Label-free detection of single nucleotide polymorphisms utilizing the differential transfer function of field-effect transistors

A Portable Readout System for Biomarker Detection with Aptamer-Modified CMOS ISFET Array

Biosensors based on ion-sensitive field effect transistors (ISFETs) combined with aptamers offer a promising and convenient solution for point-of-care testing applications due to the ability for fast and label-free detection of a wide range of biomarkers. Mobile and easy-to-use readout devices for the ISFET aptasensors would contribute to further development of the field. In this paper, the development of a portable PC-controlled device for detecting aptamer-target interactions using ISFETs is described. The device assembly allows selective modification of individual ISFETs with different oligonucleotides. Ta2O5-gated ISFET structures were optimized to minimize trapped charge and capacitive attenuation. Integrated CMOS readout circuits with linear transfer function were used to minimize the distortion of the original ISFET signal. An external analog signal digitizer with constant voltage and superimposed high-frequency sine wave reference voltage capabilities was designed to increase sensitivity when reading ISFET signals. The device performance was demonstrated with the aptamer-driven detection of troponin I in both reference voltage setting modes. The sine wave reference voltage measurement method reduced the level of drift over time and enabled a lowering of the minimum detectable analyte concentration. In this mode (constant voltage 2.4 V and 10 kHz 0.1Vp-p), the device allowed the detection of troponin I with a limit of detection of 3.27 ng/mL. Discrimination of acute myocardial infarction was demonstrated with the developed device. The ISFET device provides a platform for the multiplexed detection of different biomarkers in point-of-care testing.

Signal transduction interfaces for field-effect transistor-based biosensors

Biosensors based on field-effect transistors (FETs) are suitable for use in miniaturized and cost-effective healthcare devices. Various semiconductive materials can be applied as FET channels for biosensing, including one- and two-dimensional materials. The signal transduction interface between the biosample and the channel of FETs plays a key role in translating electrochemical reactions into output signals, thereby capturing target ions or biomolecules. In this Review, distinctive signal transduction interfaces for FET biosensors are introduced, categorized as chemically synthesized, physically structured, and biologically induced interfaces. The Review highlights that these signal transduction interfaces are key in controlling biosensing parameters, such as specificity, selectivity, binding constant, limit of detection, signal-to-noise ratio, and biocompatibility.

Technical Perspectives on Applications of Biologically Coupled Gate Field-Effect Transistors

Biosensing technologies are required for point-of-care testing (POCT). We determine some physical parameters such as molecular charge and mass, redox potential, and reflective index for measuring biological phenomena. Among such technologies, biologically coupled gate field-effect transistor (Bio-FET) sensors are a promising candidate as a type of potentiometric biosensor for the POCT because they enable the direct detection of ionic and biomolecular charges in a miniaturized device. However, we need to reconsider some technical issues of Bio-FET sensors to expand their possible use for biosensing in the future. In this perspective, the technical issues of Bio-FET sensors are pointed out, focusing on the shielding effect, pH signals, and unique parameters of FETs for biosensing. Moreover, other attractive features of Bio-FET sensors are described in this perspective, such as the integration and the semiconductive materials used for the Bio-FET sensors.

State of the Art of Chemosensors in a Biomedical Context

Healthcare is undergoing large transformations, and it is imperative to leverage new technologies to support the advent of personalized medicine and disease prevention. It is now well accepted that the levels of certain biological molecules found in blood and other bodily fluids, as well as in exhaled breath, are an indication of the onset of many human diseases and reflect the health status of the person. Blood, urine, sweat, or saliva biomarkers can therefore serve in early diagnosis of diseases such as cancer, but also in monitoring disease progression, detecting metabolic disfunctions, and predicting response to a given therapy. For most point-of-care sensors, the requirement that patients themselves can use and apply them is crucial not only regarding the diagnostic part, but also at the sample collection level. This has stimulated the development of such diagnostic approaches for the non-invasive analysis of disease-relevant analytes. Considering these timely efforts, this review article focuses on novel, sensitive, and selective sensing systems for the detection of different endogenous target biomarkers in bodily fluids as well as in exhaled breath, which are associated with human diseases.

Solution-Gated Ultrathin Channel Indium Tin Oxide-Based Field-Effect Transistor Fabricated by a One-Step Procedure that Enables High-Performance Ion Sensing and Biosensing

In this paper, we propose a one-step procedure for fabricating a solution-gated ultrathin channel indium tin oxide (ITO)-based field-effect transistor (FET) biosensor, thus providing an ″all-by-ITO″ technology. A thin-film sheet was placed on both ends of a metal shadow mask, which were contacted with a glass substrate. That is, the bottom of the metal shadow mask corresponding to the channel was slightly raised from the substrate, resulting in the creeping of some particles into the gap during sputtering. Owing to this modified metal shadow mask, a thin ITO channel (<30-40 nm) and thick ITO source/drain electrodes (ca. 100 nm) were simultaneously fabricated during the one-step sputtering. The thickness of ITO films was critical for them to be semiconductive, depending on the maximum depletion width (∼30-40 nm for the ITO channel), similarly to 2D materials. The ultrathin ITO channel worked as an ion-sensitive membrane as well owing to the intrinsic oxidated surface directly contacting with an electrolyte solution. The solution-gated 20-nm-thick channel ITO-based FET, with a steep subthreshold slope (SS) of 55 mV/dec (pH 7.41) attributable to the electric double-layer capacitance at the electrolyte solution/channel interface and the absence of interfacial traps among electrodes formed in one step, demonstrated an ideal pH responsivity (∼56 mV/pH), resulting in the real-time monitoring of cellular respiration and the long-term stability of electrical properties for 1 month. Moreover, the chemical modification of the ITO channel surface is expected to contribute to biomolecular recognition with ultrahigh sensitivity owing to the remarkably steep SS, which provided the exponential pH sensitivity in the subthreshold regime. Our new device produced in this one-step manner has a great future potential in bioelectronics.

Comprehensive Understanding of Silicon-Nanowire Field-Effect Transistor Impedimetric Readout for Biomolecular Sensing

Impedance sensing with silicon nanowire field-effect transistors (SiNW-FETs) shows considerable potential for label-free detection of biomolecules. With this technique, it might be possible to overcome the Debye-screening limitation, a major problem of the classical potentiometric readout. We employed an electronic circuit model in Simulation Program with Integrated Circuit Emphasis (SPICE) for SiNW-FETs to perform impedimetric measurements through SPICE simulations and quantitatively evaluate influences of various device parameters to the transfer function of the devices. Furthermore, we investigated how biomolecule binding to the surface of SiNW-FETs is influencing the impedance spectra. Based on mathematical analysis and simulation results, we proposed methods that could improve the impedimetric readout of SiNW-FET biosensors and make it more explicable.

Molecular-Charge-Contact-Based Ion-Sensitive Field-Effect Transistor Sensor in Microfluidic System for Protein Sensing

In this paper, we demonstrate the possibility of direct protein sensing beyond the Debye length limit using a molecular-charge-contact (MCC)-based ion-sensitive field-effect transistor (ISFET) sensor combined with a microfluidic device. Different from the MCC method previously reported, biotin-coated magnetic beads are set on the gate insulator of an ISFET using a button magnet before the injection of target molecules such as streptavidin. Then, the streptavidin—a biotin interaction, used as a model of antigen—antibody reaction is expected at the magnetic beads/gate insulator nanogap interface, changing the pH at the solution/dielectric interface owing to the weak acidity of streptavidin. In addition, the effect of the pH or ionic strength of the measurement solutions on the electrical signals of the MCC-based ISFET sensor is investigated. Furthermore, bound/free (B/F) molecule separation with a microfluidic device is very important to obtain an actual electrical signal based on the streptavidin–biotin interaction. Platforms based on the MCC method are suitable for exploiting the advantages of ISFETs as pH sensors, that is, direct monitoring systems for antigen–antibody reactions in the field of in vitro diagnostics.

Biologically Coupled Gate Field-Effect Transistors Meet in Vitro Diagnostics

In this paper, recent works on biologically coupled gate field-effect transistor (bio-FET) sensors are introduced and compared to provide a perspective. Most biological phenomena are closely related to behaviors of ions and biomolecules. This is why biosensing devices for detecting ionic and biomolecular charges contribute to the direct analysis of biological phenomena in a label-free and enzyme-free manner. Potentiometric biosensors such as bio-FET sensors, which allow the direct detection of these charges on the basis of the field effect, meet this requirement and have been developed as simple devices for in vitro diagnostics (IVD). A variety of biological ionic behaviors generated by biomolecular recognition events and cellular activities are being targeted for clinical diagnostics as well as the study of neuroscience using the bio-FET sensors. To realize these applications, bioelectrical interfaces should be formed between the electrolyte solution and the gate electrode by modifying artificially synthesized and biomimetic membranes, resulting in the selective detection of targets based on intrinsic molecular charges. Various types of semiconducting materials, not only inorganic semiconductors but also organic semiconductors, can be selected for use in bio-FET sensors, depending on the application field. In addition, a semiconductor integrated circuit device is ideal for the massively parallel detection of multiple samples. Thus, platforms based on bio-FET sensors are suitable for use in simple and miniaturized electrical circuit systems for IVD to enable the prevention and early detection of diseases.

Label-free discrimination of single nucleotide changes in DNA by reflectometric interference Fourier transform spectroscopy

Phenotypic variation - such as disease susceptibility and differential drug response - has a strong genetic component. Substantial effort has therefore been made to identify causal genomic variants explaining such variation among humans. Point mutations (PMs), which are single nucleotide changes in the genome, have been identified to be the most abundant form of causal genomic variants, making them useful, reliable diagnostic markers. Methods developed to genotype PMs have moved towards solid-phase assays, which not only show greater sensitivity and specificity, but also enable scalability and faster processing time. Most current assays are, however, based on fluorescent probes, which makes them relatively expensive. To develop a more cost-effective label-free genotyping method, we used a porous silicon (PSi) base as an efficient support for DNA biosensing and coupled it with reflectometric interference Fourier transform spectroscopy (RIFTS). To assess the versatility of this approach, we tested both a single nucleotide substitution in VKORC1 (-1639G > A; rs9923231) and a single nucleotide insertion in BRCA1 (5382insC; rs80357906). We demonstrate that the PSi-RIFTS method can efficiently detect both PM types with high sensitivity where hybridization of complementary DNA can be quantifiably differentiated from mismatch and non-complementary hybridization events. In addition, we show that the PSi base with immobilized DNA not only can be re-used to type further samples, but it also remains stable for 14 days, suggesting its potential for high-throughput applications.

Label-free real-time optical monitoring of DNA hybridization using SiN Mach-Zehnder interferometer-based integrated biosensing platform

We report on the label-free real-time optical monitoring of DNA hybridization upon exposure to a flow of complementary DNA at different concentrations. The biosensor is composed of a silicon nitride integrated unbalanced Mach-Zehnder interferometer (MZI), with an integrated arrayed waveguide grating as a spectral filter. This MZI has been shown to have both sufficient multiplexing capability and limit of detection on the order of 10  -  6 RIU. Probe DNA, consisting of a 36-mer fragment is covalently immobilized on the silicon nitride integrated biosensor. The wavelength shift is monitored upon complementary DNA targets being flown over the sensor. Concentrations of 1 pM can be easily detected. Also, an alternative route to modify the sensor surface with carboxylic groups using the photochemical reaction of fatty acids is proposed and preliminary XPS results are presented. Moreover, preliminary results for DNA obtained from a rolling circle amplification (RCA-DNA) process and spiked in a realistic amplification buffer are presented.

Surface regeneration and reusability of label-free DNA biosensors based on weak polyelectrolyte-modified capacitive field-effect structures

The reusability of capacitive field-effect electrolyte-insulator-semiconductor (EIS) sensors modified with a cationic weak polyelectrolyte (poly(allylamine hydrochloride) (PAH)) for the label-free electrical detection of single-stranded DNA (ssDNA), in-solution- and on-chip-hybridized double-stranded DNA (dsDNA) has been studied. It has been demonstrated that via simply regeneration of the gate surface of the EIS sensor by means of an electrostatic adsorption of a new PAH layer, the same biosensor can be reused for at least five DNA-detection measurements. Because of the reversal of the charge sign of the outermost layer after each surface modification with the cationic PAH or negatively charged DNA molecules, the EIS-biosensor signal exhibits a zigzag-like behavior. The amplitude of the signal changes has a tendency to decrease with increasing number of macromolecular layers. The direction of the EIS-signal shifts can serve as an indicator for a successful DNA-immobilization or -hybridization process. In addition, we observed that the EIS-signal changes induced by each surface-modification step (PAH adsorption, immobilization of ssDNA or dsDNA molecules and on-chip hybridization of complementary target cDNA) is decreased with increasing the ionic strength of the measurement solution, due to the more efficient macromolecular charge-screening by counter ions. The results of field-effect experiments were supported by fluorescence-intensity measurements of the PAH- or DNA-modified EIS surface using various fluorescence dyes.

Real-time wash-free detection of unlabeled PNA-DNA hybridization using discrete FET sensor

We demonstrate an electrochemical sensor for detection of unlabeled single-stranded DNA using peptide nucleic acid (PNA) probes coupled to the field-effect transistor (FET) gate. The label-free detection relies on the intrinsic charge of the DNA backbone. Similar detection schemes have mainly concentrated on sensitivity improvement with an emphasis on new sensor structures. Our approach focuses on using an extended-gate that separates the FET and the sensing electrode yielding a simple and mass fabricable device. We used PNA probes for efficient hybridization in low salt conditions that is required to avoid the counter ion screening. As a result, significant part of the target DNA lies within the screening length of the sensor. With this, we achieved a wash-free detection where  typical gate potential shifts are more than 70 mV with 1 µM target DNA. We routinely obtained a real-time, label- and wash-free specific detection of target DNA in nanomolar concentration with low-cost electronics and the responses were achieved within minutes after introducing targets to the solution. Furthermore, the results suggest that the sensor performance is limited by specificity rather than by sensitivity and using low-cost electronics does not limit the sensor performance in the presented sensor configuration.

Systematic Approach to the Development of Microfabricated Biosensors: Relationship between Gold Surface Pretreatment and Thiolated Molecule Binding

Despite the increasing popularity of microfabricated biosensors due to advances in technologic and surface functionalization strategies, their successful implementation is partially inhibited by the lack of consistency in their analytical characteristics. One of the main causes for the discrepancies is the absence of a systematic and comprehensive approach to surface functionalization. In this article microfabricated gold electrodes aimed at biosensor development have been systematically characterized in terms of surface pretreatment, thiolated molecule binding, and reproducibility by means of X-ray photoelectron scattering (XPS) and cyclic voltammetry (CV). It has been shown that after SU-8 photolithography gold surfaces were markedly contaminated, which decreased the effective surface area and surface coverage of a model molecule mercaptohexanol (MCH). Three surface pretreatment methods compatible with microfabricated devices were compared. The investigated methods were (i) cyclic voltammetry in dilute H₂SO₄, (ii) gentle basic piranha followed by linear sweep voltammetry in dilute KOH, and (iii) oxygen plasma treatment followed by incubation in ethanol. It was shown that all three methods significantly decreased the contamination and increased MCH surface coverage. Most importantly, it was also revealed that surface pretreatments may induce structural changes to the gold surfaces. Accordingly, these alterations influence the characteristics of MCH functionalization.

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.

Biologically sensitive field-effect transistors: from ISFETs to NanoFETs

Biologically sensitive field-effect transistors (BioFETs) are one of the most abundant classes of electronic sensors for biomolecular detection. Most of the time these sensors are realized as classical ion-sensitive field-effect transistors (ISFETs) having non-metallized gate dielectrics facing an electrolyte solution. In ISFETs, a semiconductor material is used as the active transducer element covered by a gate dielectric layer which is electronically sensitive to the (bio-)chemical changes that occur on its surface. This review will provide a brief overview of the history of ISFET biosensors with general operation concepts and sensing mechanisms. We also discuss silicon nanowire-based ISFETs (SiNW FETs) as the modern nanoscale version of classical ISFETs, as well as strategies to functionalize them with biologically sensitive layers. We include in our discussion other ISFET types based on nanomaterials such as carbon nanotubes, metal oxides and so on. The latest examples of highly sensitive label-free detection of deoxyribonucleic acid (DNA) molecules using SiNW FETs and single-cell recordings for drug screening and other applications of ISFETs will be highlighted. Finally, we suggest new device platforms and newly developed, miniaturized read-out tools with multichannel potentiometric and impedimetric measurement capabilities for future biomedical applications.

PEDOT:PSS organic electrochemical transistor arrays for extracellular electrophysiological sensing of cardiac cells

Electrophysiological biosensors embedded in planar devices represent a state of the art approach to measure and evaluate the electrical activity of biological systems. This measurement method allows for the testing of drugs and their influences on cells or tissues, cytotoxicity, as well as the direct implementation into biological systems in vivo for signal transduction. Multi-electrode arrays (MEAs) with metal or metal-like electrodes on glass substrates are one of the most common, well-established platforms for this purpose. In recent years organic electrochemical transistors (OECTs) made of poly(2,3-dihydrothieno-1,4-dioxin)-poly(styrenesulfonate) (PEDOT:PSS) have as well shown their value in transducing and amplifying the ionic signals in biological systems. We developed OECT devices in a wafer-scale process and used them as electrophysiological biosensors measuring electrophysiological activity of the cardiac cell line HL-1. Our optimized devices show very promising properties such as good signal-to-noise ratio as well as the ability to record fast components of extracellular signals. Combined with an easy, cost effective fabrication and the transparency of the polymer, this platform offers a valuable alternative to traditional MEA systems for future cell sensing applications.

On the Use of Scalable NanoISFET Arrays of Silicon with Highly Reproducible Sensor Performance for Biosensor Applications

As a prerequisite to the development of real label-free bioassay applications, a high-throughput top-down nanofabrication process is carried out with a combination of nanoimprint lithography, anisotropic wet-etching, and photolithography methods realizing nanoISFET arrays that are then analyzed for identical sensor characteristics. Here, a newly designed array-based sensor chip exhibits 32 high aspect ratio silicon nanowires (SiNWs) laid out in parallel with 8 unit groups that are connected to a very highly doped, Π-shaped common source and individual drain contacts. Intricately designed contact lines exert equal feed-line resistances and capacitances to homogenize the sensor response as well as to minimize parasitic transport effects and to render easy integration of a fluidic layer on top. The scalable nanofabrication process as outlined in this article casts out a total of 2496 nanowires (NWs) on a 4 inch p-type silicon-on-insulator (SOI) wafer, yielding 78 sensor chips based on nanoISFET arrays. The sensor platform exhibiting high-performance transistor characteristics in buffer solutions is thoroughly characterized using state-of-the-art surface and electrical measurement techniques. Deploying a pH sensor in liquid buffers after high-quality gas-phase silanization, nanoISEFT arrays demonstrate typical pH sensor behavior with sensitivity as high as 43 ± 3 mV·pH^-1 and a device-to-device variation of 7% at the wafer scale. Demonstration of a high-density sensor platform with uniform characteristics such as nanoISFET arrays of silicon (Si) in a routine and refined nanofabrication process may serve as an ideal solution deployable for real assay-based applications.

DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer

Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization. The negatively charged probe single-stranded DNA (ssDNA) molecules were electrostatically adsorbed onto the positively charged PAH layer, resulting in a preferentially flat orientation of the ssDNA molecules within the Debye length, thus yielding a reduced charge-screening effect and a higher sensor signal. Each sensor-surface modification step (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), reducing an unspecific adsorption by a blocking agent, incubation with noncomplementary DNA (ncDNA) solution) was monitored by means of capacitance-voltage and constant-capacitance measurements. In addition, the surface morphology of the PAH layer was studied by atomic force microscopy and contact-angle measurements. High hybridization signals of 34 and 43 mV were recorded in low-ionic strength solutions of 10 and 1 mM, respectively. In contrast, a small signal of 4 mV was recorded in the case of unspecific adsorption of fully mismatched ncDNA. The density of probe ssDNA and dsDNA molecules as well as the hybridization efficiency was estimated using the experimentally measured DNA immobilization and hybridization signals and a simplified double-layer capacitor model. The results of field-effect experiments were supported by fluorescence measurements, verifying the DNA-immobilization and hybridization event.

Field effect sensors for nucleic Acid detection: recent advances and future perspectives

In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET) are the basis for the development of radical new approaches for the specific detection and characterization of DNA due to FETs’ greater signal-to-noise ratio, fast measurement capabilities, and possibility to be included in portable instrumentation. Reliable molecular characterization of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. FET biosensors may become a relevant tool for molecular diagnostics and at point-of-care. The development of these devices and strategies should be carefully designed, as biomolecular recognition and detection events must occur within the Debye length. This limitation is sometimes considered to be fundamental for FET devices and considerable efforts have been made to develop better architectures. Herein we review the use of field effect sensors for nucleic acid detection strategies—from production and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics lab.

Electrical cell-substrate impedance sensing with field-effect transistors is able to unravel cellular adhesion and detachment processes on a single cell level

We introduce a novel technique of impedimetric sensing of cellular adhesion, which might have the potential to supplement the well-known technique of Electrical Cell-substrate Impedance Sensing (ECIS) in cell culture assays. In contrast to the already commercialized ECIS method, we are using ion-sensitive field-effect transistor (ISFET) devices. The standard gold microelectrode size in ECIS is in the range of 100-250 μm in diameter. Reason for this limitation is that when downscaling the sensing electrodes, their effective impedance governed by the metal-liquid interface impedance is becoming very large and hence the currents to be measured are becoming very small reaching the limit of standard instrumentation. This is the main reason why typical assays with ECIS are focusing on applications like cell-cell junctions in confluent cultures. Single cell resolution is barely reachable with these systems. Here we use impedance spectroscopy with ISFET devices having gate dimensions of only 16 × 2 μm(2), which is enabling a real single cell resolution. We introduce an electrically equivalent circuit model, explain the measured effects upon single cell detachment, and present different cellular detachment scenarios. Our approach might supplement the field of ECIS with an alternative tool opening up a route for novel cell-substrate impedance sensing assays with so far unreachable lateral resolution.

Micro- and nano-structure based oligonucleotide sensors

This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.

Neurodegeneration through oxidative stress: monitoring hydrogen peroxide induced apoptosis in primary cells from the subventricular zone of BALB/c mice using field-effect transistors

Dementia is one of the big medical challenges of our time with Alzheimer's, Huntington's and Parkinson's disease among its most common forms. In year 2000, 4.5 million people were diagnosed with Alzheimer's disease in the United States. In the case of Alzheimer's disease one of many contributing factors is a metabolic imbalance that leads to elevated oxidative stress levels. Consequences of this imbalance can be symptoms like apraxia, agnosia or sundowning. The use of field-effect transistors is a novel approach to study the effects of external stimuli on cells in vitro to provide researchers with a new tool for high resolution and high throughput studies to better understand cellular interaction and the effects of pharmacological compounds. In our study we use ion-sensitive field-effect transistors (FETs) to analyze the apoptosis inducing effects of hydrogen peroxide treatment on primary cells obtained from the subventricular zone of postnatal BALB/c mice. Upon apoptosis, the cell-substrate adhesion of the neurons is gradually weakened until complete detachment. In former studies we used our FET devices to conduct Electrical Cell-substrate Impedance Sensing (ECIS) experiments on the single cell level using morphologically different cell lines. Here we demonstrate that our novel approach of ECIS using FET devices can be expanded to primary neuronal tissue with high prospects for further studies in the field of pharmacological research.

Ag nanoclusters as probes for turn-on fluorescence recognition of TpG dinucleotide with a high selectivity

CpG dinucleotide in DNA has a great tendency to mutate to TpG dinucleotide and this transition can cause some serious diseases. In this work, fluorescent Ag nanoclusters (Ag NCs) were employed as useful inorganic fluorophores for the potential of selectively discriminating TpG dinucleotide from CpG dinucleotide. Opposite the base Y of interest in YpG dinucleotide (Y=C or T), a bulge site was introduced so as to make the base Y to be unpaired and ready for Ag(+) binding. Such that the unpaired Y and context base pairs can provide a specific space suitable for creating fluorescent Ag NCs. We found that in comparison with CpG dinucleotide, TpG dinucleotide is much more efficient in growing fluorescent Ag NCs. Therefore, mutation of CpG dinucleotide to TpG can be identified by a turn-on fluorescence response and a high selectivity. More interestingly, Ag NCs exhibit a better performance in the TpG recognition over the other dinucleotides (Y=A and G) than the previously used organic fluorophores. Additionally, the effectiveness of the bulge site design in discriminating these dinucleotides was evidenced by control DNAs having the abasic site structure. We expect that a practical method for TpG dinucleotide recognition with a high selectivity can be developed using the bulge site-grown fluorescent Ag NCs as novel probes.

Human T cells monitored by impedance spectrometry using field-effect transistor arrays: a novel tool for single-cell adhesion and migration studies

Cytotoxic T lymphocytes (CTLs) play an important role in the immune system by recognizing and eliminating pathogen-infected and tumorigenic cells. In order to achieve their function, T cells have to migrate throughout the whole body and identify the respective targets. In conventional immunology studies, interactions between CTLs and targets are usually investigated using tedious and time-consuming immunofluorescence imaging. However, there is currently no straightforward measurement tool available to examine the interaction strengths. In the present study, adhesion strengths and migration of single human CD8(+) T cells on pre-coated field-effect transistor (FET) devices (i.e. fibronectin, anti-CD3 antibody, and anti-LFA-1 antibody) were measured using impedance spectroscopy. Adhesion strengths to different protein and antibody coatings were compared. By fitting the data to an electronically equivalent circuit model, cell-related parameters (cell membrane capacitance referring to cell morphology and seal resistance referring to adhesion strength) were obtained. This electronically-assessed adhesion strength provides a novel, fast, and important index describing the interaction efficiency. Furthermore, the size of our detection transistor gates as well as their sensitivity reaches down to single cell resolution. Real-time motions of individually migrating T cells can be traced using our FET devices. The in-house fabricated FETs used in the present study are providing a novel and very efficient insight to individual cell interactions.

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.

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.

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

The chemoreceptive neuron metal-oxide-semiconductor transistor described in the preceding paper is further used to monitor the adsorption and interaction of DNA molecules and subsequently manipulate the adsorbed biomolecules with injected static charge. Adsorption of DNA molecules onto poly-L-lysine-coated sensing gates (SGs) modulates the floating gate (FG) potential ψ(O), which is reflected as a threshold voltage shift measured from the control gate (CG) V(th_CG). The asymmetric capacitive coupling between the CG and SG to the FG results in V(th_CG) amplification. The electric field in the SG oxide E(SG_ox) is fundamentally different when we drive the current readout with V(CG) and V(ref) (i.e., the potential applied to the CG and reference electrode, respectively). The V(CG)-driven readout induces a larger E(SG_ox), leading to a larger V(th_CG) shift when DNA is present. Simulation studies indicate that the counterion screening within the DNA membrane is responsible for this effect. The DNA manipulation mechanism is enabled by tunneling electrons (program) or holes (erase) onto FGs to produce repulsive or attractive forces. Programming leads to repulsion and eventual desorption of DNA, while erasing reestablishes adsorption. We further show that injected holes or electrons prior to DNA addition either aids or disrupts the immobilization process, which can be used for addressable sensor interfaces. To further substantiate DNA manipulation, we used impedance spectroscopy with a split ac-dc technique to reveal the net interface impedance before and after charge injection.

Label-free detection of single-nucleotide polymorphisms associated with myeloid differentiation-2 using a nanostructured biosensor

House dust mites are the major source of indoor allergens that are responsible for asthma. The major dust mite allergen is the group II allergen, Der p2. Myeloid differentiation-2 (MD-2) acts as an essential component in the CD14-TLR4 (toll-like receptor)/MD-2 receptor complex for Der p2 recognition. Mutations of the MD-2 associated gene on chromosome 8 degrade a human's innate responses. In this study, we report the effective detection of mutations to the MD-2 gene promoter, using a sensitive nanostructured biosensor with a sensing electrode of gold nanoparticles (GNPs) uniformly deposited in a nanohemisphere array. The 70 mer MD-2 expressed gene fragment was used to probe gene mutation. The complementary target, containing 156 mer nucleotide, was prepared using the fresh blood from patients with allergic disease. A total of 37 target samples, including 19 gene mutated samples and 18 normal samples, were prepared by a 20 cycles PCR process, and used for discrimination experiments. Experimental results illustrated that the nanostructured biosensor clearly discriminates between mutated and non-mutated MD-2 allergy genes.

High-throughput label-free detection of DNA hybridization and mismatch discrimination using interferometric reflectance imaging sensor

Optical label-free biosensors have demonstrated advantages over fluorescent-based detection methods by allowing accurate quantification while also being capable of measuring dynamic bimolecular interactions. A simple, high-throughput, solid-phase, and label-free technique, interferometric reflectance imaging sensor (IRIS), can quantify the mass density of DNA with pg/mm(2) sensitivity by measuring the optical path difference. We present the design of the IRIS instrument and complementary microarrays that can be used to perform a quantitative analysis of DNA microarrays. Finally, we present methods to accurately calculate the hybridization efficiency and identify SNPs from dynamic measurements, as well as supporting software algorithms needed for robust data processing.

Interpretation of protein adsorption through its intrinsic electric charges: a comparative study using a field-effect transistor, surface plasmon resonance, and quartz crystal microbalance

We describe the highly sensitive detection of the nonspecific adsorption of proteins onto a 1-undecanethiol self-assembled monolayer (SAM)-formed gold electrode by parallel analysis using field effect transistor (FET), surface plasmon resonance (SPR), and quartz crystal microbalance (QCM) sensors. The FET sensor detects the innate electric charges of the adsorbed protein at the electrode/solution interface, transforming the change in charge density into a potentiometric signal in real time, without the requirement for labels. In particular, using the Debye-Huckel model, the degree of potential shift was proportional to the dry mass of adsorbed albumin and β-casein. A comparison of the FET signal with SPR and QCM data provided information on the conformation and orientation of the surface-bound protein by observing characteristic break points in the correlation slopes between the signals. These slope transitions reflect a multistage process that occurs upon protein adsorption as a function of protein concentration, including interim coverage, film dehydration, and monolayer condensation. The FET biosensor, in combination with SPR and QCM, represents a new technology for interrogating protein-material interactions both quantitatively and qualitatively.

Monitoring nanoparticle induced cell death in H441 cells using field-effect transistors

In this work we propose the use of field-effect transistors (FETs) to examine the reaction of individual tumor cells to treatment with cell death inducing nanoparticles for future use in cancer therapy.For our analysis the human cancer cell line H441 (a human lung adenocarcinoma epithelial cell line) was cultivated on fibronectin coated FETs and treated with various concentrations of silicon nanoparticles. The cell line was cultivated under standard conditions. The reactions of the cells to the nanoparticles were analyzed via transfer function measurements, microscopic examination and standard MTT viability assays. Microscopic examination showed a clear change of morphology to round cells, which accompanies detachment from the surface of the substrate. Cell detachment could also be observed as a signal shift in the transfer function.The results of our study indicate the applicability of FETs for cancer research and analyzing pharmacological effects of new compounds. In addition our results implicate the usefulness of silicon nanoparticle based compounds in cancer therapy.

Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA

In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA.

Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction. The interaction of the polar amino group(s) of the base(s) of ss-DNA with a negatively charged surface also contributes significantly to the system stability.

Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices

We introduce a label-free approach for sensing polymerase reactions on deoxyribonucleic acid (DNA) using a chelator-modified silicon-on-insulator field-effect transistor (SOI-FET) that exhibits selective and reversible electrical response to pyrophosphate anions. The chemical modification of the sensor surface was designed to include rolling-circle amplification (RCA) DNA colonies for locally enhanced pyrophosphate (PPi) signal generation and sensors with immobilized chelators for capture and surface-sensitive detection of diffusible reaction by-products. While detecting arrays of enzymatic base incorporation reactions is typically accomplished using optical fluorescence or chemiluminescence techniques, our results suggest that it is possible to develop scalable and portable PPi-specific sensors and platforms for broad biomedical applications such as DNA sequencing and microbe detection using surface-sensitive electrical readout techniques.

Fluorescence light-up recognition of DNA nucleotide based on selective abasic site binding of an excited-state intramolecular proton transfer probe

DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.

DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

Rapid assessment of the stability of DNA duplexes by impedimetric real-time monitoring of chemically induced denaturation

In this article, we report on the electronic monitoring of DNA denaturation by NaOH using electrochemical impedance spectroscopy in combination with fluorescence imaging as a reference technique. The probe DNA consisting of a 36-mer fragment was covalently immobilized on nanocrystalline-diamond electrodes and hybridized with different types of 29-mer target DNA (complementary, single-nucleotide defects at two different positions, and a non-complementary random sequence). The mathematical separation of the impedimetric signals into the time constant for NaOH exposure and the intrinsic denaturation-time constants gives clear evidence that the denaturation times reflect the intrinsic stability of the DNA duplexes. The intrinsic time constants correlate with calculated DNA-melting temperatures. The impedimetric method requires minimal instrumentation, is label-free and fast with a typical time scale of minutes and is highly reproducible. The sensor electrodes can be used repetitively. These elements suggest that the monitoring of chemically induced denaturation at room temperature is an interesting approach to measure DNA duplex stability as an alternative to thermal denaturation at elevated temperatures, used in DNA-melting experiments and single nucleotide polymorphism (SNP) analysis.

Microfluidic-based biosensors toward point-of-care detection of nucleic acids and proteins

This article reviews state-of-the-art microfluidic biosensors of nucleic acids and proteins for point-of-care (POC) diagnostics. Microfluidics is capable of analyzing small sample volumes (10^-9-10^-18 l) and minimizing costly reagent consumption as well as automating sample preparation and reducing processing time. The merger of microfluidics and advanced biosensor technologies offers new promises for POC diagnostics, including high-throughput analysis, portability and disposability. However, this merger also imposes technological challenges on biosensors, such as high sensitivity and selectivity requirements with sample volumes orders of magnitude smaller than those of conventional practices, false response errors due to non-specific adsorption, and integrability with other necessary modules. There have been many prior review articles on microfluidic-based biosensors, and this review focuses on the recent progress in last 5 years. Herein, we review general technologies of DNA and protein biosensors. Then, recent advances on the coupling of the biosensors to microfluidics are highlighted. Finally, we discuss the key challenges and potential solutions for transforming microfluidic biosensors into POC diagnostic applications.

A non-labeled DNA biosensor based on light addressable potentiometric sensor modified with TiO2 thin film

Titanium dioxide (TiO(2)) thin film was deposited on the surface of the light addressable potentiometric sensor (LAPS) to modify the sensor surface for the non-labeled detection of DNA molecules. To evaluate the effect of ultraviolet (UV) treatment on the silanization level of TiO(2) thin film by 3-aminopropyltriethoxysilane (APTS), fluorescein isothiocyanate (FITC) was used to label the amine group on the end of APTS immobilized onto the TiO(2) thin film. We found that, with UV irradiation, the silanization level of the irradiated area of the TiO(2) film was improved compared with the non-irradiated area under well-controlled conditions. This result indicates that TiO(2) can act as a coating material on the biosensor surface to improve the effect and efficiency of the covalent immobilization of biomolecules on the sensor surface. The artificially synthesized probe DNA molecules were covalently linked onto the surface of TiO(2) film. The hybridization of probe DNA and target DNA was monitored by the recording of I-V curves that shift along the voltage axis during the process of reaction. A significant LAPS signal can be detected at 10 micromol/L of target DNA sample.