An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease.

Celiac disease (CeD) is an autoimmune disorder induced by consuming gluten proteins from wheat, barley, and rye. Glutens resist gastrointestinal proteolysis, resulting in peptides that elicit inflammation in patients with CeD. Despite well-established connections between glutens and CeD, chemically defined, bioavailable peptides produced from dietary proteins have never been identified from humans in an unbiased manner. This is largely attributable to technical challenges, impeding our knowledge of potentially diverse peptide species that encounter the immune system. Here, we develop a liquid chromatographic-mass spectrometric workflow for untargeted sequence analysis of the urinary peptidome. We detect over 600 distinct dietary peptides, of which ~35% have a CeD-relevant T cell epitope and ~5% are known to stimulate innate immune responses. Remarkably, gluten peptides from patients with CeD qualitatively and quantitatively differ from controls. Our results provide a new foundation for understanding gluten immunogenicity, improving CeD management, and characterizing the dietary and urinary peptidomes.

Cholestyramine as a promising, strong anion exchange resin for direct capture of genetic biomarkers from raw pancreatic fluids.

The ability to capture cell-free DNA from the gastrointestinal tract, in a minimally invasive manner, could enhance our ability to diagnose gastrointestinal disease, or gain a better understanding of the spatial mapping of the intestinal microbiota. We, therefore, sought to identify a class of capture agents that could directly and efficiently sequester genetic material from intestinal fluids. As a particular case study, we examined the ability to capture DNA from pancreatic secretions, for potential application in enabling the sequestration of early, genetic biomarkers of pancreatic disease. We hypothesized that the cholestyramine series of strong cation exchange resins, which are FDA approved for the treatment of high cholesterol, may be capable of capturing DNA from pancreatic secretions. We identified a particular cholestyramine resin, DOWEX 1 × 2 100-200 mesh, which is able to efficiently capture and purify DNA from pancreatic fluid. Using only 200 µL of pancreatic secretions, we are able to recover 247 ± 182 ng of amplifiable human DNA, giving an estimated pancreatic fluid DNA content of 1.23 ± 0.91 ng/µL. To our knowledge, this is the first demonstration of a material that can effectively capture and purify DNA directly from untreated pancreatic fluids. Thus, our approach could hold high utility for the in vivo capture of DNA and disease biomarkers if incorporated into an appropriate sampling device. Biotechnol. Bioeng. 2017;114: 934-938. © 2016 Wiley Periodicals, Inc.

Role of hypoxia-induced transglutaminase 2 in pulmonary artery smooth muscle cell proliferation.

We previously reported that transglutaminase 2 (TG2) activity is markedly elevated in lungs of hypoxia-exposed rodent models of pulmonary hypertension (PH). Since vascular remodeling of pulmonary artery smooth muscle cells (PASMCs) is important in PH, we undertook the present study to determine whether TG2 activity is altered in PASMCs with exposure to hypoxia and whether that alteration participates in their proliferative response to hypoxia. Cultured distal bovine (b) and proximal human (h) PASMCs were exposed to hypoxia (3% O2) or normoxia (21% O2). mRNA and protein expression were determined by PCR and Western blot analyses. TG2 activity and function were visualized and determined by fluorescent labeled 5-pentylamine biotin incorporation and immunoblotting of serotonylated fibronectin. Cell proliferation was assessed by [(3)H]thymidine incorporation assay. At 24 h, both TG2 expression and activity were stimulated by hypoxia in bPASMCs. Activation of TG2 by hypoxia was blocked by inhibition of the extracellular calcium-sensing receptor or the transient receptor potential channel V4. In contrast, TG2 expression was blocked by inhibition of the transcription factor hypoxia-inducible factor-1α, supporting the presence of separate mechanisms for stimulation of activity and expression of TG2. Pulmonary arterial hypertension patient-derived hPASMCs were found to proliferate significantly more rapidly and respond to hypoxia more strongly than control-derived hPASMCs. Similar to bovine cells, hypoxia-induced proliferation of patient-derived cells was blocked by inhibition of TG2 activity. Our results suggest an important role for TG2, mediated by intracellular calcium fluxes and HIF-1α, in hypoxia-induced PASMC proliferation and possibly in vascular remodeling in PH.

Plant nanobionics approach to augment photosynthesis and biochemical sensing.

The interface between plant organelles and non-biological nanostructures has the potential to impart organelles with new and enhanced functions. Here, we show that single-walled carbon nanotubes (SWNTs) passively transport and irreversibly localize within the lipid envelope of extracted plant chloroplasts, promote over three times higher photosynthetic activity than that of controls, and enhance maximum electron transport rates. The SWNT-chloroplast assemblies also enable higher rates of leaf electron transport in vivo through a mechanism consistent with augmented photoabsorption. Concentrations of reactive oxygen species inside extracted chloroplasts are significantly suppressed by delivering poly(acrylic acid)-nanoceria or SWNT-nanoceria complexes. Moreover, we show that SWNTs enable near-infrared fluorescence monitoring of nitric oxide both ex vivo and in vivo, thus demonstrating that a plant can be augmented to function as a photonic chemical sensor. Nanobionics engineering of plant function may contribute to the development of biomimetic materials for light-harvesting and biochemical detection with regenerative properties and enhanced efficiency.

Formation of High-Aspect-Ratio Helical Nanorods via Chiral Self-Assembly of Fullerodendrimers.

Two novel, asymmetric methanofullerenes are presented, which self-assemble in cyclohexane upon thermal cycling to 80 °C. We show that, through the introduction of a dipeptide sequence to one terminus of the dendritic methanofullerene, it is possible to transform the assembly behavior of these molecules from poorly formed aggregates to high-aspect-ratio nanorods. These nanorods have diameters of 3.76 ± 0.52 nm and appear to be composed of interwoven helices of dendritic fullerenes. As evidenced by circular dichroism, the helicity is characterized by a preferential handedness of assembly, which is imparted by the dipeptide moiety.

A rapid, direct, quantitative, and label-free detector of cardiac biomarker troponin T using near-infrared fluorescent single-walled carbon nanotube sensors.

Patients with chest pain account for 10% of US emergency room visits according to data from the Center for Disease Control and Prevention (2013). For triage of these patients, cardiac biomarkers troponin I and T are endorsed as standard indicators for acute myocardial infarction (AMI, or heart attack). Thus, there is significant interest in developing a rapid, point-of-care (POC) device for troponin detection. In this work, a rapid, quantitative, and label-free assay, which is specific for cardiac troponin T (cTnT) detection, using fluorescent single-walled carbon nanotubes (SWCNTs), is demonstrated. Chitosan-wrapped carbon nanotubes are cross-linked to form a thin gel that is further functionalized with nitrilotriacetic acid (NTA) moieties. Upon chelation of Ni(2+) , the Ni(2+) -NTA group binds to a hexa-histidine-modified troponin antibody, which specifically recognizes the target protein, troponin T. As the troponin T binds to the antibody, the local environment of the sensor changes, allowing direct troponin detection through intensity changes in SWCNT bandgap fluorescence. This platform represents the first near-infrared SWCNT sensor array for cTnT detection. Detection can be completed within 5 min, demonstrating a linear response to cTnT concentration and an experimental detection limit of 100 ng mL(-1) (2.5 nm). This platform provides a promising new tool for POC AMI detection in the future. Moreover, the work presents two new methods of quantifying the number of amines and carboxylic groups, respectively, in a carbon hydrogel matrices.

Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes.

Understanding molecular recognition is of fundamental importance in applications such as therapeutics, chemical catalysis and sensor design. The most common recognition motifs involve biological macromolecules such as antibodies and aptamers. The key to biorecognition consists of a unique three-dimensional structure formed by a folded and constrained bioheteropolymer that creates a binding pocket, or an interface, able to recognize a specific molecule. Here, we show that synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymer-nanotube recognition complexes for riboflavin, L-thyroxine and oestradiol. In each case, the recognition was predicted using a two-dimensional thermodynamic model of surface interactions in which the dissociation constants can be tuned by perturbing the chemical structure of the heteropolymer. Moreover, these complexes can be used as new types of spatiotemporal sensors based on modulation of the carbon nanotube photoemission in the near-infrared, as we show by tracking riboflavin diffusion in murine macrophages.

Carbon nanotubes as optical biomedical sensors.

Biosensors are important tools in biomedical research. Moreover, they are becoming an essential part of modern healthcare. In the future, biosensor development will become even more crucial due to the demand for personalized-medicine, point-of care devices and cheaper diagnostic tools. Substantial advances in sensor technology are often fueled by the advent of new materials. Therefore, nanomaterials have motivated a large body of research and such materials have been implemented into biosensor devices. Among these new materials carbon nanotubes (CNTs) are especially promising building blocks for biosensors due to their unique electronic and optical properties. Carbon nanotubes are rolled-up cylinders of carbon monolayers (graphene). They can be chemically modified in such a way that biologically relevant molecules can be detected with high sensitivity and selectivity. In this review article we will discuss how carbon nanotubes can be used to create biosensors. We review the latest advancements of optical carbon nanotube based biosensors with a special focus on near-infrared (NIR)-fluorescence, Raman-scattering and fluorescence quenching.

Charge transfer structure-reactivity dependence of fullerene-single-walled carbon nanotube heterojunctions.

Charge transfer at the interface between single-walled carbon nanotubes (SWCNTs) of distinct chiral vectors and fullerenes of various molecular weights is of interest both fundamentally and because of its importance in emerging photovoltaic and optoelectronic devices. One approach for generating isolated, discretized fullerene-SWCNT heterojunctions for spectroscopic investigation is to form an amphiphile, which is able to disperse the latter at the single-SWCNT level in aqueous solution. Herein, we synthesize a series of methanofullerene amphiphiles, including derivatives of C60, C70, and C84, and investigated their electron transfer with SWCNT of specific chirality, generating a structure-reactivity relationship. In the cases of two fullerene derivatives, lipid-C61-polyethylene glycol (PEG) and lipid-C71-PEG, band gap dependent, incomplete quenching was observed across all SWCNT species, indicating that the driving force for electron transfer is small. This is further supported by a variant of Marcus theory, which predicts that the energy offsets between the nanotube conduction bands and the C61 and C71 LUMO levels are less than the exciton binding energy in SWCNT. In contrast, upon interfacing nanotubes with C85 methanofullerene, a complete quenching of all semiconducting SWCNT is observed. This enhancement in quenching efficiency is consistent with the deeper LUMO level of C85 methanofullerene in comparison with the smaller fullerene adducts, and suggests its promise as for SWCNT-fullerene heterojunctions.

A kinetic model for the deterministic prediction of gel-based single-chirality single-walled carbon nanotube separation.

We propose a kinetic model that describes the separation of single-chirality semiconducting carbon nanotubes based on the chirality-selective adsorption to specific hydrogels. Experimental elution profiles of the (7,3), (6,4), (6,5), (8,3), (8,6), (7,5), and (7,6) species are well described by an irreversible, first-order site association kinetic model with a single rate constant describing the adsorption of each SWNT to the immobile gel phase. Specifically, we find first-order binding rate constants for seven experimentally separated nanotubes normalized by the binding site molarity (M(θ)): k7,3 = 3.5 × 10⁻5 M(θ)⁻¹ s⁻¹, k6,4 = 7.7 × 10⁻8 M(θ)⁻¹ s⁻¹, k8,3 = 2.3 × 10⁻9 M(θ)⁻¹ s⁻¹, k6,5 = 3.8 × 10⁻9 M(θ)⁻¹ s⁻¹, k7,5 = 1.9 × 10⁻¹¹ M(θ)⁻¹ s⁻¹, k8,6 = 7.7 × 10⁻¹² M(θ)⁻¹ s⁻¹, and k7,6 = 3.8 × 10⁻¹² M(θ)⁻¹ s⁻¹. These results, as well as additional control experiments, unambiguously identify the separation process as a selective adsorption. Unlike certain chromatographic processes with retention time dependence, this separation procedure can be scaled to arbitrarily large volumes, as we demonstrate. This study provides a foundation for both the mechanistic understanding of gel-based SWNT separation as well as the potential industrial-scale realization of single-chirality production of carbon nanotubes.

A structure-function relationship for the optical modulation of phenyl boronic acid-grafted, polyethylene glycol-wrapped single-walled carbon nanotubes.

Phenyl boronic acids (PBA) are important binding ligands to pendant diols useful for saccharide recognition. The aromatic ring can also function to anchor an otherwise hydrophilic polymer backbone to the surface of hydrophobic graphene or carbon nanotube. In this work, we demonstrate both functions using a homologous series of seven phenyl boronic acids conjugated to a polyethylene glycol, eight-membered, branched polymer (PPEG8) that allows aqueous dispersion of single-walled carbon nanotubes (SWNT) and quenching of the near-infrared fluorescence in response to saccharide binding. We compare the 2-carboxyphenylboronic acid (2CPBA); 3-carboxy- (3CPBA) and 4-carboxy- (4CPBA) phenylboronic acids; N-(4-phenylboronic)succinamic acid (4SCPBA); 5-bromo-3-carboxy- (5B3CPBA), 3-carboxy-5-fluoro- (5F3CPBA), and 3-carboxy-5-nitro- (5N3CPBA) phenylboronic acids, demonstrating a clear link between SWNT photoluminescence quantum yield and boronic acid structure. Surprisingly, quantum yield decreases systematically with both the location of the BA functionality and the inclusion of electron-withdrawing or -donating substituents on the phenyl ring. For three structural isomers (2CPBA, 3CPBA, and 4CPBA), the highest quantum yields were measured for para-substituted PBA (4CPBA), much higher than ortho- (2CPBA) and meta- (3CPBA) substituted PBA, indicating the first such dependence on molecular structure. Electron-withdrawing substituents such as nitro groups on the phenyl ring cause higher quantum yield, while electron-donating groups such as amides and alkyl groups cause a decrease. The solvatochromic shift of up to 10.3 meV was used for each case to estimate polymer surface coverage on an areal basis using a linear dielectric model. Saccharide recognition using the nIR photoluminescence of SWNT is demonstrated, including selectivity toward pentoses such as arabinose, ribose, and xylose to the exclusion of the expected fructose, which has a high selectivity on PBA due to the formation of a tridentate complex between fructose and PBA. This study is the first to conclusively link molecular structure of an adsorbed phase to SWNT optical properties and modulation in a systematic manner.

Understanding and controlling the substrate effect on graphene electron-transfer chemistry via reactivity imprint lithography.

Graphene has exceptional electronic, optical, mechanical and thermal properties, which provide it with great potential for use in electronic, optoelectronic and sensing applications. The chemical functionalization of graphene has been investigated with a view to controlling its electronic properties and interactions with other materials. Covalent modification of graphene by organic diazonium salts has been used to achieve these goals, but because graphene comprises only a single atomic layer, it is strongly influenced by the underlying substrate. Here, we show a stark difference in the rate of electron-transfer reactions with organic diazonium salts for monolayer graphene supported on a variety of substrates. Reactions proceed rapidly for graphene supported on SiO(2) and Al(2)O(3) (sapphire), but negligibly on alkyl-terminated and hexagonal boron nitride (hBN) surfaces, as shown by Raman spectroscopy. We also develop a model of reactivity based on substrate-induced electron-hole puddles in graphene, and achieve spatial patterning of chemical reactions in graphene by patterning the substrate.

Polymer-free near-infrared photovoltaics with single chirality (6,5) semiconducting carbon nanotube active layers.

We demonstrate a polymer-free carbon-based photovoltaic device that relies on exciton dissociation at the SWNT/C(60) interface, as shown in the figure. Through the construction of a carbon-based photovoltaic completely free of polymeric active or transport layers, we show both the feasibility of this novel device as well as inform the mechanisms for inefficiencies in SWNTs and carbon based solar cells.

Molecular perspective on diazonium adsorption for controllable functionalization of single-walled carbon nanotubes in aqueous surfactant solutions.

Functionalization of single-walled carbon nanotubes (SWCNTs) using diazonium salts allows modification of their optical and electronic properties for a variety of applications, ranging from drug-delivery vehicles to molecular sensors. However, control of the functionalization process remains a challenge, requiring molecular-level understanding of the adsorption of diazonium ions onto heterogeneous, charge-mobile SWCNT surfaces, which are typically decorated with surfactants. In this paper, we combine molecular dynamics (MD) simulations, experiments, and equilibrium reaction modeling to understand and model the extent of diazonium functionalization of SWCNTs coated with various surfactants (sodium cholate, sodium dodecyl sulfate, and cetyl trimethylammonium bromide). We show that the free energy of diazonium adsorption, determined using simulations, can be used to rank surfactants in terms of the extent of functionalization attained following their adsorption on the nanotube surface. The difference in binding affinities between linear and rigid surfactants is attributed to the synergistic binding of the diazonium ion to the local "hot/cold spots" formed by the charged surfactant heads. A combined simulation-modeling framework is developed to provide guidance for controlling the various sensitive experimental conditions needed to achieve the desired extent of SWCNT functionalization.

Role of adsorbed surfactant in the reaction of aryl diazonium salts with single-walled carbon nanotubes.

Because covalent chemistry can diminish the optical and electronic properties of single-walled carbon nanotubes (SWCNTs), there is significant interest in developing methods of controllably functionalizing the nanotube sidewall. To date, most attempts at obtaining such control have focused on reaction stoichiometry or strength of oxidative treatment. Here, we examine the role of surfactants in the chemical modification of single-walled carbon nanotubes with aryl diazonium salts. The adsorbed surfactant layer is shown to affect the diazonium derivatization of carbon nanotubes in several ways, including electrostatic attraction or repulsion, steric exclusion, and direct chemical modification of the diazonium reactant. Electrostatic effects are most pronounced in the cases of anionic sodium dodecyl sulfate and cationic cetyltrimethylammonium bromide, where differences in surfactant charge can significantly affect the ability of the diazonium ion to access the SWCNT surface. For bile salt surfactants, with the exception of sodium cholate, we find that the surfactant wraps tightly enough such that exclusion effects are dominant. Here, sodium taurocholate exhibits almost no reactivity under the explored reaction conditions, while for sodium deoxycholate and sodium taurodeoxycholate, we show that the greatest extent of reaction is observed among a small population of nanotube species, with diameters between 0.88 and 0.92 nm. The anomalous reaction of nanotubes in this diameter range seems to imply that the surfactant is less effective at coating these species, resulting in a reduced surface coverage on the nanotube. Contrary to the other bile salts studied, sodium cholate enables high selectivity toward metallic species and small band gap semiconductors, which is attributed to surfactant-diazonium coupling to form highly reactive diazoesters. Further, it is found that the rigidity of anionic surfactants can significantly influence the ability of the surfactant layer to stabilize the diazonium ion near the nanotube surface. Such Coulombic and surfactant packing effects offer promise toward employing surfactants to controllably functionalize carbon nanotubes.

Near-infrared fluorescent sensors based on single-walled carbon nanotubes for life sciences applications.

Many properties of single-walled carbon nanotubes (SWCNTs) make them ideal candidates for sensors, particularly for biological systems. Both their fluorescence in the near-infrared range of 820-1600 nm, where absorption by biological tissues is often minimal, and their inherent photostability are desirable attributes for the design of in vitro and in vivo sensors. The mechanisms by which a target molecule can selectively alter the fluorescent emission include primarily changes in emission wavelength (i.e., solvatochromism) and intensity, including effects such as charge-transfer transition bleaching and exciton quenching. The central challenge lies in engineering the nanotube interface to be selective for the analyte of interest. In this work, we review the recent development in this area over the past few years, and describe the design rules that we have developed for detecting various analytes, ranging from stable small molecules and reactive oxygen species (ROS) or reactive nitrogen species (RNS) to macromolecules. Applications to in vivo sensor measurements using these sensors are also described. In addition, the emerging field of SWCNT-based single-molecule detection using band gap fluorescence and the recent efforts to accurately quantify and utilize this unique class of stochastic sensors are also described in this article.

Label-free, single protein detection on a near-infrared fluorescent single-walled carbon nanotube/protein microarray fabricated by cell-free synthesis.

Excessive sample volumes continue to be a major limitation in the analysis of protein-protein interactions, motivating the search for label-free detection methods of greater sensitivity. Herein, we report the first chemical approach for selective protein recognition using fluorescent single-walled carbon nanotubes (SWNTs) enabling label-free microarrays capable of single protein detection. Hexahistidine-tagged capture proteins directly expressed by cell-free synthesis on SWNT/chitosan microarray are bound to a Ni(2+) chelated by Nα,Nα-bis(carboxymethyl)-L-lysine grafted to chitosan surrounding the SWNT. The Ni(2+) acts as a proximity quencher with the Ni(2+)/SWNT distance altered upon docking of analyte proteins. This ability to discern single protein binding events decreases the apparent detection limit from 100 nM, for the ensemble average, to 10 pM for an observation time of 600 s. This first use of cell-free synthesis to functionalize a nanosensor extends this method to a virtually infinite number of capture proteins. To demonstrate this, the SWNT microarrays are used to analyze a network of 1156 protein-protein interactions in the staurosporine-induced apoptosis of SH-SY5Y cells, confirming literature predictions.

Single molecule detection of nitric oxide enabled by d(AT)15 DNA adsorbed to near infrared fluorescent single-walled carbon nanotubes.

We report the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT)(15) oligonucleotides, adsorbed to an array of near-infrared fluorescent semiconducting single-walled carbon nanotubes (AT(15)-SWNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)(15) imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT(15)-SWNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in the estimated rate constants is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-site NO adsorption rate constant is 0.001 s(-1) µM NO(-1). The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation.

A kinetic Monte Carlo analysis for the production of singularly tethered carbon nanotubes.

Nanoparticles that possess a single covalent tether to either another particle or a surface play an increasingly important role in nanotechnology, serving as a foundation for aggregation-based plasmonic sensors, chemically assembled framework structures, and scanning probe tips. Using a theoretical approach, we explore the reaction conditions necessary to maximize singular tethering for several cases of homogeneously dispersed nanoparticles, with a particular focus on single-walled carbon nanotubes. In the limit of particles of monodisperse size and equal site reactivity, the number of tethers versus the reaction conversion is statistically described by the well-known binomial distribution, with a variance that is minimal for the single tether case. However, solutions of nanoparticles often deviate from this ideal, and reaction events can introduce steric hindrance to neighboring sites or alter particle electronic properties, both of which can influence local reactivity. In order to study these cases we use the electron transfer reactions of single-walled carbon nanotubes. We find that the distribution in the number of monofunctional tubes, as a function of conversion, is largely dependent on the distribution of nanotube rate constants, and therefore tube chiralities, in the initial solution. As a contemporary example, we examine the implications of this result on the metallic-semiconductor separation of carbon nanotubes using electron transfer chemistry.