Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions

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.

Native diffusion of fluorogenic turn-on dyes accurately report interfacial chemical reaction locations

Single-molecule fluorescence microscopy with "turn-on" dyes that change fluorescent state after a reaction report on the chemistry of interfaces relevant to analytical and bioanalytical chemistry. Paramount to accurately understanding the phenomena at the ultimate detection limit of a single molecule is ensuring fluorophore properties such as diffusion do not obscure the chemical reaction of interest. Here, we develop Monte Carlo simulations of a dye that undergoes reduction to turn-on at the cathode of a corroded iron surface taking into account the diffusion of the dye molecules in a total internal reflection fluorescence (TIRF) excitation volume, location of the cathode, and chemical reactions. We find, somewhat counterintuitively, that a fast diffusion coefficient of D = 10⁸ nm²/s, corresponding to the dye in aqueous solution, accurately reports the location of single reaction sites. The dyes turn on and are present for the acquisition of a single frame allowing for localization before diffusing out of the thin TIRF excitation volume axially. Previously turned-on (i.e., activated) dyes can also randomly hit the surface surrounding the reaction site leading to a uniform increase in the background. Using concentrations that lead to high turnover rates at the reaction site can achieve signal-to-background ratios of  ~100 in our simulation. Therefore, the interplay between diffusion, turn-on reaction rate, and concentration of the dye must be strategically considered to produce accurate images of reaction locations. This work demonstrates that modeling can assist in the design of single-molecule microscopy experiments to understand interfaces related to analytical chemistry such as electrode, nanoparticle, and sensor surfaces.

Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing

The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.

Tuning IgE: IgE-Associating Molecules and Their Effects on IgE-Dependent Mast Cell Reactions

The recent emergence of anti-immunoglobulin E (IgE) drugs and their candidates for humans has endorsed the significance of IgE-dependent pathways in allergic disorders. IgE is distributed locally in the tissues or systemically to confer a sensory mechanism in a domain of adaptive immunity to the otherwise innate type of effector cells, namely, mast cells and basophils. Bound on the high-affinity IgE receptor FcεRI, IgE enables fast memory responses against revisiting threats of venoms, parasites, and bacteria. However, the dysregulation of IgE-dependent reactions leads to potentially life-threatening allergic diseases, such as asthma and anaphylaxis. Therefore, reactivity of the IgE sensor is fine-tuned by various IgE-associating molecules. In this review, we discuss the mechanistic basis for how IgE-dependent mast cell activation is regulated by the IgE-associating molecules, including the newly developed therapeutic candidates.

Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications

Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets-IgA, IgM, IgG and IgE-have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.

Biophysical Characterization of Aptamer-Target Interactions

Aptamers are single-stranded nucleic acid molecules forming well-defined 3D structures. Aptamers typically bind to their ligands with high affinity and specificity. They are capable of interacting with various kinds of ligands: ions, small molecules, peptides, proteins, viruses, bacteria, and even cells. Therefore, aptamers are in widespread use as sensor molecules or as targeting agents in diagnostics and pharmaceutics. As a prerequisite for their use in these economic high-value areas, aptamers must be studied in detail with respect to different biophysical characteristics. Of central importance are basic binding parameters of the aptamer-target interaction, such as binding affinity and kinetics. Numerous biophysical methods with different features, characteristics, and capabilities are used in the field today for this purpose.This chapter provides an overview of the current state-of-the-art technologies for studying interactions between aptamers and targets and discusses their advantages as well as drawbacks. Furthermore, essential aspects influencing any aptamer characterization strategy will be presented. Finally, issues of comparability of binding data between different aptamer characterization technologies will be discussed. Graphical Abstract.

Measurements of aptamer-protein binding kinetics using graphene field-effect transistors

Quantifying interactions between biomolecules subject to various environmental conditions is essential for applications such as drug discovery and precision medicine. This paper presents an investigation of the kinetics of environmentally dependent biomolecular binding using an electrolyte-gated graphene field-effect transistor (GFET) nanosensor. In this approach, biomolecular binding occurring on and in the vicinity of a graphene surface induces a change in carrier concentration, whose resulting conductance change is measured. This allows a systematic study of the kinetic properties of the binding system. We apply this approach to the specific binding of human immunoglobulin E (IgE), an antibody involved in parasite immunity, with an aptamer at different ionic strengths (Na⁺ and Mg²⁺) and temperatures. Experimental results demonstrate increased-rate binding kinetics at higher salt-ion concentrations and temperatures. In particular, the divalent cation Mg²⁺ yields more pronounced changes in the conformational structure of the aptamer than the monovalent cation Na⁺. In addition, the dissociation of the aptamer-protein complex at room temperature is found to be characterized by large unfavorable changes in the activation enthalpy and entropy.

A graphene aptasensor for biomarker detection in human serum

This paper presents an affinity graphene nanosensor for detection of biomarkers in undiluted and non-desalted human serum. The affinity nanosensor is a field-effect transistor in which graphene serves as the conducting channel. The graphene surface is sequentially functionalized with a nanolayer of the polymer polyethylene glycol (PEG) and a biomarker-specific aptamer. The aptamer is able to specifically bind with and capture unlabeled biomarkers in serum. A captured biomarker induces a change in the electric conductivity of the graphene, which is measured in a buffer of optimally chosen ionic strength to determine the biomarker concentration. The PEG layer effectively rejects nonspecific adsorption of background molecules in serum while still allowing the aptamer to be readily accessible to serum-borne biomarkers and increases the effective Debye screening length on the graphene surface. Thus, the aptamer-biomarker binding sensitively changes the graphene conductivity, thereby achieving specific and label-free detection of biomarkers with high sensitivity and without the need to dilute or desalt the serum. Experimental results demonstrate that the graphene nanosensor is capable of specifically capturing human immunoglobulin E (IgE), used as a representative biomarker, in human serum in the concentration range of 50 pM-250 nM, with a resolution of 14.5 pM and a limit of detection of 47 pM.

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

Interactions of DNA with proteins are essential for key biological processes and have both a fundamental and practical significance. In particular, DNA binding to anti-DNA antibodies is a pathogenic mechanism in autoimmune pathology, such as systemic lupus erythematosus. Here we measured at the single-molecule level binding and forced unbinding of surface-attached DNA and a monoclonal anti-DNA antibody MRL4 from a lupus erythematosus mouse. In optical trap-based force spectroscopy, a microscopic antibodycoated latex bead is trapped by a focused laser beam and repeatedly brought into contact with a DNA-coated surface. After careful discrimination of non-specific interactions, we showed that the DNA-antibody rupture force spectra had two regimes, reflecting formation of weaker (20-40 pN) and stronger (>40 pN) immune complexes that implies the existence of at least two bound states with different mechanical stability. The two-dimensional force-free off-rate for the DNA-antibody complexes was ~2.2 × 10^-3 s^-1, the transition state distance was ~0.94 nm, the apparent on-rate was ~5.26 s^-1, and the stiffness of the DNA-antibody complex was characterized by a spring constant of 0.0021 pN/nm, suggesting that the DNA-antibody complex is a relatively stable, but soft and deformable macromolecular structure. The stretching elasticity of the DNA molecules was characteristic of single-stranded DNA, suggesting preferential binding of the MRL4 antibody to one strand of DNA. Collectively, the results provide fundamental characteristics of formation and forced dissociation of DNA-antibody complexes that help to understand principles of DNA-protein interactions and shed light on the molecular basis of autoimmune diseases accompanied by formation of anti-DNA antibodies.

Recent Advances in Aptamers Targeting Immune System

The immune system plays important role in protecting the organism by recognizing non-self molecules from pathogen such as bacteria, parasitic worms, and viruses. When the balance of the host defense system is disturbed, immunodeficiency, autoimmunity, and inflammation occur. Nucleic acid aptamers are short single-stranded DNA (ssDNA) or RNA ligands that interact with complementary molecules with high specificity and affinity. Aptamers that target the molecules involved in immune system to modulate their function have great potential to be explored as new diagnostic and therapeutic agents for immune disorders. This review summarizes recent advances in the development of aptamers targeting immune system. The selection of aptamers with superior chemical and biological characteristics will facilitate their application in the diagnosis and treatment of immune disorders.