Potentiometric Detection of Single Nucleotide Polymorphism by Using a Genetic Field-effect transistor

Control of interface functions in solid-state biosensors for stable detection of molecular recognition

Significant progress has been achieved in the field of solid-state biosensors over the past 50 years. Various sensing devices with high-density integration and flexible configuration, as well as new applications for clinical diagnosis and healthcare, have been developed using blood, serum, and other body fluids such as sweat, tears, and saliva. A high-density array of ion-sensitive field effect transistors was developed by exploiting the advantages of advanced semiconductor technologies and commercialized in combination with an enzymatic primer extension reaction as a DNA sequencer in 2011. Different types of materials such as inorganic materials, metals, polymers, and biomolecules are mixed together on the surface of the gate while maintaining their own functions; therefore, compatibility among different materials has to be optimized so that the best detection performance of solid-state biosensors, including stability and reliability, is achieved as designed. Solid-state biosensors are suitable for the rapid, cost-effective, and noninvasive identification of biomarkers at various timepoints over the course of a disease.

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.

Hydrogel-Coated Gate Field-Effect Transistor for Real-Time and Label-Free Monitoring of β-Amyloid Aggregation and Its Inhibition

In this paper, we propose a hydrogel-coated gate field-effect transistor (FET) for the real-time and label-free monitoring of β-amyloid (Aβ) aggregation and its inhibition. The hydrogel used in this study is composed of poly tetramethoxysilane (TMOS), in which Aβ monomers are entrapped and then aggregate, and coated on the gate insulator; that is, Aβ aggregation is induced in the vicinity of the sensing surface. With the Aβ hydrogel-coated gate FET, the steplike decrease in the surface potential of the Aβ hydrogel-coated gate electrode is electrically monitored in real time, according to the stepwise aggregation of Aβ monomers to form into fibrils through oligomers and so forth in stages. This is because the capacitance of the Aβ-hydrogel membrane decreases depending on the stage of aggregation; that is, the hydrophobicity of the Aβ-hydrogel membrane increases stepwise depending on the amount of Aβ aggregates. The formation of Aβ fibrils is also confirmed in the measurement solution using a fluorescent dye, thioflavin T, which selectively binds to the Aβ fibrils. Moreover, the addition of daunomycin, an inhibitor of Aβ aggregation, to the measurement solution suppresses the stepwise electrical response of the Aβ hydrogel-coated gate FET. Thus, a platform based on the Aβ hydrogel-coated gate FET is suitable for a simple screening system for inhibitors of Aβ aggregation, which may lead the identification of potential therapeutic agents for Alzheimer's disease.

In Situ Electrical Monitoring of Methylated DNA Based on Its Conformational Change to G-Quadruplex Using a Solution-Gated Field-Effect Transistor

Methylated DNA is not only a diagnostic but also a prognostic biomarker for early-stage cancer. However, sodium bisulfite sequencing as a "gold standard" method for detection of methylation markers has some drawbacks such as its time-consuming and labor-intensive procedures. Therefore, simple and reliable methods are required to analyze DNA sequences with or without methylated residues. Herein, we propose a simple and direct method for detecting DNA methylation through its conformation transition to G-quadruplex using a solution-gated field-effect transistor (SG-FET) without using labeled materials. The BCL-2 gene, which is involved in the development of various human tumors, contains G-rich segments and undergoes a conformational change to G-quadruplex depending on the K⁺ concentration. Stacked G-quadruplex strands move close to the SG-FET sensor surface, resulting in large electrical signals based on intrinsic molecular charges. In addition, a dense hydrophilic polymer brush is grafted using surface-initiated atom transfer radical polymerization onto the SG-FET sensor surface to reduce electrical noise based on nonspecific adsorption of interfering species. In particular, control of the polymer brush thickness induces electrical signals based on DNA molecular charges in the diffusion layer, according to the Debye length limit. A platform based on the SG-FET sensor with a well-defined polymer brush is suitable for in situ monitoring of methylated DNA and realizes a point-of-care device with a high signal-to-noise ratio and without the requirement for additional processes such as bisulfite conversion and polymerase chain reaction.

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.

Biocompatible and Na+-sensitive thin-film transistor for biological fluid sensing

In this study, we develop a Na⁺-sensitive thin-film transistor (TFT) for a biocompatible ion sensor and investigate its cytotoxicity. A transparent amorphous oxide semiconductor composed of amorphous In-Ga-Zn-oxide (a-InGaZnO) is utilized as a channel of the Na⁺-sensitive TFT, which includes an indium tin oxide (ITO) film as the source and drain electrodes and a Ta₂O₅ thin-film gate, onto which a Na⁺-sensitive membrane is coated. As one of the Na⁺-sensitive membranes, the polyvinyl chloride (PVC) membrane with bis(12-crown-4) as the ionophore used on the TFT sensors shows good sensitivity and selectivity to changes in Na⁺ concentration but has high cytotoxicity owing to the leaching of its plasticizer to the solution; the plasticizer is added to solve and entrap the ionophore in the PVC membrane. On the other hand, a plasticizer-free Na⁺-sensitive membrane, the fluoropolysilicone (FPS) membrane with the bis(12-crown-4) ionophore, also reduces cell viability owing to the leaching of the ionophore. However, the FPS membrane with calix[4]arene as the ionophore on the gate of TFT sensors exhibits not only favorable electrical properties but also the lack of cytotoxicity. Thus, considering structural flexibility of TFTs, a platform based on TFT sensors coated with the Na⁺-sensitive FPS membrane containing calix[4]arene is suitable as a biocompatible Na⁺ sensing system for the continuous monitoring of ionic components in biological fluids such as sweat and tears.

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.

Biocompatible Poly(catecholamine)-Film Electrode for Potentiometric Cell Sensing

Surface-coated poly(catecholamine) (pCA) films have attracted attention as biomaterial interfaces owing to their biocompatible and physicochemical characteristics. In this paper, we report that pCA-film-coated electrodes are useful for potentiometric biosensing devices. Four different types of pCA film, l-dopa, dopamine, norepinephrine, and epinephrine, with thicknesses in the range of 7-27 nm were electropolymerized by oxidation on Au electrodes by using cyclic voltammetry. By using the pCA-film electrodes, the pH responsivities were found to be 39.3-47.7 mV/pH within the pH range of 1.68 to 10.01 on the basis of the equilibrium reaction with hydrogen ions and the functional groups of the pCAs. The pCA films suppressed nonspecific signals generated by other ions (Na⁺, K⁺, Ca²⁺) and proteins such as albumin. Thus, the pCA-film electrodes can be used in pH-sensitive and pH-selective biosensors. HeLa cells were cultivated on the surface of the pCA-film electrodes to monitor cellular activities. The surface potential of the pCA-film electrodes changed markedly because of cellular activity; therefore, the change in the hydrogen ion concentration around the cell/pCA-film interface could be monitored in real time. This was caused by carbon dioxide or lactic acid that is generated by cellular respiration and dissolves in the culture medium, resulting in the change of hydrogen concentration. pCA-film electrodes are suitable for use in biocompatible and pH-responsive biosensors, enabling the more selective detection of biological phenomena.

Programming a nonvolatile memory-like sensor for KRAS gene sensing and signal enhancement

A programmable field effect-based electrolyte-insulator-semiconductor (EIS) sensor constructed with a nonvolatile memory-like structure is proposed for KRAS gene DNA hybridization detection. This programmable EIS structure was fabricated with silicon oxide (SiO2)/silicon nitride (Si3N4)/silicon oxide on a p-type silicon wafer, namely electrolyte-oxide-nitride-oxide-Si (EONOS). In this research, voltage stress programming from 4 to 20V was applied to trigger holes confinement in the nitride-trapping layer that, consequently, enhances the DNA attachment onto the sensing surface due to additional electrostatic interaction. Not solely resulting from the higher DNA load, the programming may affect the orientation of the DNA that finally contributes to the change in capacitance. Findings have shown that a higher voltage program is able to increase the total capacitance and results in ~3.5- and ~5.5-times higher sensitivities for a series of concentrations for complementary DNA and wild type versus mutant DNA hybridization detection, respectively. Overall, it has been proven that the voltage program on the nonvolatile memory-like structure of EONOS is a notable candidate for genosensor development, scoping the diagnosis of a single nucleotide polymorphism (SNP)-related disease.

Advanced LSI-based amperometric sensor array with light-shielding structure for effective removal of photocurrent and mode selectable function for individual operation of 400 electrodes

We have developed a large-scale integrated (LSI) complementary metal-oxide semiconductor (CMOS)-based amperometric sensor array system called "Bio-LSI" as a platform for electrochemical bio-imaging and multi-point biosensing with 400 measurement points. In this study, we newly developed a Bio-LSI chip with a light-shield structure and a mode-selectable function with the aim of extending the application range of Bio-LSI. The light shield created by the top metal layer of the LSI chip significantly reduces the noise generated by the photocurrent, whose value is less than 1% of the previous Bio-LSI without the light shield. The mode-selectable function enables the individual operation of 400 electrodes in off, electrometer, V1, and V2 mode. The off-mode cuts the electrode from the electric circuit. The electrometer-mode reads out the electrode potential. The V1-mode and the V2-mode set the selected sensor electrode at two different independent voltages and read out the current. We demonstrated the usefulness of the mode-selectable function. First, we displayed a dot picture based on the redox reactions of 2.0 mM ferrocenemethanol at 400 electrodes by applying two different independent voltages using the V1 and V2 modes. Second, we carried out a simultaneous detection of O2 and H2O2 using the V1 and V2 modes. Third, we used the off and V1 modes for the modification of the osmium-polyvinylpyridine gel polymer containing horseradish peroxidase (Os-HRP) at the selected electrodes, which act as sensors for H2O2. These results confirm that the advanced version of Bio-LSI is a promising tool that can be applied to a wide range of analytical fields.

Self-oriented immobilization of DNA polymerase tagged by titanium-binding peptide motif

We developed a titanium-binding-peptide-1 (TBP-1)-tagged DNA polymerase, for self-oriented immobilization onto a titanium oxide (TiO2) substrate. The enzymatic function of a polymerase immobilized on a solid state device is strongly dependent on the orientation of the enzyme. The TBP-tagged DNA polymerase, which was derived from a hyperthermophilic archaeon, was designed to incorporate the RKLPDA peptide at the N-terminus, and synthesized by translation processes in Escherichia coli (E. coli). The specific binding of the TBP-tagged DNA polymerase onto a TiO2 substrate was clearly monitored by surface plasmon resonance spectroscopy (SPR) and by surface potential detection with an extended-gate field effect transistor (FET). In the SPR analyses, constant quantities of the DNA polymerase were stably immobilized on the titanium substrate under flow conditions, regardless of the concentration of the DNA polymerase, and could be completely removed by a 4 M MgCl2 wash after measurement. The FET signal showed the contribution of the molecular charge in the TBP motif to the binding with TiO2. In addition, the TBP-tagged DNA polymerase-tethered TiO2 gate electrode enabled the effective detection of the positive charges of hydrogen ions produced by the DNA extension reaction, according to the FET principle. Therefore, the self-oriented immobilization platform based on the motif-inserted enzyme is suitable for the quick and stable immobilization of functional enzymes on biosensing devices.

Donnan potential caused by polyelectrolyte monolayers

The Donnan potential is successfully isolated from ion pair potential on a ferrocene-labeled polyelectrolyte (DNA) monolayer. The isolated Donnan potential shifts negatively upon the increase in NaClO4 concentration with a slope of -58.8 mV/decade. With the salt concentration grown up to 1 M, the stretched DNA chains in low salt concentration are found to experience a gradual conformation relaxing process. At salt concentrations higher than 2 M, Donnan breakdown occurs where only the ion pair effect modulates the apparent potential. The apparent formal potential also shows strong dependence on solution pH, which reveals that the charge density in the polyelectrolyte monolayer plays an important role in the establishment of Donnan equilibrium.

Electronic hybridization detection in microarray format and DNA genotyping

We describe an approach to substituting a fluorescence microarray with a surface made of an arrangement of electrolyte-gated field effect transistors. This was achieved using a dedicated blocking of non-specific interactions and comparing threshold voltage shifts of transistors exhibiting probe molecules of different base sequence. We apply the approach to detection of the 35delG mutation, which is related to non-syndromic deafness and is one of the most frequent mutations in humans. The process involves barcode sequences that are generated by Tas-PCR, a newly developed replication reaction using polymerase blocking. The barcodes are recognized by hybridization to surface attached probes and are directly detected by the semiconductor device.

Current and emerging challenges of field effect transistor based bio-sensing

Field-effect-transistor (FET) based electrical signal transduction is an increasingly prevalent strategy for bio-sensing. This technique, often termed "Bio-FETs", provides an essentially label-free and real-time based bio-sensing platform effective for a variety of targets. This review highlights recent progress and challenges in the field. A special focus is on the comprehension of emerging nanotechnology-based approaches to facilitate signal-transduction and amplification. Some new targets of Bio-FETs and the future perspectives are also discussed.

Simple and robust strategy for potentiometric detection of glucose using fluorinated phenylboronic acid self-assembled monolayer

BACKGROUND

Field effect transistor (FET) based signal-transduction (Bio-FET) is an emerging technique for label-free and real-time basis biosensors for a wide range of targets. Glucose has constantly been of interest due to its clinical relevance. Use of glucose oxidase (GOD) and a lectin protein Concanavalin A are two common strategies to generate glucose-dependent electrochemical events. However, these protein-based materials are intolerant of long-term usage and storage due to their inevitable denaturing.

METHODS

A phenylboronic acid (PBA) modified self-assembled monolayer (SAM) on a gold electrode with an optimized disassociation constant of PBA, that is, 3-fluoro-4-carbamoyl-PBA possessing its pKa of 7.1, was prepared and utilized as an extended gate electrode for Bio-FET.

RESULTS

The prepared electrode showed a glucose-dependent change in the surface potential under physiological conditions, thus providing a remarkably simple rationale for the glyco-sensitive Bio-FET. Importantly, the PBA modified electrode showed tolerance to relatively severe heat and drying treatments; conditions under which protein based materials would surely be denatured.

CONCLUSIONS

A PBA modified SAM with optimized disassociation constant (pKa) can exhibit a glucose-dependent change in the surface potential under physiological conditions, providing a remarkably simple but robust method for the glyco-sensing.

GENERAL SIGNIFICANCE

This protein-free, totally synthetic glyco-sensing strategy may offer cheap, robust and easily accessible platform that may be useful in developing countries. This article is part of a Special Issue entitled Organic Bioelectronics-Novel Applications in Biomedicine.

Electrochemical DNA methylation detection for enzymatically digested CpG oligonucleotides

We describe the electrochemical detection of DNA methylation through the direct oxidation of both 5-methylcytosine (mC) and cytosine (C) in 5'-CG-3' sequence (CpG) oligonucleotides using a sputtered nanocarbon film electrode after digesting a longer CpG oligonucleotide with endonuclease P1. Direct electrochemistry of the longer CpG oligonucleotides was insufficient for obtaining the oxidation currents of these bases because the CG rich sequence inhibited the direct oxidation of each base in the longer CpG oligonucleotides, owing to the conformational structure and its very low diffusion coefficient. To detect C methylation with better quantitativity and sensitivity in the relatively long CpG oligonucleotides, we successfully used an endonuclease P1 to digest the target CpG oligonucleotide and yield an identical mononucleotide 2'-deoxyribonucleoside 5'-monophosphate (5'-dNMP). Compared with results obtained without P1 treatment, we achieved 4.4 times higher sensitivity and a wider concentration range for mC detection with a resolution capable of detecting a subtle methylated cytosine difference in the CpG oligonucleotides (60mer).

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.

Aptamer-based biosensor for sensitive PDGF detection using diamond transistor

The detection of platelet-derived growth factor (PDGF) via a solution-gate field-effect transistor (SGFET) has been demonstrated for the first time using aptamers immobilized on a diamond surface. Upon introduction of PDGF to the immobilized aptamer, a shift of 31.7 mV in the negative direction is observed at a source-drain current of -50 μA. A shift of 32.3 mV in the positive direction is detected after regeneration by SDS solution, indicating that the static measurement returns to its original value. These SGFETs operate stably within the large potential window of diamond (>3.0 V), and hence the surface channel does not need passivating with a thick insulating layer. Thereof, the immobilized aptamer channels have been exposed directly to the electrolyte solution without a gate insulator. Immobilization is achieved via aptamers covalently bonding to amine sites, thereby increasing the sensitivity of the biosensors. Diamond SGFETs have potential for the detection of PDGF and show durability against biological degradation after repeated usage and regeneration.

Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures

Biomolecular recognition is versatile, specific, and high affinity, qualities that have motivated decades of research aimed at adapting biomolecules into a general platform for molecular sensing. Despite significant effort, however, so-called "biosensors" have almost entirely failed to achieve their potential as reagentless, real-time analytical devices; the only quantitative, reagentless biosensor to achieve commercial success so far is the home glucose monitor, employed by millions of diabetics. The fundamental stumbling block that has precluded more widespread success of biosensors is the failure of most biomolecules to produce an easily measured signal upon target binding. Antibodies, for example, do not change their shape or dynamics when they bind their recognition partners, nor do they emit light or electrons upon binding. It has thus proven difficult to transduce biomolecular binding events into a measurable output signal, particularly one that is not readily spoofed by the binding of any of the many potentially interfering species in typical biological samples. Analytical approaches based on biomolecular recognition are therefore mostly cumbersome, multistep processes relying on analyte separation and isolation (such as Western blots, ELISA, and other immunochemical methods); these techniques have proven enormously useful, but are limited almost exclusively to laboratory settings. In this Account, we describe how we have refined a potentially general solution to the problem of signal detection in biosensors, one that is based on the binding-induced "folding" of electrode-bound DNA probes. That is, we have developed a broad new class of biosensors that employ electrochemistry to monitor binding-induced changes in the rigidity of a redox-tagged probe DNA that has been site-specifically attached to an interrogating electrode. These folding-based sensors, which have been generalized to a wide range of specific protein, nucleic acid, and small-molecule targets, are rapid (responding in seconds to minutes), sensitive (detecting sub-picomolar to micromolar concentrations), and reagentless. They are also greater than 99% reusable, are supported on micrometer-scale electrodes, and are readily fabricated into densely packed sensor arrays. Finally, and critically, their signaling is linked to a binding-specific change in the physics of the probe DNA, and not simply to adsorption of the target onto the sensor head. Accordingly, they are selective enough to be employed directly in blood, crude soil extracts, cell lysates, and other grossly contaminated clinical and environmental samples. Indeed, we have recently demonstrated the ability to quantitatively monitor a specific small molecule in real-time directly in microliters of flowing, unmodified blood serum. Because of their sensitivity, substantial background suppression, and operational convenience, these folding-based biosensors appear potentially well suited for electronic, on-chip applications in pathogen detection, proteomics, metabolomics, and drug discovery.

Device considerations for development of conductance-based biosensors

Design and fabrication of electronic biosensors based on field-effect-transistor (FET) devices require understanding of interactions between semiconductor surfaces and organic biomolecules. From this perspective, we review practical considerations for electronic biosensors with emphasis on molecular passivation effects on FET device characteristics upon immobilization of organic molecules and an electrostatic model for FET-based biosensors.

Feasibility studies on si-based biosensors

The aim of this paper is to summarize the efforts carried out so far in the fabrication of Si-based biosensors by a team of researchers in Catania, Italy. This work was born as a collaboration between the Catania section of the Microelectronic and Microsystem Institute (IMM) of the CNR, the Surfaces and Interfaces laboratory (SUPERLAB) of the Consorzio Catania Ricerche and two departments at the University of Catania: the Biomedical Science and the Biological Chemistry and Molecular Biology Departments. The first goal of our study was the definition and optimization of an immobilization protocol capable of bonding the biological sensing element on a Si-based surface via covalent chemical bonds. We chose SiO(2) as the anchoring surface due to its biocompatibility and extensive presence in microelectronic devices. The immobilization protocol was tested and optimized, introducing a new step, oxide activation, using techniques compatible with microelectronic processing. The importance of the added step is described by the experimental results. We also tested different biological molecule concentrations in the immobilization solutions and the effects on the immobilized layer. Finally a MOS-like structure was designed and fabricated to test an electrical transduction mechanism. The results obtained so far and the possible evolution of the research field are described in this review paper.

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

We present a label-free method for the detection of DNA hybridization, which is monitored by non-metallized silicon field-effect transistors (FET) in a microarray approach. The described method enables a fast and fully electronic readout of ex situ binding assays. The label-free detection utilizing the field-effect is based on the intrinsic charge of the DNA molecules and/or on changes of the solid-liquid interface impedance, when biomolecules bind to the sensor surface. With our sensor system, usually a time-resolved, dc readout is used. In general, this FET signal suffers from sensor drift, temperature drift, changes in electrolyte composition or pH value, influence of the reference electrode, etc. In this article, we present a differential ac readout concept for FET microarrays, which enables a stable operation of the sensor against many of these side-parameters, reliable readout and a possibility for a quick screening of large sensor arrays. We present the detection of point mutations in short DNA samples with this method in an ex situ binding assay.

Sequence-specific, electronic detection of oligonucleotides in blood, soil, and foodstuffs with the reagentless, reusable E-DNA sensor

The ability to detect specific oligonucleotides in complex, contaminant-ridden samples, without the use of exogenous reagents and using a reusable, fully electronic platform could revolutionize the detection of pathogens in the clinic and in the field. Here, we characterize a label-free, electronic sensor, termed E-DNA, for its ability to simultaneously meet these challenging demands. We find that because signal generation is coupled to a hybridization-linked conformational change, rather than to only adsorption to the sensor surface, E-DNA is selective enough to detect oligonucleotides in complex, multicomponent samples, such as blood serum and soil. Moreover, E-DNA signaling is monotonically related to target complementarity, allowing the sensor to discriminate between mismatched targets: we readily detect the complementary 17-base target against a 50 000-fold excess of genomic DNA, can distinguish a three-base mismatch from perfect target directly in blood serum, and under ideal conditions, observe statistically significant differences between single-base mismatches. Finally, because the sensing components are linked to the electrode surface, E-DNA is reusable: a 30-s room temperature wash recovers >99% of the sensor signal. This work further supports the utility of E-DNA as a rapid, specific, and convenient method for the detection of DNA and RNA sequences.

Peptide-nucleic acid-modified ion-sensitive field-effect transistor-based biosensor for direct detection of DNA hybridization

Here, we report the development of a peptide-nucleic acid (PNA)-modified ion-sensitive field-effect transistor (IS-FET)-based biosensor that takes advantage of the change in the surface potential upon hybridization of a negatively charged DNA. PNA was immobilized on a silicon nitride gate insulator by an addition reaction between a maleimide group introduced on the gate surface, the succinimide group of N-(6-maleimidocaproyloxy) succinimide, and the thiol group of the terminal cysteine in PNA. The surface was characterized after each step of the reaction by X-ray photoelectron spectroscopy analysis, and the kinetic analysis of the hybridization events was assessed by surface plasmon resonance. In addition, we measured the -potential before and after PNA-DNA hybridization in the presence of counterions to investigate the change in surface charge density at the surface-solution interface within the order of the Debye length. On the basis of the zeta-potential, the surface charge density, DeltaQ, calculated using the Grahame equation was approximately 4.0 x 10(-3) C/m2 and the estimated number of hybridized molecules was at least 1.7 x 10(11)/cm2. The I-V characteristics revealed that the PNA-DNA duplexes induce a positive shift in the threshold voltage, VT, and a decrease in the saturated drain current, ID. These results demonstrate that direct detection of DNA hybridization should be possible using a PNA-modified IS-FET-based biosensor. PNA is particularly advantageous for this system because it enables highly specific and selective binding at low ionic strength.

An enzymatic bionanotransduction system for multianalyte biological detection

AIM

The aim of this study was to develop and optimize a system for the detection of multiple biological targets in a single sample based on enzymatic bionanotransduction.

METHOD AND RESULTS

We used biological recognition elements (antibodies, DNA sequences) linked to DNA templates with T7 promoter regions for detection of specific target molecules. In vitro transcription of DNA templates bound to target molecules produced RNA nanosignals specific for every target in the sample. An enzyme-linked oligonucleotide fluorescence assay (ELOFA) provided a correlation between nanosignal profiles and target concentrations. The system was capable of detecting and distinguishing three species of specific immunoglobulin G (IgG) molecules at a level of 0.2 ng, mixed protein and DNA targets and single sample detection of Escherichia coli O157 micro-organisms and Staphylococcal enterotoxin B (SEB).

CONCLUSIONS

This report provided proof of concept for the use of enzymatic bionanotransduction with multianalyte biological detection based on differential nanosignal hybridization along with the application of this system to pathogen/toxin detection.

SIGNIFICANCE AND IMPACT OF THE STUDY

This system has the potential to be used as a tool for detection of multiple foodborne and environmental pathogens, toxins and targets of interest in a single sample.

Stable immobilization of an oligonucleotide probe on a gold substrate using tripodal thiol derivatives

We proposed an interface molecule for immobilization of DNA probes on solid substrates of DNA chips. We have designed and synthesized tripodal thiol derivatives for stable immobilization of oligonucleotide probes on a gold surface. On the basis of the tetrahedral structure of tripod, the tripodal thiol derivatives were bonded upright to the gold substrate, which would control the orientation of oligonucleotide probes. When the gold substrate with oligonucleotide probes tethered using the thiol derivatives was exposed to deionized water at higher temperatures, the tripodal interface molecules were attached to the gold surface more stably than the single contact molecules. The DNA chip platform combined with the functional interface molecule is suitable for a reproducible, inexpensive, and high-throughput detection system for genetic analyses in clinical diagnostics.

Signal enhancement in electronic detection of DNA hybridization

Electronic detection of the specific recognition between complementary DNA sequences is investigated. DNA probes are immobilized at different lateral positions on a Poly( L -lysine)-coated surface of an integrated silicon transistor array. Hybridization and field effect detection are done with the solid surface immersed in electrolyte solutions. Differential measurements are performed, where DNA hybridization leads to surface potential shifts between the transistors of the array. We experimentally show that these differential signals of hybridization can be enhanced significantly by changing the salt concentration between hybridization and detection.

DNA Detection by an Extended-Gate FET Sensor with a High-Frequency Voltage Superimposed onto a Reference Electrode

An extended-gate field-effect-transistor (FET) sensor with a gold-sensing electrode, to which a gold-thiol bond could easily be applied, was developed for DNA detection. Because the gold electrode is located in a different area from the FET, it can be operated without a light-shielding box by masking only the FET. However, when the FET sensor is used in an aqueous solution, fluctuation of the interface potential on the gold surface occurs, which results in decreased sensitivity. In DNA detection, 1 h or more was required to stabilize the drain current of the FET sensor after dipping it into the solution. To improve the sensitivity by reducing the fluctuation, we devised a measurement technique using a high-frequency voltage superimposed onto a reference electrode. With a superimposed high frequency voltage of over 1 kHz, the time required to stabilize the drain current of the FET sensor after dipping it in the solution was not only shortened to 5 min, but the fluctuation of the drain current was also reduced. As a result of applying this method, the FET sensor could successfully detect DNA hybridization and the extension reaction.

Direct transduction of allele-specific primer extension into electrical signal using genetic field effect transistor

We have developed a genetic field effect transistor (FET) for single nucleotide polymorphism (SNP) genotyping, which is based on potentiometric detection of molecular recognition on the gate insulator. Here, we report direct transduction of allele-specific primer extension on the gate surface into electrical signal using the genetic FETs. This method is based on detection of intrinsic negative charges of polynucleotide synthesized by DNA polymerase. The charge density change at the gate surface could be monitored during primer extension reaction. Moreover, three different genotypes could be successfully distinguished without any labeling for target DNA by the use of the genetic FET in combination with allele-specific primer extension. The platform based on the genetic FETs is suitable for a simple, accurate and inexpensive system for SNP genotyping in clinical diagnostics.