Programmable ion-sensitive transistor interfaces. II. Biomolecular sensing and manipulation

Ultrasensitive dopamine detection with graphene aptasensor multitransistor arrays

Detecting physiological levels of neurotransmitters in biological samples can advance our understanding of brain disorders and lead to improved diagnostics and therapeutics. However, neurotransmitter sensors for real-world applications must reliably detect low concentrations of target analytes from small volume working samples. Herein, a platform for robust and ultrasensitive detection of dopamine, an essential neurotransmitter that underlies several brain disorders, based on graphene multitransistor arrays (gMTAs) functionalized with a selective DNA aptamer is presented. High-yield scalable methodologies optimized at the wafer level were employed to integrate multiple graphene transistors on small-size chips (4.5 × 4.5 mm). The multiple sensor array configuration permits independent and simultaneous replicate measurements of the same sample that produce robust average data, reducing sources of measurement variability. This procedure allowed sensitive and reproducible dopamine detection in ultra-low concentrations from small volume samples across physiological buffers and high ionic strength complex biological samples. The obtained limit-of-detection was 1 aM (10–18) with dynamic detection ranges spanning 10 orders of magnitude up to 100 µM (10–8), and a 22 mV/decade peak sensitivity in artificial cerebral spinal fluid. Dopamine detection in dopamine-depleted brain homogenates spiked with dopamine was also possible with a LOD of 1 aM, overcoming sensitivity losses typically observed in ion-sensitive sensors in complex biological samples. Furthermore, we show that our gMTAs platform can detect minimal changes in dopamine concentrations in small working volume samples (2 µL) of cerebral spinal fluid samples obtained from a mouse model of Parkinson’s Disease. The platform presented in this work can lead the way to graphene-based neurotransmitter sensors suitable for real-world academic and pre-clinical pharmaceutical research as well as clinical diagnosis.

A new approach towards the Debye length challenge for specific and label-free biological sensing based on field-effect transistors

Biologically-modified field-effect transistors (BioFETs) are promising platforms for specific and label-free biosensing due to their sub-micron footprint suitable for multiplexing in ultra-small samples, low noise levels, inherent amplification, etc. Debye screening length is a well-recognized challenge for any BioFET-based technology. The screening length is the smallest at the double layer, where the solution ion population is higher than the bulk population. One way to address the small double layer screening length is to electrostatically modify the potential drop across the solution such as to minimize the potential drop over the double layer. This will decrease the population of the double layer ions and increase the screening length. However, this is not possible with BioFETs as voltage application to the reference electrode simultaneously affects both the double layer and the BioFET conducting channel. The current study addresses the screening length challenge with the novel Meta-Nano-Channel (MNC) BioFET. The MNC BioFET, which is fabricated in a complementary-metal-oxide-silicon (CMOS) process, allows decoupling of the electrostatics of the double layer from the electrodynamics of the conducting channel. The study explores the mechanism of sensing with the MNC BioFET, and demonstrates how the double layer can be electrostatically tuned in order to optimize the screening length without affecting the conducting channel. Finally, specific and label-free sensing of 10 ng ml^-1 prostate specific antigen (PSA) is demonstrated. It is shown that by electrostatically increasing the double layer screening length, the sensing signal increases from 70 mV to 133 mV.

Computer Simulation of a Surface Charge Nanobiosensor with Internal Signal Integration

The ionized states of molecular analytes located on solid surfaces require profound investigation and better understanding for applications in the basic sciences in general, and in the design of nanobiosensors, in particular. Such ionized states are induced by the interactions of molecules between them in the analyzed substance and with the target surface. Here, computer simulations using COMSOL Multiphysics software show the effect of surface charge density and distribution on the output generation in a dynamic PIN diode with gate control. This device, having built-in potential barriers, has a unique internal integration of output signal generation. The identified interactions showed the possibility of a new design for implementing a nanobiosensor based on a dynamic PIN diode in a mode with surface charge control.

VLSI Structures for DNA Sequencing-A Survey

DNA sequencing is a critical functionality in biomedical research, and technical advances that improve it have important implications for human health. Novel methods by which sequencing can be accomplished in more accurate, high-throughput, and faster ways are in development. Here, we review VLSI biosensors for nucleotide detection and DNA sequencing. Implementation strategies are discussed and split into function-specific architectures that are presented for reported design examples from the literature. Lastly, we briefly introduce a new approach to sequencing using Gate All-Around (GAA) nanowire Metal Oxide Semiconductor Field Effect Transistors (MOSFETs) that has significant implications for the field.

Electrostatically Governed Debye Screening Length at the Solution-Solid Interface for Biosensing Applications

Biosensors based on field-effect devices (bioFETs) offer numerous advantages over current technologies and therefore have attracted immense research over the decades. However, short Debye screening length in highly ionic physiological solutions remains the main obstacle for bioFET realization. This challenge becomes considerably more acute at the electrolyte-oxide interface of the sensing area due to high ion concentration induced by the charged amphoteric sites, which prohibits any attempt to employ the field-effect mechanism to "sense" any charged biomolecules. In this work, we present an electrostatic approach by which the double layer (DL) excess ion concentration is removed, thus forcing the DL ion concentration to match the bulk concentration, which subsequently forces bulk screening length at the DL, thereby "exposing" target biomolecules to the underlying bioFET. To this end, we employ local tunable surface electric fields, introduced to the DL using surface passivated-metal electrodes. We examine numerically and analytically the effect of these electric fields on the DL ion distribution. We also numerically demonstrate the feasibility of the proposed approach for a fully depleted silicon-on-insulator based bioFET and show how the threshold voltage shift induced by the presence of target molecules increases by almost two orders of magnitude upon the removal of the surface excess ion population.

Electrodiffusion models of synaptic potentials in dendritic spines

The biophysical properties of dendritic spines play a critical role in neuronal integration but are still poorly understood, due to experimental difficulties in accessing them. Spine biophysics has been traditionally explored using theoretical models based on cable theory. However, cable theory generally assumes that concentration changes associated with ionic currents are negligible and, therefore, ignores electrodiffusion, i.e. the interaction between electric fields and ionic diffusion. This assumption, while true for large neuronal compartments, could be incorrect when applied to femto-liter size structures such as dendritic spines. To extend cable theory and explore electrodiffusion effects, we use here the Poisson (P) and Nernst-Planck (NP) equations, which relate electric field to charge and Fick's law of diffusion, to model ion concentration dynamics in spines receiving excitatory synaptic potentials (EPSPs). We use experimentally measured voltage transients from spines with nanoelectrodes to explore these dynamics with realistic parameters. We find that (i) passive diffusion and electrodiffusion jointly affect the dynamics of spine EPSPs; (ii) spine geometry plays a key role in shaping EPSPs; and, (iii) the spine-neck resistance dynamically decreases during EPSPs, leading to short-term synaptic facilitation. Our formulation, which complements and extends cable theory, can be easily adapted to model ionic biophysics in other nanoscale bio-compartments.

Field-effect sensors - from pH sensing to biosensing: sensitivity enhancement using streptavidin-biotin as a model system

Field-Effect Transistor sensors (FET-sensors) have been receiving increasing attention for biomolecular sensing over the last two decades due to their potential for ultra-high sensitivity sensing, label-free operation, cost reduction and miniaturisation. Whilst the commercial application of FET-sensors in pH sensing has been realised, their commercial application in biomolecular sensing (termed BioFETs) is hindered by poor understanding of how to optimise device design for highly reproducible operation and high sensitivity. In part, these problems stem from the highly interdisciplinary nature of the problems encountered in this field, in which knowledge of biomolecular-binding kinetics, surface chemistry, electrical double layer physics and electrical engineering is required. In this work, a quantitative analysis and critical review has been performed comparing literature FET-sensor data for pH-sensing with data for sensing of biomolecular streptavidin binding to surface-bound biotin systems. The aim is to provide the first systematic, quantitative comparison of BioFET results for a single biomolecular analyte, specifically streptavidin, which is the most commonly used model protein in biosensing experiments, and often used as an initial proof-of-concept for new biosensor designs. This novel quantitative and comparative analysis of the surface potential behaviour of a range of devices demonstrated a strong contrast between the trends observed in pH-sensing and those in biomolecule-sensing. Potential explanations are discussed in detail and surface-chemistry optimisation is shown to be a vital component in sensitivity-enhancement. Factors which can influence the response, yet which have not always been fully appreciated, are explored and practical suggestions are provided on how to improve experimental design.

Detection principles of biological and chemical FET sensors

The seminal importance of detecting ions and molecules for point-of-care tests has driven the search for more sensitive, specific, and robust sensors. Electronic detection holds promise for future miniaturized in-situ applications and can be integrated into existing electronic manufacturing processes and technology. The resulting small devices will be inherently well suited for multiplexed and parallel detection. In this review, different field-effect transistor (FET) structures and detection principles are discussed, including label-free and indirect detection mechanisms. The fundamental detection principle governing every potentiometric sensor is introduced, and different state-of-the-art FET sensor structures are reviewed. This is followed by an analysis of electrolyte interfaces and their influence on sensor operation. Finally, the fundamentals of different detection mechanisms are reviewed and some detection schemes are discussed. In the conclusion, current commercial efforts are briefly considered.

Dynamic behaviour of the silica-water-bio electrical double layer in the presence of a divalent electrolyte

Molecular dynamics simulation of the electric double layer at the silica-water-bio interface in mixed electrolyte. Water orientation and charge distribution showed a significant effect on the electrostatics at the interface.

Non-Faradaic Electrochemical Detection of Exocytosis from Mast and Chromaffin Cells Using Floating-Gate MOS Transistors

We present non-faradaic electrochemical recordings of exocytosis from populations of mast and chromaffin cells using chemoreceptive neuron MOS (CνMOS) transistors. In comparison to previous cell-FET-biosensors, the CνMOS features control (CG), sensing (SG) and floating gates (FG), allows the quiescent point to be independently controlled, is CMOS compatible and physically isolates the transistor channel from the electrolyte for stable long-term recordings. We measured exocytosis from RBL-2H3 mast cells sensitized by IgE (bound to high-affinity surface receptors FcεRI) and stimulated using the antigen DNP-BSA. Quasi-static I-V measurements reflected a slow shift in surface potential () which was dependent on extracellular calcium ([Ca]_o) and buffer strength, which suggests sensitivity to protons released during exocytosis. Fluorescent imaging of dextran-labeled vesicle release showed evidence of a similar time course, while un-sensitized cells showed no response to stimulation. Transient recordings revealed fluctuations with a rapid rise and slow decay. Chromaffin cells stimulated with high KCl showed both slow shifts and extracellular action potentials exhibiting biphasic and inverted capacitive waveforms, indicative of varying ion-channel distributions across the cell-transistor junction. Our approach presents a facile method to simultaneously monitor exocytosis and ion channel activity with high temporal sensitivity without the need for redox chemistry.

Programmable ion-sensitive transistor interfaces. III. Design considerations, signal generation, and sensitivity enhancement

We report on factors that affect DNA hybridization detection using ion-sensitive field-effect transistors (ISFETs). Signal generation at the interface between the transistor and immobilized biomolecules is widely ascribed to unscreened molecular charges causing a shift in surface potential and hence the transistor output current. Traditionally, the interaction between DNA and the dielectric or metal sensing interface is modeled by treating the molecular layer as a sheet charge and the ionic profile with a Poisson-Boltzmann distribution. The surface potential under this scenario is described by the Graham equation. This approximation, however, often fails to explain large hybridization signals on the order of tens of mV. More realistic descriptions of the DNA-transistor interface which include factors such as ion permeation, exclusion, and packing constraints have been proposed with little or no corroboration against experimental findings. In this study, we examine such physical models by their assumptions, range of validity, and limitations. We compare simulations against experiments performed on electrolyte-oxide-semiconductor capacitors and foundry-ready floating-gate ISFETs. We find that with weakly charged interfaces (i.e., low intrinsic interface charge), pertinent to the surfaces used in this study, the best agreement between theory and experiment exists when ions are completely excluded from the DNA layer. The influence of various factors such as bulk pH, background salinity, chemical reactivity of surface groups, target molecule concentration, and surface coatings on signal generation is studied. Furthermore, in order to overcome Debye screening limited detection, we suggest two signal enhancement strategies. We first describe frequency domain biosensing, highlighting the ability to sort short DNA strands based on molecular length, and then describe DNA biosensing in multielectrolytes comprising trace amounts of higher-valency salt in a background of monovalent saline. Our study provides guidelines for optimized interface design, signal enhancement, and the interpretation of FET-based biosensor signals.

Point-of-care nucleic acid detection using nanotechnology

Recent developments in nanotechnology have led to significant advancements in point-of-care (POC) nucleic acid detection. The ability to sense DNA and RNA in a portable format leads to important applications for a range of settings, from on-site detection in the field to bedside diagnostics, in both developing and developed countries. We review recent innovations in three key process components for nucleic acid detection: sample preparation, target amplification, and read-out modalities. We discuss how the advancements realized by nanotechnology are making POC nucleic acid detection increasingly applicable for decentralized and accessible testing, in particular for the developing world.

Programmable ion-sensitive transistor interfaces. I. Electrochemical gating

Electrochemical gating is the process by which an electric field normal to the insulator electrolyte interface shifts the surface chemical equilibrium and further affects the charge in solution [Jiang and Stein, Langmuir 26, 8161 (2010)]. The surface chemical reactivity and double-layer charging at the interface of electrolyte-oxide-semiconductor (EOS) capacitors is investigated. We find a strong pH-dependent hysteresis upon dc potential cycling. Varying salinity at a constant pH does not change the hysteretic window, implying that field-induced surface pH regulation is the dominant cause of hysteresis. We propose and investigate this mechanism in foundry-made floating-gate ion-sensitive field-effect transistors, which can serve as both an ionic sensor and an actuator. Termed the chemoreceptive neuron metal-oxide-semiconductor (CνMOS) transistor, it features independently driven control gates (CGs) and sensing gates (SGs) that are capacitively coupled to an extended floating gate (FG). The SG is exposed to fluid, the CG is independently driven, and the FG is capable of storing charge Q(FG) of either polarity. Asymmetric capacitive coupling between the CG and SG to FG results in intrinsic amplification of the measured surface potential shifts and influences the FG charge injection mechanism. This modified SG surface condition was monitored through transient recordings of the output current, performed under alternate positive and negative CG pulses. Transient recordings revealed a hysteresis where the current was enhanced under negative pulsing and reduced after positive pulsing. This hysteresis effect is similar to that observed with EOS capacitors, suggesting a field-dependent surface charge regulation mechanism at play. At high CG biases, nonvolatile charge Q(FG) tunneling into the FG occurs, which creates a larger field and tunes the pH response and the point of zero charge. This mechanism gives rise to surface programmability. In this paper we describe the operational principles, tunneling mechanism, and role of electrolyte composition under field modulation. The experimental findings are then modeled by a Poisson-Boltzmann formulation with surface pH regulation. We find that surface ionization constants play a dominant role in determining the pH tuning effect. In the following paper [K. Jayant et al., Phys. Rev. E 88, 012802 (2013)] we extend the dual-gate operation to molecular sensing and demonstrate the use of Q(FG) to achieve manipulation of surface-adsorbed DNA.