Divalent Metal Cation Optical Sensing Using Single-Walled Carbon Nanotube Corona Phase Molecular Recognition.

Colloidal single-walled carbon nanotubes (SWCNTs) offer a promising platform for the nanoscale engineering of molecular recognition. Optical sensors have been recently designed through the modification of noncovalent corona phases (CPs) of SWCNTs through a phenomenon known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe constructs, DNA CPs are of great interest due to the breadth of the design space and our ability to control these molecules with sequence specificity at scale. Utilizing these constructs for metal ion sensing is a natural extension of this technology due to DNA's well-known coordination chemistry. Additionally, understanding metal ion interactions of these constructs allows for improved sensor design for use in complex aqueous environments. In this work, we study the interactions between a panel of 9 dilute divalent metal cations and 35 DNA CPs under the most controlled experimental conditions for SWCNT optical sensing to date. We found that best practices for the study of colloidal SWCNT analyte responses involve mitigating the effects of ionic strength, dilution kinetics, laser power, and analyte response kinetics. We also discover that SWCNT with DNA CPs generally offers two unique sensing states at pH 6 and 8. The combined set of sensors in this work allowed for the differentiation of Hg2+, Pb2+, Cr2+, and Mn2+. Finally, we implemented Hg2+ sensing in the context of portable detection within fish tissue extract, demonstrating nanomolar level detection.

A synthetic mimic of phosphodiesterase type 5 based on corona phase molecular recognition of single-walled carbon nanotubes.

Molecular recognition binding sites that specifically identify a target molecule are essential for life science research, clinical diagnoses, and therapeutic development. Corona phase molecular recognition is a technique introduced to generate synthetic recognition at the surface of a nanoparticle corona, but it remains an important question whether such entities can achieve the specificity of natural enzymes and receptors. In this work, we generate and screen a library of 24 amphiphilic polymers, preselected for molecular recognition and based on functional monomers including methacrylic acid, acrylic acid, and styrene, iterating upon a poly(methacrylic acid-co-styrene) motif. When complexed to a single-walled carbon nanotube, some of the resulting corona phases demonstrate binding specificity remarkably similar to that of phosphodiesterase type 5 (PDE5), an enzyme that catalyzes the hydrolysis of secondary messenger. The corona phase binds selectively to a PDE5 inhibitor, Vardenafil, as well as its molecular variant, but not to other potential off-target inhibitors. Our work herein examines the specificity and sensitivity of polymer "mutations" to the corona phase, as well as direct competitions with the native binding PDE5. Using structure perturbation, corona surface characterization, and molecular dynamics simulations, we show that the molecular recognition is associated with the unique three-dimensional configuration of the corona phase formed at the nanotube surface. This work conclusively shows that corona phase molecular recognition can mimic key aspects of biological recognition sites and drug targets, opening up possibilities for pharmaceutical and biological applications.

Characterization of Protein Aggregation Using Hydrogel-Encapsulated nIR Fluorescent Nanoparticle Sensors.

The monitoring of biopharmaceutical critical quality attributes in-process, at both the process development and manufacturing stages, is necessary for the implementation of process analytical technology and quality-by-design principles. Among these attributes, it is important to monitor and control protein aggregation during the manufacturing of biological therapeutics to prevent adverse immunogenic responses and minimize negative impacts on drug deliverability. In this work, we explore hydrogel-encapsulated, label-free fluorescent nanosensors for the characterization of protein aggregation. A mathematical model is used to describe the diffusion and binding of a series of stressed pharmaceutical samples to such sensors, describing their dynamic response. We use mathematical modeling to map the influence of hydrogel properties on the separation performance, given the composition of UV-stressed IgG1 samples. Using this modified model, the compositions of light-stressed IgG1 samples were fit to experimental data and correlated with size-exclusion chromatography data. The results demonstrate the ability to detect the presence of high-molecular-weight protein species at a concentration as low as 1%. This work represents a significant step toward the development and deployment of rapid process analytical technologies for biopharmaceutical characterization.

Immobilization and Function of nIR-Fluorescent Carbon Nanotube Sensors on Paper Substrates for Fluidic Manipulation.

Nanoparticle-based optical sensors are capable of highly sensitive and selective chemical interactions and can form the basis of molecular recognition for various classes of analytes. However, their incorporation into standardized in vitro assays has been limited by their incompatibility with packaging or form factors necessary for specific applications. Here, we have developed a technique for immobilizing nIR-fluorescent single-walled carbon nanotube (SWCNT) sensors on seven different types of paper substrates including nitrocellulose, nylon, poly(vinylidene fluoride), and cellulose. Sensors remain functional upon immobilization and exhibit nIR fluorescence in nonaqueous solvent systems. We then extend this system to the Corona Phase Molecular Recognition (CoPhMoRe) approach of synthetic molecular recognition by screening ssDNA-wrapped SWCNTs with different sequences against a panel of fat-soluble vitamins in canola oil, identifying a sensor which responds to ß-carotene with a dissociation constant of 2.2 µM. Moreover, we pattern hydrophobic regions onto nitrocellulose using the wax printing method and form one-dimensional sensor barcodes for rapid multiplexing. Using a sensor array of select ssDNA wrappings, we are able to distinguish between Cu(II), Cd(II), Hg(II), and Pb(II) at a concentration of 100 µM. Finally, we demonstrate that immobilized sensors remain fluorescent and responsive for nearly 60 days when stability is addressed. This work represents a significant step toward the deployment of fluorescent nanoparticle sensors for point-of-use applications.

Measuring the Accessible Surface Area within the Nanoparticle Corona Using Molecular Probe Adsorption.

The corona phase-the adsorbed layer of polymer, surfactant, or stabilizer molecules around a nanoparticle-is typically utilized to disperse nanoparticles into a solution or solid phase. However, this phase also controls molecular access to the nanoparticle surface, a property important for catalytic activity and sensor applications. Unfortunately, few methods can directly probe the structure of this corona phase, which is subcategorized as either a hard, immobile corona or a soft, transient corona in exchange with components in the bulk solution. In this work, we introduce a molecular probe adsorption (MPA) method for measuring the accessible nanoparticle surface area using a titration of a quenchable fluorescent molecule. For example, riboflavin is utilized to measure the surface area of gold nanoparticle standards, as well as corona phases on dispersed single-walled carbon nanotubes and graphene sheets. A material balance on the titration yields certain surface coverage parameters, including the ratio of the surface area to dissociation constant of the fluorophore, q/KD, as well as KD itself. Uncertainty, precision, and the correlation of these parameters across different experimental systems, preparations, and modalities are all discussed. Using MPA across a series of corona phases, we find that the Gibbs free energy of probe binding scales inversely with the cube root of surface area, q. In this way, MPA is the only technique to date capable of discerning critical structure-property relationships for such nanoparticle surface phases. Hence, MPA is a rapid quantitative technique that should prove useful for elucidating corona structure for nanoparticles across different systems.

Analysis of Multiplexed Nanosensor Arrays Based on Near-Infrared Fluorescent Single-Walled Carbon Nanotubes.

The high-throughput, label-free detection of biomolecules remains an important challenge in analytical chemistry with the potential of nanosensors to significantly increase the ability to multiplex such assays. In this work, we develop an optical sensor array, printable from a single-walled carbon nanotube/chitosan ink and functionalized to enable a divalent ion-based proximity quenching mechanism for transducing binding between a capture protein or an antibody with the target analyte. Arrays of 5 × 6, 200 µm near-infrared (nIR) spots at a density of ≈300 spots/cm2 are conjugated with immunoglobulin-binding proteins (proteins A, G, and L) for the detection of human IgG, mouse IgM, rat IgG2a, and human IgD. Binding kinetics are measured in a parallel, multiplexed fashion from each sensor spot using a custom laser scanning imaging configuration with an nIR photomultiplier tube detector. These arrays are used to examine cross-reactivity, competitive and nonspecific binding of analyte mixtures. We find that protein G and protein L functionalized sensors report selective responses to mouse IgM on the latter, as anticipated. Optically addressable platforms such as the one examined in this work have potential to significantly advance the real-time, multiplexed biomolecular detection of complex mixtures.

Ionic Strength-Mediated Phase Transitions of Surface-Adsorbed DNA on Single-Walled Carbon Nanotubes.

Single-stranded DNA oligonucleotides have unique, and in some cases sequence-specific molecular interactions with the surface of carbon nanotubes that remain the subject of fundamental study. In this work, we observe and analyze a generic, ionic strength-mediated phase transition exhibited by over 25 distinct oligonucleotides adsorbed to single-walled carbon nanotubes (SWCNTs) in colloidal suspension. The phase transition occurs as monovalent salts are used to modify the ionic strength from 500 mM to 1 mM, causing a reversible reduction in the fluorescence quantum yield by as much as 90%. The phase transition is only observable by fluorescence quenching within a window of pH and in the presence of dissolved O2, but occurs independently of this optical quenching. The negatively charged phosphate backbone increases (decreases) the DNA surface coverage on an areal basis at high (low) ionic strength, and is well described by a two-state equilibrium model. The resulting quantitative model is able to describe and link, for the first time, the observed changes in optical properties of DNA-wrapped SWCNTs with ionic strength, pH, adsorbed O2, and ascorbic acid. Cytosine nucleobases are shown to alter the adhesion of the DNA to SWCNTs through direct protonation from solution, decreasing the driving force for this phase transition. We show that the phase transition also changes the observed SWCNT corona phase, modulating the recognition of riboflavin. These results provide insight into the unique molecular interactions between DNA and the SWCNT surface, and have implications for molecular sensing, assembly, and nanoparticle separations.

High-resolution imaging of cellular dopamine efflux using a fluorescent nanosensor array.

Intercellular communication via chemical signaling proceeds with both spatial and temporal components, but analytical tools, such as microfabricated electrodes, have been limited to just a few probes per cell. In this work, we use a nonphotobleaching fluorescent nanosensor array based on single-walled carbon nanotubes (SWCNTs) rendered selective to dopamine to study its release from PC12 neuroprogenitor cells at a resolution exceeding 20,000 sensors per cell. This allows the spatial and temporal dynamics of dopamine release, following K+ stimulation, to be measured at exceedingly high resolution. We observe localized, unlabeled release sites of dopamine spanning 100 ms to seconds that correlate with protrusions but not predominately the positive curvature associated with the tips of cellular protrusions as intuitively expected. The results illustrate how directionality of chemical signaling is shaped by membrane morphology, and highlight the advantages of nanosensor arrays that can provide high spatial and temporal resolution of chemical signaling.

Mechanism of immobilized protein A binding to immunoglobulin G on nanosensor array surfaces.

Protein A is often used for the purification and detection of antibodies such as immunoglobulin G (IgG) because of its quadrivalent domains that bind to the Fc region of these macromolecules. However, the kinetics and thermodynamics of the binding to many sensor surfaces have eluded mechanistic description due to complexities associated with multivalent interactions. In this work, we use a near-infrared (nIR) fluorescent single-walled carbon nanotube sensor array to obtain the kinetics of IgG binding to protein A, immobilized using a chelated Cu(2+)/His-tag chemistry to hydrogel dispersed sensors. A bivalent binding mechanism is able to describe the concentration dependence of the effective dissociation constant, KD,eff, which varies from 100 pM to 1 µM for IgG concentrations from 1 ng mL(-1) to 100 µg mL(-1), respectively. The mechanism is shown to describe the unusual concentration-dependent scaling demonstrated by other sensor platforms in the literature as well, and a comparison is made between resulting parameters. For comparison, we contrast IgG binding with that of human growth hormone (hGH) to its receptor (hGH-R) which displays an invariant dissociation constant at KD = 9 µM. These results should aid in the use of protein A and other recognition elements in a variety of sensor types.