Multiplex enzymatic synthesis of DNA with single-base resolution.

Enzymatic DNA synthesis (EDS) is a promising benchtop and user-friendly method of nucleic acid synthesis that, instead of solvents and phosphoramidites, uses mild aqueous conditions and enzymes. For applications such as protein engineering and spatial transcriptomics that require either oligo pools or arrays with high sequence diversity, the EDS method needs to be adapted and certain steps in the synthesis process spatially decoupled. Here, we have used a synthesis cycle comprising a first step of site-specific silicon microelectromechanical system inkjet dispensing of terminal deoxynucleotidyl transferase enzyme and 3' blocked nucleotide, and a second step of bulk slide washing to remove the 3' blocking group. By repeating the cycle on a substrate with an immobilized DNA primer, we show that microscale spatial control of nucleic acid sequence and length is possible, which, here, are assayed by hybridization and gel electrophoresis. This work is distinctive for enzymatically synthesizing DNA in a highly parallel manner with single base control.

An Aqueous Analog MAC Machine.

Using ions in aqueous milieu for signal processing, like in biological circuits, may potentially lead to a bioinspired information processing platform. Studies, however, have focused on individual ionic diodes and transistors rather than circuits comprising many such devices. Here a 16 × 16 array of new ionic transistors is developed in an aqueous quinone solution. Each transistor features a concentric ring electrode pair with a disk electrode at the center. The electrochemistry of these electrodes in the solution provides the basis for the transistor operation. The ring pair electrochemically tunes the local electrolytic concentration to modulate the disk's Faradaic reaction rate. Thus, the disk current as a Faradaic reaction to the disk voltage is gated by the ring pair. The 16 × 16 array of these transistors performs analog multiply-accumulate (MAC) operations, a computing modality hotly pursued for low-power artificial neural networks. This exploits the transistor's operating regime where the disk current is a multiplication of the disk voltage and a weight parameter tuned by the ring pair gating. Such disk currents from multiple transistors are summated in a global reference electrode to complete a MAC task. This ionic circuit demonstrating analog computing is a step toward sophisticated aqueous ionics.

CMOS electrochemical pH localizer-imager.

pH controls a large repertoire of chemical and biochemical processes in water. Densely arrayed pH microenvironments would parallelize these processes, enabling their high-throughput studies and applications. However, pH localization, let alone its arrayed realization, remains challenging because of fast diffusion of protons in water. Here, we demonstrate arrayed localizations of picoliter-scale aqueous acids, using a 256-electrochemical cell array defined on and operated by a complementary metal oxide semiconductor (CMOS)-integrated circuit. Each cell, comprising a concentric pair of cathode and anode with their current injections controlled with a sub-nanoampere resolution by the CMOS electronics, creates a local pH environment, or a pH "voxel," via confined electrochemistry. The system also monitors the spatiotemporal pH profile across the array in real time for precision pH control. We highlight the utility of this CMOS pH localizer-imager for high-throughput tasks by parallelizing pH-gated molecular state encoding and pH-regulated enzymatic DNA elongation at any selected set of cells.

Antibody recognition of a human chorionic gonadotropin epitope (hCGbeta66-80) depends on local structure retained in the free peptide.

Human chorionic gonadotropin (hCG) is an important biomarker in pregnancy and oncology, where it is routinely detected and quantified by specific immunoassays. Intelligent epitope selection is essential to achieving the required assay performance. We present binding affinity measurements demonstrating that a typical ß3-loop-specific monoclonal antibody (8G5) is highly selective in competitive immunoassays and distinguishes between hCGß(66-80) and the closely related luteinizing hormone (LH) fragment LHß(86-100), which differ only by a single amino acid residue. A combination of optical spectroscopic measurements and atomistic computer simulations on these free peptides reveals differences in turn type stabilized by specific hydrogen bonding motifs. We propose that these structural differences are the basis for the observed selectivity in the full protein.

The rational development of molecularly imprinted polymer-based sensors for protein detection.

The detection of specific proteins as biomarkers of disease, health status, environmental monitoring, food quality, control of fermenters and civil defence purposes means that biosensors for these targets will become increasingly more important. Among the technologies used for building specific recognition properties, molecularly imprinted polymers (MIPs) are attracting much attention. In this critical review we describe many methods used for imprinting recognition for protein targets in polymers and their incorporation with a number of transducer platforms with the aim of identifying the most promising approaches for the preparation of MIP-based protein sensors (277 references).

Polymer- and colloid-mediated bioassays, sensors and diagnostics.

Synthetic polymers and colloids are increasingly being exploited in bioassays to help measure gene expression, sequence genomes, monitor metabolic disorders and detect the presence of disease. This can be attributed to their potential to reduce reaction scales, improve throughput, lower costs and improve the sensitivity, selectivity, stability and reproducibility of assays. This review highlights the newest application areas, including some of the strategies employed, as well as major technical challenges and future opportunities. The move away from conventional assay approaches is being driven by a desire to improve our basic understanding of human biology, to diagnose diseases earlier, and to manage healthcare resources more efficiently. These endeavors are important owing to a rising world population and an increasing average life span.

MiS-MALDI: microgel-selected detection of protein biomarkers by MALDI-ToF mass spectrometry.

Intensified efforts to decipher the origin of disease at the molecular level stimulate the emergence of more efficient proteomic technologies. To complement this, attempts are being made to identify new predictive biomarkers for building more reliable biomarker patterns. As biomarker research gathers pace an immediate interest becomes focused on platforms, which although based on mainstream approaches, are more amenable to specialist tasks. Particularly relevant this is for disease-specific biomarkers, which are present at very low concentrations in multicomponent biological fluids and require depletion protocols enabling their separation from high-abundance components. In this report, we describe a new strategy allowing the rapid detection of target protein biomarkers by MALDI-ToF mass spectrometry. The approach relies on selective sequestering of target proteins from complex media by engineered microgels, which select proteins by their size (<30 kDa) and isoelectric points (protein pI <6.5). Subsequently, biomarker-loaded microgels are subjected to direct mass-spectrometric analysis without the need for preceding protein extraction. Exemplified by a natural protein-folding motif, coiled-coil, the monitoring of hierarchical folding-dependent macromolecular systems by the approach is also shown. The described strategy offers a general rationale for versatile platforms for high throughput proteomics and holds promise for proteome fingerprinting of biomolecular interactions.

Measurement of glucose in blood with a phenylboronic acid optical sensor.

BACKGROUND: Current methods of glucose monitoring rely predominantly on enzymes such as glucose oxidase for detection. Phenylboronic acid receptors have been proposed as alternative glucose binders. A unique property of these molecules is their ability to bind glucose in a fully reversible covalent manner that facilitates direct continuous measurements. We examined (1) the ability of a phenylboronic-based sensor to measure glucose in blood and blood plasma and (2) the effect on measurement accuracy of a range of potential interferents. We also showed that the sensor is able to track glucose fluctuations occurring at rates mimicking those experienced in vivo. METHOD: In vitro static measurements of glucose in blood and blood plasma were conducted using holographic sensors containing acrylamide, N,N'-methylenebisacrylamide, 3-acrylamidophenylboronic acid, and (3-acrylamidopropyl) trimethylammonium chloride. The same sensors were also used for in vitro measurements performed under flow conditions. RESULTS: The opacity of the liquid had no affect on the ability of the optical sensor to measure glucose in blood or blood plasma. The presence of common antibiotics, diabetic drugs, pain killers, and endogenous substances did not affect the measurement accuracy, as shown by error grid analysis. Ex vivo flow experiments showed that the sensor is able to track changes accurately in concentration occurring in real time without lag or evidence of hysteresis. CONCLUSIONS: The ability of phenylboronic acid sensors to measure glucose in whole blood was demonstrated for the first time. Holographic sensors are ideally suited to continuous blood glucose measurements, being physically and chemically robust and potentially calibration free.

pH-sensitive holograms for continuous monitoring in plasma.

Conventional electrochemical methods of determining the pH of body fluids have drawbacks. Newer optical methods offer the promise of miniaturisation and continuous in vivo measurements without drift. This report examines the ability of a holographic sensor based on a thin-film, biocompatible hydrogel (approximately 10 microm) of poly(2-hydroxyethyl methacrylate) and ionisable 2-(dimethylaminoethyl) methacrylate to accurately measure the pH of blood plasma ex vivo. It is found that the sensors behave in a fully reversible manner. After an initial calibration with buffers, they can measure pH over extended periods (more than 40 h).

Continuous blood glucose monitoring with a thin-film optical sensor.

BACKGROUND: We recently described a holographic optical sensor with improved selectivity for glucose over fructose that was based on a thin-film polymer hydrogel containing phenylboronic acid receptors. The aim of the present work was to measure glucose in human blood plasma as opposed to simple buffers and track changes in concentration at a rate mimicking glucose changes in vivo. METHODS: We used holographic sensors containing acrylamide, N,N'-methylenebisacrylamide, 3-acrylamidophenylboronic acid, and (3-acrylamidopropyl)trimethylammonium chloride to measure 7 human blood plasma samples at different glucose concentrations (3-33 mmol/L) in static mode. Separately, using a flow cell, the glucose concentration was varied at approximately 0.17-0.28 mmol(-1) x L(-1) x min(-1), and the sensor's ability to continuously monitor glucose was investigated over an extended period. RESULTS: We subjected the results of the ex vivo static measurements to error grid analysis. Of 46 measurements, 42 (91.3%) fell in zone A of a Clarke error grid, and the remainder (8.7%) fell in zone B. The ex vivo flow experiments showed that the sensor is able to accurately track changes in concentration occurring in real time without lag or evidence of hysteresis. CONCLUSIONS: We demonstrate the ability of a phenylboronic acid-based sensor to measure glucose in human blood plasma for the 1st time in vitro. Holographic glucose sensors can be used without recourse to recalibration. Their robust nature, coupled with their format flexibility, makes them an attractive alternative to conventional electrochemical enzyme-based methods of glucose monitoring for people with diabetes.

Selective holographic detection of glucose using tertiary amines.

Introducing tertiary amine monomers into holographic sensors containing phenylboronic acids gives greatly improved selectivity for glucose.

Crosslinking of phenylboronic acid receptors as a means of glucose selective holographic detection.

A holographic sensor for the detection of glucose has been developed that is based on a hydrogel film containing phenylboronic acid receptors. Changes to the replay wavelength of the hologram were used to characterise the swelling and de-swelling behaviour of the hydrogel matrix upon receptor-ligand binding. The effect of introducing a fixed positive charge into the polymer matrix by modification of the hydrogel with a quaternary amine group (3-acrylamidopropyl)trimethylammonium chloride (ATMA), was investigated for a range of sugars and the alpha-hydroxy acid, lactate, at physiological pH. The quaternary amine-modified hydrogel matrix was found to contract in the presence of glucose, whereas, it was minimally responsive to other saccharides. The selectivity of the sensor for glucose compared to lactate was also significantly improved compared to the unmodified film. A crosslinking mechanism is proposed to explain the enhanced selectivity to glucose.

Physicochemical perspectives on DNA microarray and biosensor technologies.

Detection and sequence-identification of nucleic acid molecules is often performed by binding, or hybridization, of specimen "target" strands to immobilized, complementary "probe" strands. A familiar example is provided by DNA microarrays used to carry out thousands of solid-phase hybridization reactions simultaneously to determine gene expression patterns or to identify genotypes. The underlying molecular process, namely sequence-specific recognition between complementary probe and target molecules, is fairly well understood in bulk solution. However, this knowledge proves insufficient to adequately understand solid-phase hybridization. For example, equilibrium binding constants for solid-phase hybridization can differ by many orders of magnitude relative to solution values. Kinetics of probe-target binding are affected. Surface interactions, electrostatics and polymer phenomena manifest themselves in ways not experienced by hybridizing strands in bulk solution. The emerging fundamental understanding provides important insights into application of DNA microarray and biosensor technologies.

Reaction of N-phenyl maleimide with aminosilane monolayers.

Reaction of N-phenyl maleimide (NPM) with silica surfaces modified with a self-assembled monolayer of (aminopropyl)triethoxysilane (APTES) was investigated using infrared spectroscopy (FTIR), elemental analysis, and titration assays. This reaction is of interest as a test case for using amine-maleimide coupling for immobilization of biomolecules. Addition of NPM to surface APTES residues was consistently sub-stoichiometric, with typical yields of about 75% on monolayers with a coverage of 1.15 APTES residues/nm2. Titration analysis found negligible presence of imide alkene C=C bonds in modified supports, indicating that addition of NPM to APTES proceeded via amine attack at the imide olefinic bond. FTIR measurements also revealed presence of amide bands which intensified over periods of 10 h. These observations were attributed to a slower secondary process in which APTES amines attack imide carbonyls to produce amide linkages. Stability of NPM-modified surfaces was examined under room temperature storage in pH 7 buffer up to 72 h and for 2 h exposure to buffer at temperatures up to 90 degrees C. It was found that stability was determined by robustness of APTES-silica attachment, with about 30% loss under the harshest conditions investigated.

Poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers: preparation and aqueous solution properties.

A series of water-soluble, amphiphilic graft copolymers has been prepared by free-radical copolymerization of methoxypoly(ethylene glycol) macromonomers, with either methyl methacrylate or butyl methacrylate as the comonomers, in water/ethanol solvent mixtures. Lower molecular weight copolymers were obtained by increasing the concentration of the initiator, azobisisobutyronitrile (AIBN), used in the polymerization reaction. However, the route used also led to the formation of significant quantities of tetramethylsuccinodinitrile, a toxic byproduct resulting from the cage reaction of AIBN. Static fluorescence measurements using pyrene as a probe, along with 1H NMR experiments, showed that the graft copolymers form aggregates in water at very low concentrations (approximately 0.01 g l(-1)) with the pendant hydrophilic graft chains forming a stabilizing shell around the hydrophobic backbone. An increase in the hydrophile-lipophile balance of the graft copolymers was found to lead to smaller aggregates with lower aggregation numbers and highly swollen hydrophilic shells, as revealed by small angle neutron scattering (SANS).

Polystyrene nanoparticles based on poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers.

The solubilization of styrene by poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers has been examined. From turbidity measurements the solubility limit of the monomer in the micelles was obtained and the distribution coefficients were evaluated. Dynamic light scattering revealed that below the solubility limit, solubilization leads to a slight increase in micelle size, while above the solubility limit, there is a dramatic increase in particle size and turbidity as oil-in-water emulsions are formed through coalescence of monomer-swollen micelles. Polymerizations carried out below the solubility limit using the graft copolymer micelles as templates resembled microemulsion polymerizations in nature and led to very fine sterically stabilized polystyrene latex particles. Through careful control of the monomer concentration and the polymerization temperature it was possible to obtain spherical nanosize latex particles with similar size to those of the micelle precursors (10 nm) up to 11% monomer by weight. Polymerizations above the solubility limit, on the other hand, showed similarities with emulsion polymerizations and resulted in larger particles with higher polydispersity.