SOI nanowire for the high-sensitive detection of HBsAg and α-fetoprotein

The Study of Performance of a Nanoribbon Biosensor, Sensitized with Aptamers and Antibodies, upon Detection of Core Antigen of Hepatitis C Virus

The development of highly sensitive diagnostic systems for the early revelation of diseases in humans is one of the most important tasks of modern biomedical research, and the detection of the core antigen of the hepatitis C virus (HCVcoreAg)-a protein marker of the hepatitis C virus-is just the case. Our study is aimed at testing the performance of the nanoribbon biosensor in the case of the use of two different types of molecular probes: the antibodies and the aptamers against HCVcoreAg. The nanoribbon sensor chips employed are based on "silicon-on-insulator structures" (SOI-NR). Two different HCVcoreAg preparations are tested: recombinant β-galactosidase-conjugated HCVcoreAg ("Virogen", Watertown, MA, USA) and recombinant HCVcoreAg ("Vector-Best", Novosibirsk, Russia). Upon the detection of either type of antigen preparation, the lowest concentration of the antigen detectable in buffer with pH 5.1 was found to be approximately equal, amounting to ~10-15 M. This value was similar upon the use of either type of molecular probes.

Nanoribbon Biosensor-Based Detection of microRNA Markers of Prostate Cancer

Prostate cancer (PC) is one of the major causes of death among elderly men. PC is often diagnosed later in progression due to asymptomatic early stages. Early detection of PC is thus crucial for effective PC treatment. The aim of this study is the simultaneous highly sensitive detection of a palette of PC-associated microRNAs (miRNAs) in human plasma samples. With this aim, a nanoribbon biosensor system based on "silicon-on-insulator" structures (SOI-NR biosensor) has been employed. In order to provide biospecific detection of the target miRNAs, the surface of individual nanoribbons has been sensitized with DNA oligonucleotide probes (oDNA probes) complementary to the target miRNAs. The lowest concentration of nucleic acids, detectable with our biosensor, has been found to be 1.1 × 10-17 M. The successful detection of target miRNAs, isolated from real plasma samples of PC patients, has also been demonstrated. We believe that the development of highly sensitive nanotechnology-based biosensors for the detection of PC markers is a step towards personalized medicine.

SOI-FET Sensors with Dielectrophoretic Concentration of Viruses and Proteins

Quick label-free virus screening and highly sensitive analytical tools/techniques are becoming extremely important in a pandemic. In this study, we developed a biosensing device based on the silicon nanoribbon multichannel and dielectrophoretic controlled sensors functionalized with SARS-CoV-2 spike antibodies for the use as a platform for the detection and studding of properties of viruses and their protein components. Replicatively defective viral particles based on vesicular stomatitis viruses and HIV-1 were used as carrier molecules to deliver the target SARS-CoV-2 spike S-proteins to sensory elements. It was shown that fully CMOS-compatible nanoribbon sensors have the subattomolar sensitivity and dynamic range of 4 orders. Specific interaction between S-proteins and antibodies leads to the accumulation of the negative charge on the sensor surface. Nonspecific interactions of the viral particles lead to the positive charge accumulation. It was shown that dielectrophoretic controlled sensors allow to estimate the effective charge of the single virus at the sensor surface and separate it from the charge associated with the binding of target proteins with the sensor surface.

The Use of Excess Electric Charge for Highly Sensitive Protein Detection: Proof of Concept

In highly sensitive bioanalytical systems intended for the detection of protein biomarkers at low and ultra-low concentrations, the efficiency of capturing target biomolecules from the volume of the analyzed sample onto the sensitive surface of the detection system is a crucial factor. Herein, the application of excess electric charge for the enhancement of transport of target biomolecules towards the sensitive surface of a detection system is considered. In our experiments, we demonstrate that an uncompensated electric charge is induced in droplets of protein-free water owing to the separation of charge in a part of the Kelvin dropper either with or without the use of an external electric field. The distribution of an excess electric charge within a protein-free water droplet is calculated. It is proposed that the efficiency of protein capturing onto the sensitive surface correlates with the sign and the amount of charge induced per every single protein biomolecule. The effect described herein can allow one to make the protein capturing controllable, enhancing the protein capturing in the desired (though small) sensitive area of a detector. This can be very useful in novel systems intended for highly sensitive detection of proteins at ultra-low (≤10−15 M) concentrations.

Nanoribbon Biosensor in the Detection of miRNAs Associated with Colorectal Cancer

A nanoribbon biosensor (NRBS) was developed to register synthetic DNAs that simulate and are analogous to miRNA-17-3p associated with colorectal cancer. Using this nanoribbon biosensor, the ability to detect miRNA-17-3p in the blood plasma of a patient diagnosed with colorectal cancer has been demonstrated. The sensing element of the NRBS was a nanochip based on a silicon-on-insulator (SOI) nanostructure. The nanochip included an array of 10 nanoribbons and was designed with the implementation of top-down technology. For biospecific recognition of miRNA-17-3p, the nanochip was modified with DNA probes specific for miRNA-17-3p. The performance of the nanochip was preliminarily tested on model DNA oligonucleotides, which are synthetic analogues of miRNA-17-3p, and a detection limit of ~10-17 M was achieved. The results of this work can be used in the development of serological diagnostic systems for early detection of colorectal cancer.

Electrochemical Impedance Spectroscopy (EIS): Principles, Construction, and Biosensing Applications

Electrochemical impedance spectroscopy (EIS) is a powerful technique used for the analysis of interfacial properties related to bio-recognition events occurring at the electrode surface, such as antibody–antigen recognition, substrate–enzyme interaction, or whole cell capturing. Thus, EIS could be exploited in several important biomedical diagnosis and environmental applications. However, the EIS is one of the most complex electrochemical methods, therefore, this review introduced the basic concepts and the theoretical background of the impedimetric technique along with the state of the art of the impedimetric biosensors and the impact of nanomaterials on the EIS performance. The use of nanomaterials such as nanoparticles, nanotubes, nanowires, and nanocomposites provided catalytic activity, enhanced sensing elements immobilization, promoted faster electron transfer, and increased reliability and accuracy of the reported EIS sensors. Thus, the EIS was used for the effective quantitative and qualitative detections of pathogens, DNA, cancer-associated biomarkers, etc. Through this review article, intensive literature review is provided to highlight the impact of nanomaterials on enhancing the analytical features of impedimetric biosensors.

Aptamer-Sensitized Nanoribbon Biosensor for Ovarian Cancer Marker Detection in Plasma

The detection of CA 125 protein in buffer solution with a silicon-on-insulator (SOI)-based nanoribbon (NR) biosensor was experimentally demonstrated. In the biosensor, sensor chips, bearing an array of 12 nanoribbons (NRs) with n-type conductance, were employed. In the course of the analysis with the NR biosensor, the target protein was biospecifically captured onto the surface of the NRs, which was sensitized with covalently immobilized aptamers against CA 125. Atomic force microscopy (AFM) and mass spectrometry (MS) were employed in order to confirm the formation of the probe–target complexes on the NR surface. Via AFM and MS, the formation of aptamer–antigen complexes on the surface of SOI substrates with covalently immobilized aptamers against CA 125 was revealed, thus confirming the efficient immobilization of the aptamers onto the SOI surface. The biosensor signal, resulting from the biospecific interaction between CA 125 and the NR-immobilized aptamer probes, was shown to increase with an increase in the target protein concentration. The minimum detectable CA 125 concentration was as low as 1.5 × 10−17 M. Moreover, with the biosensor proposed herein, the detection of CA 125 in the plasma of ovarian cancer patients was demonstrated.

Micro-Raman Characterization of Structural Features of High-k Stack Layer of SOI Nanowire Chip, Designed to Detect Circular RNA Associated with the Development of Glioma

The application of micro-Raman spectroscopy was used for characterization of structural features of the high-k stack (h-k) layer of "silicon-on-insulator" (SOI) nanowire (NW) chip (h-k-SOI-NW chip), including Al₂O₃ and HfO₂ in various combinations after heat treatment from 425 to 1000 °C. After that, the NW structures h-k-SOI-NW chip was created using gas plasma etching optical lithography. The stability of the signals from the monocrine phase of HfO₂ was shown. Significant differences were found in the elastic stresses of the silicon layers for very thick (>200 nm) Al₂O₃ layers. In the UV spectra of SOI layers of a silicon substrate with HfO₂, shoulders in the Raman spectrum were observed at 480-490 cm^-1 of single-phonon scattering. The h-k-SOI-NW chip created in this way has been used for the detection of DNA-oligonucleotide sequences (oDNA), that became a synthetic analog of circular RNA-circ-SHKBP1 associated with the development of glioma at a concentration of 1.1 × 10^-16 M. The possibility of using such h-k-SOI NW chips for the detection of circ-SHKBP1 in blood plasma of patients diagnosed with neoplasm of uncertain nature of the brain and central nervous system was shown.

AFM study of changes in properties of horseradish peroxidase after incubation of its solution near a pyramidal structure

In our present paper, the influence of a pyramidal structure on physicochemical properties of a protein in buffer solution has been studied. The pyramidal structure employed herein was similar to those produced industrially for anechoic chambers. Pyramidal structures are also used as elements of biosensors. Herein, horseradish peroxidase (HRP) enzyme was used as a model protein. HRP macromolecules were adsorbed from their solution onto an atomically smooth mica substrate, and then visualized by atomic force microscopy (AFM). In parallel, the enzymatic activity of HRP was estimated by conventional spectrophotometry. Additionally, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) has been employed in order to find out whether or not the protein secondary structure changes after the incubation of its solution either near the apex of a pyramid or in the center of its base. Using AFM, we have demonstrated that the incubation of the protein solution either in the vicinity of the pyramid’s apex or in the center of its base influences the physicochemical properties of the protein macromolecules. Namely, the incubation of the HRP solution in the vicinity of the top of the pyramidal structure has been shown to lead to an increase in the efficiency of the HRP adsorption onto mica. Moreover, after the incubation of the HRP solution either near the top of the pyramid or in the center of its base, the HRP macromolecules adsorb onto the mica surface predominantly in monomeric form. At that, the enzymatic activity of HRP does not change. The results of our present study are useful to be taken into account in the development of novel biosensor devices (including those for the diagnosis of cancer in humans), in which pyramidal structures are employed as sensor, noise suppression or construction elements.

Biosensors Based on SOI Nanowire Transistors for Biomedicine and Virusology

This article contains the results of research on the topical problem of highly sensitive express registration of biological objects using field-effect transistors with the surface open for analyte access, which are made based on silicon-on-insulator (SOI) films. The possibilities of dielectrophoretic effects for controlling the concentration of the analyte in the area of sensory elements are considered on the example of the indication of viruses of nuclear polyhedrosis and vaccinia. It is shown that the use of the dielectrophoresis (DEPh) effect makes it possible to solve (1) the key tasks for creating sensor systems: increasing the detecting ability, as well as exrtacting and verifying the signal from the target particles; and (2) the fundamental task: determining the charge state of the analyte in solutions without modifying the sensors’ surface. The problems and prospects of the mass application of nanowire (NW) biosensors, including those with the dielectrophoretic effect, in biotechnology, virology, etc., are discussed.

Detection of Influenza Virus Using a SOI-Nanoribbon Chip, Based on an N-Type Field-Effect Transistor

The detection of influenza A virions with a nanoribbon detector (NR detector) has been demonstrated. Chips for the detector have been fabricated based on silicon-on-insulator nanoribbon structures (SOI nanoribbon chip), using a complementary metal-oxide-semiconductor (CMOS)-compatible technology—by means of gas-phase etching and standard optical photolithography. The surface of the SOI nanoribbon chip contains a matrix of 10 nanoribbon (NR) sensor elements. SOI nanoribbon chips of n-type conductance have been used for this study. For biospecific detection of target particles, antibodies against influenza virus have been covalently immobilized onto NRs. Influenza A virus detection was performed by real-time registration of the source-drain current through the NRs. The detection of the target viral particles was carried out in buffer solutions at the target particles concentration within the range from 10⁷ to 10³ viral particles per milliliter (VP/mL). The lowest detectable concentration of the target viral particles was 6 × 10⁻¹⁶ M (corresponding to 10⁴ VP/mL). The use of solutions containing ~10⁹ to 10¹⁰ VP/mL resulted in saturation of the sensor surface with the target virions. In the saturation mode, detection was impossible.

Raman Spectroscopy-Based Quality Control of "Silicon-On-Insulator" Nanowire Chips for the Detection of Brain Cancer-Associated MicroRNA in Plasma

Application of micro-Raman spectroscopy for the monitoring of quality of nanowire sensor chips fabrication has been demonstrated. Nanowire chips have been fabricated on the basis of «silicon-on-insulator» (SOI) structures (SOI-NW chips). The fabrication of SOI-NW chips was performed by optical litography with gas-phase etching. The so-fabricated SOI-NW chips are intended for highly sensitive detection of brain cancer biomarkers in humans. In our present study, two series of experiments have been conducted. In the first experimental series, detection of a synthetic DNA oligonucleotide (oDNA) analogue of brain cancer-associated microRNA miRNA-363 in purified buffer solution has been performed in order to demonstrate the high detection sensitivity. The second experimental series has been performed in order to reveal miRNA-363 itself in real human plasma samples. To provide detection biospecificity, the SOI-NW chip surface was modified by covalent immobilization of probe oligonucleotides (oDNA probes) complementary to the target biomolecules. Using the SOI-NW sensor chips proposed herein, the concentration detection limit of the target biomolecules at the level of 3.3 × 10-17 M has been demonstrated. Thus, the approach employing the SOI-NW chips proposed herein represents an attractive tool in biomedical practice, aimed at the early revelation of oncological diseases in humans.

Optical Monitoring of the Production Quality of Si-Nanoribbon Chips Intended for the Detection of ASD-Associated Oligonucleotides

Gas-phase etching and optical lithography were employed for the fabrication of a silicon nanoribbon chip (Si-NR chip). The quality of the so-fabricated silicon nanoribbons (Si-NRs) was monitored by optical Raman scattering spectroscopy. It was demonstrated that the structures of the Si-NRs were virtually defect-free, meaning they could be used for highly sensitive detection of biological macromolecules. The Si-NR chips were then used for the highly sensitive nanoelectronics detection of DNA oligonucleotides (oDNAs), which represent synthetic analogs of 106a-5p microRNA (miR-106a-5p), associated with the development of autism spectrum disorders in children. The specificity of the analysis was attained by the sensitization of the Si-NR chip sur-face by covalent immobilization of oDNA probes, whose nucleotide sequence was complementary to the known sequence of miR-106a-5p. The use of the Si-NR chip was demonstrated to al-low for the rapid label-free real-time detection of oDNA at ultra-low (~10⁻¹⁷ M) concentrations.

Highly Sensitive Detection of CA 125 Protein with the Use of an n-Type Nanowire Biosensor

The detection of CA 125 protein in a solution using a silicon-on-insulator (SOI)-nanowire biosensor with n-type chip has been experimentally demonstrated. The surface of nanowires was modified by covalent immobilization of antibodies against CA 125 in order to provide the biospecificity of the target protein detection. We have demonstrated that the biosensor signal, which results from the biospecific interaction between CA 125 and the covalently immobilized antibodies, increases with the increase in the protein concentration. At that, the minimum concentration, at which the target protein was detectable with the SOI-nanowire biosensor, amounted to 1.5 × 10⁻¹⁶ M.

SOI-Nanowire Biosensor for the Detection of Glioma-Associated miRNAs in Plasma

Herein, we report the development of a highly sensitive nanotechnology-based system—silicon-on-insulator nanowire biosensor for the revelation of microRNAs (miRNAs), associated with the development of glioma in the human. In this system, a sensor chip, bearing an array of silicon nanowire structures, is employed. The sensor chip is fabricated using a top-down technology. In our experiments reported herein, we demonstrated the detection of DNA oligonucleotide (oDNA), which represents a synthetic analogue of microRNA-363 associated with the development of glioma. To provide biospecific detection of the target oligonucleotides, the surface of the nanowire structures is modified with oligonucleotide probes; the latter are complementary to the target ones. The concentration limit of the target oligonucleotide detection, attained using our nanowire biosensor, is at the level of DL~10−17 M. The revelation of the elevated level of glioma-associated miRNA in plasma is also demonstrated.

Nanowire Aptamer-Sensitized Biosensor Chips with Gas Plasma-Treated Surface for the Detection of Hepatitis C Virus Core Antigen

Herein, we have demonstrated highly sensitive real-time biospecific detection of a protein marker of hepatitis C—the core antigen of hepatitis C virus (HCVcoreAg)—using a nanowire (NW) biosensor. The primary element of the NW-biosensor is a chip with p-type conductance, bearing silicon-on-insulator (SOI) nanowire structures on its surface. The nanowire structures are fabricated by gas-plasma treatment and electron beam lithography. The detection specificity was provided by sensitization of the sensor surface with aptamers against HCVcoreAg. The influence of buffer pH on the sensor response signal was studied. The effect of reverse polarity of the biosensor response signal with change from the acidic buffer pH to the neutral one was found. The lowest detectable HCVcoreAg concentration was determined to be 2.0 × 10−15 M in both acidic (pH 5.1) and neutral (pH 7.4) buffer solution. The proposed aptamer-sensitized sensor was also successfully applied to detect HCVcoreAg in serum samples of hepatitis C patients.

Covalent Protein Immobilization onto Muscovite Mica Surface with a Photocrosslinker

Muscovite mica with an amino silane-modified surface is commonly used as a substrate in atomic force microscopy (AFM) studies of biological macromolecules. Herein, the efficiency of two different protein immobilization strategies employing either (N-hydroxysuccinimide ester)-based crosslinker (DSP) or benzophenone-based photoactivatable crosslinker (SuccBB) has been compared using AFM and mass spectrometry analysis. Two proteins with different physicochemical properties—human serum albumin (HSA) and horseradish peroxidase enzyme protein (HRP)—have been used as model objects in the study. In the case of HRP, both crosslinkers exhibited high immobilization efficiency—as opposed to the case with HSA, when sufficient capturing efficiency has only been observed with SuccBB photocrosslinker. The results obtained herein can find their application in commonly employed bioanalytical systems and in the development of novel highly sensitive chip-based diagnostic platforms employing immobilized proteins. The obtained data can also be of interest for other research areas in medicine and biotechnology employing immobilized biomolecules.

The Dependence of Spontaneous Charge Generation in Water on its Flow Rate in a Flow-Based Analytical System

Highly sensitive biosensor systems are particularly sensitive to the charge state of an analyte. This charge state can have either a positive (for instance, in case of increasing the efficiency of fishing of low-abundant proteins) or negative effect (for instance, in case of the appearance of charge jumps upon the injection of analyte solution into a measuring cell, what can cause undesirable parasitic signals). Previously, it was demonstrated that upon the pumping of analyte solution through polymeric communications of biosensors with a peristaltic pump at a low (~1 mL/min) flow rate, an accumulation of charge, transferred by the liquid drops from the feeding system into the measuring cell, is observed. At this point, the time dependence of charge accumulation has a linear-stepwise form. In the present study, the influence of the flow rate of water on the parameters of the time dependence of the accumulation of charge in such a system—including the influence on the stepwise charge accumulation—has been investigated. The measurements have been performed with a highly sensitive electrometer sensor at 38 °C, which corresponds to a pathological state of a human body. It has been found that a linear-stepwise time dependence of charge accumulation is observed in a wide range of water flow rates (V= 0.9 to 7.2 mL/min). At that point, upon increasing the flow rate with the transition from the drop-by-drop mode of water supply (0.9 mL/min) to the jet flow (7.2 mL/min), an increase in the absolute value of accumulated charge is observed, but the magnitude of the charge jumps does not change significantly. Thus, the amount of charge accumulated in the cell ambiguously depends on the water flow rate—i.e., this dependence can be non-linear. Accounting for the discovered phenomenon is important in the development of new, more accurate models describing physicochemical properties of aqueous solutions and hemodynamics. This effect should also be taken into account in the development of highly sensitive diagnostic systems intended for the detection of single biomarkers of pathologies in humans and crops, as well as in other living systems. In low-concentration systems, the occurrence of a charge can become a significant factor affecting the efficiency of detection of biomolecules and the reliability of the data obtained. The detection of biomolecules present in the solution at low concentrations is in high demand in medical diagnostics for the revelation of biomarkers at the early asymptomatic stage of various diseases, including aggressive forms of cancer.

Detection of Marker miRNAs, Associated with Prostate Cancer, in Plasma Using SOI-NW Biosensor in Direct and Inversion Modes

Information about the characteristics of measuring chips according to their storage conditions is of great importance for clinical diagnosis. In our present work, we have studied the capability of chips to detect nanowire biosensors when they are either freshly prepared or have been stored for either one or two years in a clean room. Potential to detect DNA oligonucleotides (oDNAs)-synthetic analogues of microRNAs (miRNAs) 198 and 429 that are associated with the development of prostate cancer (PCa)-in buffer solution was demonstrated using a nanowire biosensor based on silicon-on-insulator structures (SOI-NW biosensor). To provide biospecific detection, nanowire surfaces were sensitized with oligonucleotide probes (oDNA probes) complimentary to the known sequences of miRNA 183 and 484. In this study it is demonstrated that freshly prepared SOI-NW biosensor chips with n-type conductance and immobilized oDNA probes exhibit responses to the addition of complimentary oDNAs in buffer, leading to decreases in chips' conductance at a concentration of 3.3 × 10-16 M. The influence of storage time on the characteristics of SOI-NW biosensor chips is also studied herein. It is shown that a two-year storage of the chips leads to significant changes in their characteristics, resulting in "inverse" sensitivity toward negatively charged oDNA probes (i.e., through an increase in chips' conductance). It is concluded that the surface layer makes the main contribution to conductance of the biosensor chip. Our results indicate that the detection of target nucleic acid molecules can be carried out with high sensitivity using sensor chips after long-term storage, but that changes in their surface properties, which lead to inversed detection signals, must be taken into account. Examples of the applications of such chips for the detection of cancer-associated microRNAs in plasma samples of patients with diagnosed prostate cancer are given. The results obtained herein are useful for the development of highly sensitive nanowire-based diagnostic systems for the revelation of (prostate) cancer-associated microRNAs in human plasma.

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.

Ultrasensitive Detection of 2,4-Dinitrophenol Using Nanowire Biosensor

The method for the detection of 2,4-dinitrophenol (DNP) in solution is proposed. This method employs the sensors based on silicon nanowire field-effect transistors with protective layers of high-k dielectrics, whose surface is functionalized with an amino silane. Direct highly sensitive detection of DNP has been demonstrated, and the lowest detectable concentration of DNP was determined to be 10−14 M. Silicon-on-insulator nanowire (SOI-NW) sensors can well be employed for the rapid detection of a wide range of toxic and explosive compounds by selection of sensor surface modification techniques.

Multidimensional Conductive Nanofilm-Based Flexible Aptasensor for Ultrasensitive and Selective HBsAg Detection

Hepatitis B virus (HBV) infection is a major worldwide health issue causing serious liver diseases, including liver cirrhosis and hepatocellular carcinoma. Monitoring the serum hepatitis B surface antigen (HBsAg) level is pivotal to the diagnosis of HBV infection. In this study, we describe multidimensional conductive nanofilm (MCNF)-based field-effect transistor (FET) aptasensor for HBsAg detection. The MCNF, composed of vertically oriented carboxylic polypyrrole nanowires (CPPyNW) and graphene layer, is formed using electropolymerization of pyrrole on the graphene surface and following acid treatment. The amine-functionalized HBsAg-binding aptamers are then immobilized on the CPPyNW surface through covalent bonding formation (i.e., amide group). The prepared aptasensor presents highly sensitive to HBsAg as low as 10 aM among interfering biomolecules with various deformations. Moreover, the MCNF-based aptasensor has great potential for practical application in the noninvasive real-time diagnosis because of its improved sensing ability to the human serum and artificial saliva.

Micro-Raman Spectroscopy for Monitoring of Deposition Quality of High-k Stack Protective Layer onto Nanowire FET Chips for Highly Sensitive miRNA Detection

Application of micro-Raman spectroscopy for the monitoring of quality of high-k (h-k) dielectric protective layer deposition onto the surface of a nanowire (NW) chip has been demonstrated. A NW chip based on silicon-on-insulator (SOI) structures, protected with a layer of high-k dielectric ((h-k)-SOI-NW chip), has been employed for highly sensitive detection of microRNA (miRNA) associated with oncological diseases. The protective dielectric included a 2-nm-thick Al₂O₃ surface layer and a 8-nm-thick HfO₂ layer, deposited onto a silicon SOI-NW chip. Such a chip had increased time stability upon operation in solution, as compared with an unprotected SOI-NW chip with native oxide. The (h-k)-SOI-NW biosensor has been employed for the detection of DNA oligonucleotide (oDNA), which is a synthetic analogue of miRNA-21 associated with oncological diseases. To provide biospecificity of the detection, the surface of (h-k)-SOI-NW chip was modified with oligonucleotide probe molecules (oDVA probes) complementary to the sequence of the target biomolecule. Concentration sensitivity of the (h-k)-SOI-NW biosensor at the level of DL~10⁻¹⁶ M has been demonstrated.

Surface modification of SOI-FET sensors for label-free and specific detection of short RNA analyte

AIM

A new type of surface modification of SOI-FET sensors with ultrathin sensor-probe transition layer and uncharged probes for highly specific detection of short RNA (saRNA) was suggested.

MATERIALS & METHODS

Carbonyldiimidazole (CDI) or glycidoxypropyltrimethoxysilane were used as precursors of sensor-probe interface layers, together with peptide nucleic acids and new NA analogues - phosphoryl guanidine oligo(2'-OMe)ribonucleotides (PGO) as probes for RNA hybridization. RNA sequences corresponding to mRNA NELFA (NM_005663) and microRNA-29a (cancer markers) were used as saRNA targets. Real-time saRNA detection by SOI-FET sensors and fluorescence analysis were applied.

RESULTS

Highly specific response with femtomolar sensitivity to saRNA was demonstrated for CDI-PGO-modified sensors fabricated by optical lithography.

CONCLUSION

The proposed CDI-PGO protocol of modification of Si sensor surface is a promising procedure for biomedical applications.

[Atomic force microscopy fishing of gp120 on immobilized aptamer and its mass spectrometry identification]

A method of atomic force microscopy-based fishing (AFM fishing) has been developed for protein detection in the analyte solution using a chip with an immobilized aptamer. This method is based on the biospecific fishing of a target protein from a bulk solution onto the small AFM chip area with the immobilized aptamer to this protein used as the molecular probe. Such aptamer-based approach allows to increase an AFM image contrast compared to the antibody-based approach. Mass spectrometry analysis used after the biospecific fishing to identify the target protein on the AFM chip has proved complex formation. Use of the AFM chip with the immobilized aptamer avoids interference of the antibody and target protein peaks in a mass spectrum.

[AFM-based technologies as the way towards the reverse Avogadro number]

Achievement of the concentration detection limit for proteins at the level of the reverse Avogadro number determines the modern development of proteomics. In this review, the possibility of approximating the reverse Avogadro number by using nanotechnological methods (AFM-based fishing with mechanical and electrical stimulation, nanowire detectors, and other methods) are discussed. The ability of AFM to detect, count, visualize and characterize physico-chemical properties of proteins at concentrations up to 10(-17)-10(-18) M is demonstrated. The combination of AFM-fishing with mass-spectrometry allows the identification of proteins not only in pure solutions, but also in multi-component biological fluids (serum). The possibilities to improve the biospecific fishing efficiency by use of SOMAmers in both AFM and nanowire systems are discussed. The paper also provides criteria for evaluation of the sensitivity of fishing-based detection systems. The fishing efficiency depending on the detection system parameters is estimated. The practical implementation of protein fishing depending on the ratio of the sample solution volume and the surface of the detection system is discussed. The advantages and disadvantages of today's promising nanotechnological protein detection methods implemented on the basis of these schemes.

A self-amplified transistor immunosensor under dual gate operation: highly sensitive detection of hepatitis B surface antigen

Ion-sensitive field-effect transistors (ISFETs), although they have attracted considerable attention as effective immunosensors, have still not been adopted for practical applications owing to several problems: (1) the poor sensitivity caused by the short Debye screening length in media with high ion concentration, (2) time-consuming preconditioning processes for achieving the highly-diluted media, and (3) the low durability caused by undesirable ions such as sodium chloride in the media. Here, we propose a highly sensitive immunosensor based on a self-amplified transistor under dual gate operation (immuno-DG ISFET) for the detection of hepatitis B surface antigen. To address the challenges in current ISFET-based immunosensors, we have enhanced the sensitivity of an immunosensor by precisely tailoring the nanostructure of the transistor. In the pH sensing test, the immuno-DG ISFET showed superior sensitivity (2085.53 mV per pH) to both standard ISFET under single gate operation (58.88 mV per pH) and DG ISFET with a non-tailored transistor (381.14 mV per pH). Moreover, concerning the detection of hepatitis B surface antigens (HBsAg) using the immuno-DG ISFET, we have successfully detected trace amounts of HBsAg (22.5 fg mL(-1)) in a non-diluted 1× PBS medium with a high sensitivity of 690 mV. Our results demonstrate that the proposed immuno-DG ISFET can be a biosensor platform for practical use in the diagnosis of various diseases.

Highly sensitive, label-free and real-time detection of alpha-fetoprotein using a silicon nanowire biosensor

Alpha-fetoprotein (AFP) is a tumor-associated fetal protein that can be expressed in large amounts in adult tumor cells, serving as a useful clinical tumor-marker. Silicon nanowire (SiNW) biosensors have emerged as a powerful tool in detecting protein biomarkers, due to their ultrahigh sensitivity, real-time response and label-free detection. We fabricated a SiNW-based field-effect transistor (FET) according to "top-down" methodology. First, anti-AFP antibodies were immobilized onto the surface of the SiNW-FET. A polydimethylsiloxane (PDMS) microchannel was then integrated to the modified SiNW-FET. Various concentrations of AFP were then pumped through the sensing area. We observed a current change that corresponded to binding of AFP onto the surface of our anti-AFP functionalized SiNW-FET biosensor. Concentrations of AFP as low as 0.1 ng/mL were detected. The results implicate our SiNW biosensor as an effective AFP biomarker detector with promising potential in clinical applications.

Atomic force microscopy fishing and mass spectrometry identification of gp120 on immobilized aptamers

Atomic force microscopy (AFM) was applied to carry out direct and label-free detection of gp120 human immunodeficiency virus type 1 envelope glycoprotein as a target protein. This approach was based on the AFM fishing of gp120 from the analyte solution using anti-gp120 aptamers immobilized on the AFM chip to count gp120/aptamer complexes that were formed on the chip surface. The comparison of image contrasts of fished gp120 against the background of immobilized aptamers and anti-gp120 antibodies on the AFM images was conducted. It was shown that an image contrast of the protein/aptamer complexes was two-fold higher than the contrast of the protein/antibody complexes. Mass spectrometry identification provided an additional confirmation of the target protein presence on the AFM chips after biospecific fishing to avoid any artifacts.

A CMOS wireless biomolecular sensing system-on-chip based on polysilicon nanowire technology

As developments of modern societies, an on-field and personalized diagnosis has become important for disease prevention and proper treatment. To address this need, in this work, a polysilicon nanowire (poly-Si NW) based biosensor system-on-chip (bio-SSoC) is designed and fabricated by a 0.35 μm 2-Poly-4-Metal (2P4M) complementary metal-oxide-semiconductor (CMOS) process provided by a commercialized semiconductor foundry. Because of the advantages of CMOS system-on-chip (SoC) technologies, the poly-Si NW biosensor is integrated with a chopper differential-difference amplifier (DDA) based analog-front-end (AFE), a successive approximation analog-to-digital converter (SAR ADC), and a microcontroller to have better sensing capabilities than a traditional Si NW discrete measuring system. In addition, an on-off key (OOK) wireless transceiver is also integrated to form a wireless bio-SSoC technology. This is pioneering work to harness the momentum of CMOS integrated technology into emerging bio-diagnosis technologies. This integrated technology is experimentally examined to have a label-free and low-concentration biomolecular detection for both Hepatitis B Virus DNA (10 fM) and cardiac troponin I protein (3.2 pM). Based on this work, the implemented wireless bio-SSoC has demonstrated a good biomolecular sensing characteristic and a potential for low-cost and mobile applications. As a consequence, this developed technology can be a promising candidate for on-field and personalized applications in biomedical diagnosis.