Assessing Aptamer-Analyte Binding Kinetics by Microfluidic Fluorescence Microscopy.

Kinetic measurement plays a crucial role in understanding aptamer binding mechanisms and identifying appropriate aptamers for clinical and research applications. Current techniques, while well established, generally require large sample volumes, bulky and expensive instruments operated by trained personnel, and are hence not readily accessible to resource-limited research laboratories. This paper presents a fluorescence microscopy-based microfluidic assay for measuring aptamer-analyte binding kinetics in a simple and cost-effective manner. Kinetic measurements are achieved by monitoring time-course fluorescence of fluorescently labeled aptamers as they bind to the targets trapped in a microfluidic chip. Fluorescence measurements are performed on a standard fluorescence microscope and are accessible to laboratories with only modest resources. Moreover, microfluidic technology allows efficient and cost-effective immobilization of small amounts of target molecules or live cells as well as flow-based manipulation of aptamers for the measurements. Kinetic measurements of aptamer binding to immunoglobulin E protein and CCRF-CEM cells have yielded results consistent with those obtained from established methods, demonstrating the potential utility of our method for exploring aptamer-target interactions and identifying aptamers that best suit specific given biomedical applications.

A comparative study of aptamer isolation by conventional and microfluidic strategies.

Aptamers are single-stranded oligonucleotide molecules that bind with high affinity and specificity to a wide range of target molecules. The method of systematic evolution of ligands by exponential enrichment (SELEX) plays an essential role in the isolation of aptamers from a randomized oligonucleotide library. To date, significant modifications and improvements of the SELEX process have been achieved, engendering various forms of SELEX from conventional SELEX to microfluidics-based full-chip SELEX. While full-chip SELEX is generally considered advantageous over conventional SELEX, there has not yet been a conclusive comparison between the methods. Herein, we present a comparative study of three SELEX strategies for aptamer isolation, including those using conventional agarose bead-based partitioning, microfluidic affinity selection, and fully integrated microfluidic affinity selection and PCR amplification. Using immunoglobulin E (IgE) as a model target molecule, we compare these strategies in terms of the time and cost for each step of the SELEX process including affinity selection, amplification, and oligonucleotide conditioning. Target-binding oligonucleotides in the enriched pools are sequenced and compared to assess the relative efficacy of the SELEX strategies. We show that the microfluidic strategies are more time- and cost-efficient than conventional SELEX.

A Microfluidic Dual-Aptamer Sandwich Assay for Rapid and Cost-Effective Detection of Recombinant Proteins.

While monitoring expression of recombinant proteins is essential for obtaining high-quality biopharmaceutical and biotechnological products, existing assays for recombinant protein detection are laborious, time-consuming and expensive. This paper presents a microfluidic approach to rapid and cost-effective detection of tag-fused recombinant proteins via a dual-aptamer sandwich assay. Our approach addresses limitations in current methods for both dual-aptamer assays and generation of aptamers for such assays by first using microfluidic technology to isolate the aptamers rapidly and then employing these aptamers to implement a microfluidic dual-aptamer assay for tag-fused recombinant protein detection. The use of microfluidic technology enables the fast generation of aptamers and rapid detection of recombinant proteins with minimized consumption of reagents. In addition, compared with antibodies, aptamers as low-cost affinity reagents with an ability of reversible denaturation further decreases the cost of recombinant protein detection. For demonstration, an aptamer pair is isolated rapidly toward His-tagged IgE within two days, and then used in the microfluidic dual-aptamer assay for detecting His-tagged IgE in cell culture media within 10 min and with a limit of detection of 7.1 nM.

Microfluidic isolation of aptamers with affinity towards multiple myeloma monoclonal immunoglobulins.

Multiple myeloma (MM) is a bone marrow cancer of resident plasma cells that affects 125,000 patients in the U.S. with about 30,000 new cases per year. Its signature is the clonal proliferation of a single plasma cell that secretes a patient specific monoclonal immunoglobulin (M-Ig). Targeting the M-Ig in patient serum could allow sensitive and noninvasive identification of minimal residual disease in multiple myeloma. Aptamers, which are single-stranded oligonucleotides with affinity and specificity to a target molecule, have recently been introduced as affinity reagents for recognition of MM M-Igs. Here we exploit microfluidic SELEX technology to enable rapid and efficient generation of aptamers against M-Ig proteins from MM patients. We first characterize the technology by isolating aptamers with affinity towards the monoclonal antibody rituximab as a model M-Ig and then apply the technology to isolating aptamers specifically targeting M-Igs obtained from serum samples of MM patients. We demonstrate that high-affinity DNA aptamers (KD < 50 nM) for M-Ig proteins from a patient sample could be isolated via microfluidic SELEX within approximately 12 h and using less than 100 micrograms of patient M-Ig. Such aptamers can potentially be used in personalized monitoring of minimal residual disease in MM patients.

Mathematical approaches in estimating aptamer-target binding affinity.

The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Mathematical models ranging from one-site binding to multiple aptameric binding site-based models are explained in detail. Models applied in several different approaches of affinity measurements such as thermodynamics and kinetic analysis, including cooperativity and competitive-assay based mathematical models have been elaborately discussed. Mathematical models incorporating factors that could potentially affect affinity measurements are also further scrutinized.

Can oriented-attachment be an efficient growth mechanism for the synthesis of 1D nanocrystals via atomic layer deposition?

One-dimensional (1D) nanocrystals, such as nanorods and nanowires, have received extensive attention in the nanomaterials field due to their large surface areas and 1D confined transport properties. Oriented attachment (OA) is now recognized as a major growth mechanism for efficiently synthesizing 1D nanocrystals. Recently, atomic layer deposition (ALD) has been modified to be a powerful vapor-phase technique with which to synthesize 1D OA nanorods/nanowires with high efficiency and quality by increasing the temperature and purging time. In this invited mini-review, we look into the advantages of OA and high-temperature ALD, and investigate the potential of employing the OA growth mechanism for the synthesis of 1D nanocrystals via modified ALD, aiming to provide guidance to researchers in the fields of both OA and ALD for efficient synthesis of 1D nanocrystals.

Quantitative evaluation of Coulombic interactions in the oriented-attachment growth of nanotubes.

The Coulombic interaction in the oriented attachment growth of one-dimensional nanotubes is evaluated via a newly-derived analytical expression of the Coulombic interactions between a spherical attaching nanoparticle and a growing nanotube. The correlation between the interaction and the important growth parameters, including nanoparticle/nanotube size, aspect ratio, and nanoparticle-nanotube separation has been analyzed. Our work provides, for the first time, an efficient platform to investigate the growth kinetics and mechanisms of oriented attachment growth of nanotubes.

Cost-effective evaluation of Aptamer candidates in SELEX-based Aptamer isolation.

Aptamers are short, single-stranded nucleic acids with high affinity and specificity for various targets, making them valuable in diagnostics and therapeutics. Their isolation traditionally involves a time-consuming and costly process called SELEX. While SELEX methods have evolved to improve binding and amplification, the crucial step of aptamer identification from sequencing data remains expensive and often overlooked. Common identification methods require modification of aptamer candidates with labels like biotin or fluorescent dyes, which becomes costly and cumbersome for high-throughput sequencing data. This paper presents an efficient and cost-effective approach to streamline aptamer identification. It employs asymmetric polymerase chain reaction (PCR) to generate modified single-stranded DNA copies of aptamer candidates, simplifying the modification process. By using excess modified forward primers and limited reverse primers, this method reduces costs since only unmodified candidates need to be synthesized initially. The approach was demonstrated with an IgE protein aptamer and successfully applied to identify aptamers from a pool of 12 candidates against a monoclonal antibody. The validity of the results was further confirmed through the direct synthesis of fluorophore-conjugated aptamer candidates, yielding consistent outcomes while reducing the cost by threefold. This approach addresses a critical bottleneck in aptamer discovery by significantly reducing the time and cost associated with aptamer identification, facilitating aptamer-based research and making aptamers more accessible for various applications in diagnostics and therapeutics.

Rapid isolation of anti-idiotype aptamers for quantification of human monoclonal antibodies against SARS-CoV-2 spike protein.

Therapeutic antibodies that block viral entry have already proven to be important, first line drugs for treatments of viral infections. In the case of SARS-CoV-2, combinations of multiple therapeutic antibodies may need to be rapidly identified and formulated in a way that blocks each new, predominant variant of the virus. For efficient introduction of any new antibody combination into patients, it is important to be able to monitor patient-specific pharmacokinetics of individual antibodies, which would include the time course of their specific capacity to block the viral spike proteins. Here, we present three examples of microfluidic-based rapid isolation of companion reagents useful for establishing combination antibody therapies. These reagents are specific three-dimensional imprints of variable regions of individual human monoclonal antibodies against the -spike protein of SARS-CoV-2 virus in the form of oligonucleotide-based ligands (aptamers). We implement these anti-idiotypic aptamers as bioreceptors in graphene-based field-effect transistor sensors to accomplish label free, rapid, and sensitive detection of matching antibodies within minutes. Through this work we have demonstrated the general applicability of anti-idiotype aptamers as capture reagents in quantification of active forms of monoclonal antibodies in complex biological mixtures.

Microfluidic measurement of intracellular mRNA with a molecular beacon probe towards point-of-care radiation triage.

In large-scale radiation exposure events, the ability to triage potential victims by the received radiation dosage is crucial. This can be evaluated by radiation-induced biological changes. Radiation-responsive mRNA is a class of biomarkers that has been explored for dose-dependency with methods such as RT-qPCR. However, these methods are challenging to implement for point-of-care devices. We have designed and used molecular beacons as probes for the measurement of radiation-induced changes of intracellular mRNA in a microfluidic device towards determining radiation dosage. Our experiments, in which fixed TK6 cells labeled with a molecular beacon specific to BAX mRNA exhibited dose-dependent fluorescence in a manner consistent with RT-qPCR analysis, demonstrate that such intracellular molecular probes can potentially be used in point-of-care radiation biodosimetry. This proof of concept could readily be extended to any RNA-based test to provide direct measurements at the bedside.

Surface acoustic wave-assisted microfluidic isolation of aptamers.

Aptamers are synthetic single-stranded nucleic acid molecules that bind to biochemical targets with high affinity and specificity. The method of systematic evolution of ligands by exponential enrichment (SELEX) is widely used to isolate aptamers from randomized oligonucleotides. Recently, microfluidic technology has been applied to improve the efficiency and reduce the cost in SELEX processes. In this work, we present an approach that exploits surface acoustic waves to improve the affinity selection process in microfluidic SELEX. Acoustic streaming is used to enhance the interactions of the solution-based oligonucleotide molecules with microbead-immobilized target molecules, allowing the identification of high-affinity aptamer candidates in a more efficient manner. For demonstration, a DNA aptamer is isolated within three rounds of selection in 5 h to specifically bind to immunoglobulin E, a representative target protein, with an equilibrium dissociation constant of approximately 22.6 nM.

High-Polarity Fluoroalkyl Ether Electrolyte Enables Solvation-Free Li+ Transfer for High-Rate Lithium Metal Batteries.

Lithium metal batteries (LMBs) have aroused extensive interest in the field of energy storage owing to the ultrahigh anode capacity. However, strong solvation of Li+ and slow interfacial ion transfer associated with conventional electrolytes limit their long-cycle and high-rate capabilities. Herein an electrolyte system based on fluoroalkyl ether 2,2,2-trifluoroethyl-1,1,2,3,3,3-hexafluoropropyl ether (THE) and ether electrolytes is designed to effectively upgrade the long-cycle and high-rate performances of LMBs. THE owns large adsorption energy with ether-based solvents, thus reducing Li+ interaction and solvation in ether electrolytes. With THE rich in fluoroalkyl groups adjacent to oxygen atoms, the electrolyte owns ultrahigh polarity, enabling solvation-free Li+ transfer with a substantially decreased energy barrier and ten times enhancement in Li+ transference at the electrolyte/anode interface. In addition, the uniform adsorption of fluorine-rich THE on the anode and subsequent LiF formation suppress dendrite formation and stabilize the solid electrolyte interphase layer. With the electrolyte, the lithium metal battery with a LiFePO4 cathode delivers unprecedented cyclic performances with only 0.0012% capacity loss per cycle over 5000 cycles at 10 C. Such enhancement is consistently observed for LMBs with other mainstream electrodes including LiCoO2 and LiNi0.5 Mn0.3 Co0.2 O2 , suggesting the generality of the electrolyte design for battery applications.

Tellurium-Impregnated Porous Cobalt-Doped Carbon Polyhedra as Superior Cathodes for Lithium-Tellurium Batteries.

Lithium-tellurium (Li-Te) batteries are attractive for energy storage owing to their high theoretical volumetric capacity of 2621 mAh cm-3. In this work, highly nanoporous cobalt and nitrogen codoped carbon polyhedra (C-Co-N) derived from a metal-organic framework (MOF) is synthesized and employed as tellurium host for Li-Te batteries. The Te@C-Co-N cathode with a high Te loading of 77.2 wt % exhibits record-breaking electrochemical performances including an ultrahigh initial capacity of 2615.2 mAh cm-3 approaching the theoretical capacity of Te (2621 mAh cm-3), a superior cycling stability with a high capacity retention of 93.6%, a ∼99% Columbic efficiency after 800 cycles as well as rate capacities of 2160, 1327.6, and 894.8 mAh cm-3 at 4, 10, and 20 C, respectively. The redox chemistry of tellurium is revealed by in operando Raman spectroscopic analysis and density functional theory simulations. The results illustrate that the performances are attributed to the highly conductive C-Co-N matrix with an advantageous structure of abundant micropores, which provides highly efficient channels for electron transfer and ionic diffusion as well as sufficient surface area to efficiently host tellurium while mitigating polytelluride dissolution and suppressing volume expansion.

Three-Dimensional Hierarchical Reduced Graphene Oxide/Tellurium Nanowires: A High-Performance Freestanding Cathode for Li-Te Batteries.

Three-dimensional aerogel with ultrathin tellurium nanowires (TeNWs) wrapped homogeneously by reduced graphene oxide (rGO) is realized via a facile hydrothermal method. Featured with high conductivity and large flexibility, the rGO constructs a conductive three-dimensional (3D) backbone with rich porosity and leads to a free-standing, binder-free cathode for lithium-tellurium (Li-Te) batteries with excellent electrochemical performances. The cathode shows a high initial capacity of 2611 mAh cm(-3) at 0.2 C, a high retention of 88% after 200 cycles, and a high-rate capacity of 1083 mAh cm(-3) at 10 C. In particular, the 3D aerogel cathode delivers a capacity of 1685 mAh cm(-3) at 1 C after 500 cycles, showing pronounced long-cycle performance at high current density. The performances are attributed to the well-defined flexible 3D architecture with high porosity and conductivity network, which offers highly efficient channels for electron transfer and ionic diffusion while compromising volume expansion of Te in charge/discharge. Owing to such advantageous properties, the reported 3D rGO/tellurium nanowire (3DGT) aerogel presents promising application potentials as a high-performance cathode for Li-Te batteries.

From Metal-Organic Framework to Li2S@C-Co-N Nanoporous Architecture: A High-Capacity Cathode for Lithium-Sulfur Batteries.

Owing to the high theoretical specific capacity (1166 mAh g-1), lithium sulfide (Li2S) has been considered as a promising cathode material for Li-S batteries. However, the polysulfide dissolution and low electronic conductivity of Li2S limit its further application in next-generation Li-S batteries. In this report, a nanoporous Li2S@C-Co-N cathode is synthesized by liquid infiltration-evaporation of ultrafine Li2S nanoparticles into graphitic carbon co-doped with cobalt and nitrogen (C-Co-N) derived from metal-organic frameworks. The obtained Li2S@C-Co-N architecture remarkably immobilizes Li2S within the cathode structure through physical and chemical molecular interactions. Owing to the synergistic interactions between C-Co-N and Li2S nanoparticles, the Li2S@C-Co-N composite delivers a reversible capacity of 1155.3 (99.1% of theoretical value) at the initial cycle and 929.6 mAh g-1 after 300 cycles, with nearly 100% Coulombic efficiency and a capacity fading of 0.06% per cycle. It exhibits excellent rate capacities of 950.6, 898.8, and 604.1 mAh g-1 at 1C, 2C, and 4C, respectively. Such a cathode structure is promising for practical applications in high-performance Li-S batteries.