models and numerical solutions are generally applicable to a wide range of systems, which use ITP to enhance reactions. The model is also an interesting case study of the complex coupling of electric field-driven species transport and reaction kinetics.

Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders

An aptamer is a short sequence of synthetic oligonucleotides which bind to their cognate target, specifically while maintaining similar or higher sensitivity compared to an antibody. The in-vitro selection of an aptamer, applying a conjoining approach of chemistry and molecular biology, is referred as Systematic Evolution of Ligands by Exponential enrichment (SELEX). These initial products of SELEX are further modified chemically in an attempt to make them stable in biofluid, avoiding nuclease digestion and renal clearance. While the modification is incorporated, enough care should be taken to maintain its sensitivity and specificity. These modifications and several improvisations have widened the window frame of aptamer applications that are currently not only restricted to in-vitro systems, but have also been used in molecular imaging for disease pathology and treatment. In the food industry, it has been used as sensor for detection of different diseases and fungal infections. In this review, we have discussed a brief history of its journey, along with applications where its role as a therapeutic plus diagnostic (theranostic) tool has been demonstrated. We have also highlighted the potential aptamer-mediated strategies for molecular targeting of COVID-19. Finally, the review focused on its future prospective in immunotherapy, as well as in identification of novel biomarkers in stem cells and also in single cell proteomics (scProteomics) to study intra or inter-tumor heterogeneity at the protein level. Small size, chemical synthesis, low batch variation, cost effectiveness, long shelf life and low immunogenicity provide advantages to the aptamer over the antibody. These physical and chemical properties of aptamers render them as a strong biomedical tool for theranostic purposes over the existing ones. The significance of aptamers in human health was the key finding of this review.

Aptamers for Proteins Associated with Rheumatic Diseases: Progress, Challenges, and Prospects of Diagnostic and Therapeutic Applications

Nucleic acid aptamers capable of affine and specific binding to their molecular targets have now established themselves as a very promising alternative to monoclonal antibodies for diagnostic and therapeutic applications. Although the main focus in aptamers’ research and development for biomedicine is made on cardiovascular, infectious, and malignant diseases, the use of aptamers as therapeutic or diagnostic tools in the context of rheumatic diseases is no less important. In this review, we consider the main features of aptamers that make them valuable molecular tools for rheumatologists, and summarize the studies on the selection and application of aptamers for protein biomarkers associated with rheumatic diseases. We discuss the progress in the development of aptamer-based diagnostic assays and targeted therapeutics for rheumatic disorders, future prospects in the field, and issues that have yet to be addressed.

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

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

Modified DNA Aptamers for C-Reactive Protein and Lactate Dehydrogenase-5 with Sub-Nanomolar Affinities

Human C-reactive protein (CRP) and lactate dehydrogenase are important markers in clinical laboratory testing-the former is used to detect in vivo inflammation, and the latter is used to detect cell necrosis and tissue destruction. We developed aptamers that bind to human CRP and human lactate dehydrogenase-5 (LDH-5) with high affinities (dissociation constants of 6.2 pM and 235 pM, respectively), applying the systematic evolution of ligands by exponential enrichment (SELEX) method, and by using a modified DNA library containing the following base-appended base modifications: analog adenine derivative at the fifth position of uracil (U^ad), analog guanine derivative at the fifth position of uracil (U^gu), and analog adenine derivative at the seventh position of adenine (A^ad). A potential application of these aptamers as sensor elements includes high-sensitivity target detection in point-of-care testing.

Trapping of sub-100 nm nanoparticles using gigahertz acoustofluidic tweezers for biosensing applications

In this study, we present a nanoscale acoustofluidic trap (AFT) that manipulates nanoparticles in a microfluidic system actuated by a gigahertz acoustic resonator. The AFT generates independent standing closed vortices with high-speed rotation. Via careful design and optimization of geometric confinements, the AFT was able to effectively capture and enrich sub-100 nm nanoparticles with a low power consumption (0.25-5 μW μm-2) and rapid trapping (within 30 s), showing significantly enhanced particle-operating ability as compared to its acoustic and optical counterparts; using specifically functionalized nanoparticles (SFNPs) to selectively capture target molecules from the sample, the AFT led to the molecular concentration enhancement of ∼200 times. We investigated the feasibility of the SFNP-assisted AFT preconcentration method for biosensing applications and successfully demonstrated the capability of this method for the detection of serum prostate-specific antigen (PSA). The AFT was prepared via a fully CMOS-compatible process and thus could be conveniently integrated on a single chip, with potential for "lab-on-a-chip" or point-of-care (POC) nanoparticle-based biosensing applications.

Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development

Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.

Aptamers in the Therapeutics and Diagnostics Pipelines

Aptamers are short single-stranded DNA or RNA oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity, by acquiring unique three-dimensional structures. Aptamers have the advantage of being highly specific, relatively small in size, non-immunogenic and can be easily stabilized by chemical modifications, thus allowing expansion of their diagnostic and therapeutic potential. Since the invention of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like macular degeneration, cancer, thrombosis and inflammatory diseases. Furthermore, owing to the aforementioned advantages and unique adaptability of aptamers to point-of-care platforms, aptamer technology has created a stable niche in the field of in vitro diagnostics by enhancing the speed and accuracy of diagnoses. The aim of this review is to give an overview on aptamers, highlight the inherent therapeutic and diagnostic opportunities and challenges associated with them and present various aptamers that have reached therapeutic clinical trials, diagnostic markets or that have immediate translational potential for therapeutics and diagnostics applications.

Slow Off-Rate Modified Aptamer (SOMAmer) as a Novel Reagent in Immunoassay Development for Accurate Soluble Glypican-3 Quantification in Clinical Samples

Accurate quantification of soluble glypican-3 in clinical samples using immunoassays is challenging, because of the lack of appropriate antibody reagents to provide a full spectrum measurement of all potential soluble glypican-3 fragments in vivo. Glypican-3 SOMAmer (slow off-rate modified aptamer) is a novel reagent that binds, with high affinity, to a far distinct epitope of glypican-3, when compared to all available antibody reagents generated in-house. This paper describes an integrated analytical approach to rational selection of key reagents based on molecular characterization by epitope mapping, with the focus on our work using a SOMAmer as a new reagent to address development challenges with traditional antibody reagents for the soluble glypican-3 immunoassay. A qualified SOMAmer-based assay was developed and used for soluble glypican-3 quantification in hepatocellular carcinoma (HCC) patient samples. The assay demonstrated good sensitivity, accuracy, and precision. Data correlated with those obtained using the traditional antibody-based assay were used to confirm the clinically relevant soluble glypican-3 forms in vivo. This result was reinforced by a liquid chromatography tandem mass spectrometry (LC-MS/MS) assay quantifying signature peptides generated from trypsin digestion. The work presented here offers an integrated strategy for qualifying aptamers as an alternative affinity platform for immunoassay reagents that can enable speedy assay development, especially when traditional antibody reagents cannot meet assay requirements.

Amplification-free detection of DNA in a paper-based microfluidic device using electroosmotically balanced isotachophoresis

We present a novel microfluidic paper-based analytical device (μPAD) which utilizes the native high electroosmotic flow (EOF) in nitrocellulose to achieve stationary isotachophoresis (ITP) focusing. This approach decouples sample accumulation from the length of the channel, resulting in significant focusing over short channel lengths. We provide a brief theory for EOF-balanced ITP focusing under continuous injection from a depleting reservoir and present the design of a short (7 mm) paper-based microfluidic channel, which allows a 200 μL sample to be processed in approximately 6 min, resulting in a 20 000-fold increase in concentration - a full order of magnitude improvement compared to previous paper-based ITP devices. We show the stability of the assay over longer (40 min) durations of time, and using Morpholino probes, we present the applicability of the device for amplification-free detection of nucleic acids, with a limit-of-detection (LoD) of 5 pM in 10 min. Finally, we utilize the small footprint of the channel and show a multiplexed platform in which 12 assays operate in parallel in a 24-well plate format.

Assay for Listeria monocytogenes cells in whole blood using isotachophoresis and recombinase polymerase amplification

We present a new approach which enables lysis, extraction, and detection of inactivated Listeria monocytogenes cells from blood using isotachophoresis (ITP) and recombinase polymerase amplification (RPA). We use an ITP-compatible alkaline and proteinase K approach for rapid and effective lysis. We then perform ITP purification to separate bacterial DNA from whole blood contaminants using a microfluidic device that processes 25 μL sample volume. Lysis, mixing, dispensing, and on-chip ITP purification are completed in a total of less than 50 min. We transfer extracted DNA directly into RPA master mix for isothermal incubation and detection, an additional 25 min. We first validate our assay in the detection of purified genomic DNA spiked into whole blood, and demonstrate a limit of detection of 16.7 fg μL^-1 genomic DNA, the equivalent of 5 × 10³ cells per mL. We then show detection of chemically-inactivated L. monocytogenes cells spiked into whole blood, and demonstrate a limit of detection of 2 × 10⁴ cells per mL. Lastly, we show preliminary experimental data demonstrating the feasibility of the integration of ITP purification with RPA detection on a microfluidic chip. Our results suggest that ITP purification is compatible with RPA detection, and has potential to extend the applicability of RPA to whole blood.

Isotachophoresis applied to biomolecular reactions

This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids, proteins, and live cells. ITP is a versatile technique which requires no specific geometric design or material, and is compatible with a wide range of microfluidic and automated platforms. Though ITP has traditionally been used as a purification and separation technique, recent years have seen its emergence as a method to automate and speed up chemical reactions. ITP has been used to demonstrate up to 14 000-fold acceleration of nucleic acid assays, and has been used to enhance lateral flow and other immunoassays, and even whole bacterial cell detection assays. We here classify these studies into two categories: homogeneous (all reactants in solution) and heterogeneous (at least one reactant immobilized on a solid surface) assay configurations. For each category, we review and describe physical modeling and scaling of ITP-aided reaction assays, and elucidate key principles in ITP assay design. We summarize experimental advances, and identify common threads and approaches which researchers have used to optimize assay performance. Lastly, we propose unaddressed challenges and opportunities that could further improve these applications of ITP.

Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes

Nucleic acid aptamers have minimal immunogenicity, high chemical synthesis production, low cost and high chemical stability when compared with antibodies. However, the susceptibility to nuclease degradation, rapid excretion through renal filtration and insufficient binding affinity hindered their development as drug candidates for therapeutic applications. In this review, we will discuss methods to conquer these challenges and highlight recent developments of chemical modifications and technological advances that may enable early aptamers to be translated into clinical therapeutics.

A facile label-free G-quadruplex based fluorescent aptasensor method for rapid detection of ATP

The present work demonstrates a simple, rapid and label-free ATP detection method using a fluorescent aptasensor that is based on G-quadruplex formation. In the absence of ATP, the Thioflavin T (ThT) dye binds to the G-rich ATP aptamer and forms an ATP aptamer/ThT G-quadruplex complex, which results in high fluorescence intensity. Upon addition of ATP, the ATP aptamer/ThT complex will be replaced by the formation of an ATP aptamer/ATP complex. During this process, separation of the ThT dye from the ATP aptamer/ThT complex decreases the fluorescence intensity of the reaction mixture dramatically. This fluorescence aptasensor is highly sensitive and rapid, with a detection limit of 18nM and a total reaction time of only 10min. Furthermore, this method is cost-effective and simple, removing the requirement for labeling the detection reagents with a fluorophore-quencher pair.

A rapidly-prototyped microfluidic device for size-based nucleic acid fractionation using isotachophoresis

We present a novel microfluidic device for size-based nucleic acid (NA) fractionation using isotachophoresis (ITP) and an ionic spacer.

Micro- and Nanoscale Technologies for Delivery into Adherent Cells

Several recent micro- and nanotechnologies have provided novel methods for biological studies of adherent cells because the small features of these new biotools provide unique capabilities for accessing cells without the need for suspension or lysis. These novel approaches have enabled gentle but effective delivery of molecules into specific adhered target cells, with unprecedented spatial resolution. We review here recent progress in the development of these technologies with an emphasis on in vitro delivery into adherent cells utilizing mechanical penetration or electroporation. We discuss the major advantages and limitations of these approaches and propose possible strategies for improvements. Finally, we discuss the impact of these technologies on biological research concerning cell-specific temporal studies, for example non-destructive sampling and analysis of intracellular molecules.

A sandwich dipstick assay for ATP detection based on split aptamer fragments

Aptamer-based strip assay is an easy, highly efficient and low-cost detection method, which has been developed and easily applied to onsite detection. A new sensitive sandwich dipstick assay for adenosine triphosphate (ATP) detection was successfully developed based on specific recognition between split aptamer fragments and the target. In this method, the thiolated aptamer was first conjugated to the surface of gold nanoparticles (AuNPs), while the biotin-aptamer was immobilized on the surface of a nitrocellulose filter in the test line. In the presence of ATP, the thiol-aptamer/ATP/biotin-aptamer complexes were generated, which led to an obvious increase in optical signals at the test line. Under the optimal determination conditions, an excellent linear logarithmic response to the ATP concentration was obtained within the range of 0.5 μM to 5 mM. The limit of detection (LOD) of 0.5 μM was reached at a signal-to-noise ratio of 3. The dipstick assay showed a good average recovery of 96-108 % with the RSD of less than 20 % in urine samples. The proposed method exhibited high specificity against other nucleotides such as the uridine triphosphate (UTP), cytidine triphosphate (CTP), and guanosine triphosphate (GTP). The results indicated that the dipstick strip may be considered as an inexpensive screening tool for onsite ATP determination. Graphical Abstract A simple split aptamer fragments based sandwich-type dipstick assay was developed for ATP detection.

Detection of C-reactive protein using nanoparticle-enhanced surface plasmon resonance using an aptamer-antibody sandwich assay

High affinity DNA aptamers against C-reactive protein (CRP) were obtained using a microfluidic chip. The aptamers were then used for the construction of an Au nanoparticle enhanced surface plasmon resonance biosensor, which was introduced for the detection of CRP at concentrations ranging from 10 pM to 100 nM in diluted human serum.