Applications of Graphene Field Effect Biosensors for Biological Sensing.

This chapter provides a comprehensive overview of the principles, applications, and advancements in graphene field-effect transistor (gFET) biosensors for biological sensing. The unique properties of graphene that make it ideal for biosensing, including its high conductivity, chemical stability, and ability to facilitate label-free detection, will be discussed. The chapter also explores various applications of gFET biosensors, from detecting pH and salinity changes to complex protein-protein interactions and DNA/RNA sensing. It also addresses the challenges and future directions in gFET biosensor technology, emphasizing the need for scalable manufacturing, sophisticated surface chemistry, and the integration of multiomics approaches to enhance biosensing capabilities.

The promise of graphene-based transistors for democratizing multiomics studies.

As biological research has synthesized genomics, proteomics, metabolomics, and transcriptomics into systems biology, a new multiomics approach to biological research has emerged. Today, multiomics studies are challenging and expensive. An experimental platform that could unify the multiple omics approaches to measurement could increase access to multiomics data by enabling more individual labs to successfully attempt multiomics studies. Field effect biosensing based on graphene transistors have gained significant attention as a potential unifying technology for such multiomics studies. This review article highlights the outstanding performance characteristics that makes graphene field effect transistor an attractive sensing platform for a wide variety of analytes important to system biology. In addition to many studies demonstrating the biosensing capabilities of graphene field effect transistors, they are uniquely suited to address the challenges of multiomics studies by providing an integrative multiplex platform for large scale manufacturing using the well-established processes of semiconductor industry. Furthermore, the resulting digital data is readily analyzable by machine learning to derive actionable biological insight to address the challenge of data compatibility for multiomics studies. A critical stage of systems biology will be democratizing multiomics study, and the graphene field effect transistor is uniquely positioned to serve as an accessible multiomics platform.

Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor.

Simple and fast methods for the detection of target genes with single-nucleotide specificity could open up genetic research and diagnostics beyond laboratory settings. We recently reported a biosensor for the electronic detection of unamplified target genes using liquid-gated graphene field-effect transistors employing an RNA-guided catalytically deactivated CRISPR-associated protein 9 (Cas9) anchored to a graphene monolayer. Here, using unamplified genomic samples from patients and by measuring multiple types of electrical response, we show that the biosensors can discriminate within one hour between wild-type and homozygous mutant alleles differing by a single nucleotide. We also show that biosensors using a guide RNA-Cas9 orthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozygous and heterozygous DNA samples from patients with sickle cell disease, and that the biosensors can also be used to rapidly screen for guide RNA-Cas9 complexes that maximize gene-targeting efficiency.

Rapid and Electronic Identification and Quantification of Age-Specific Circulating Exosomes via Biologically Activated Graphene Transistors.

Increasing access to modern clinical practices concomitantly extends lifespan, ironically revealing new classes of degenerative and inflammatory diseases of later years. Here, an electronic graphene field-effect transistor (gFET) is reported, termed EV-chip, for label-free, rapid identification and quantification of exosomes (EV) associated with aging through specific surface markers, CD63 and CD151. Studies suggest that blood-derived exosomes carry specific biomolecules that can be used toward diagnostic applications of age and health. However, to observe improvements in patient outcomes, earlier detection at the point-of-care (POC) is required. Unfortunately, conventional techniques and other electronic-based platforms for exosome sensing are burdensome and inept for the POC distinction of aged blood factors. It is shown that EV-chip can quantitatively detect purified exosomes from plasma, with a limit of detection (LOD) of 2 × 104 particles mL-1 and a limit of quantification (LOQ) of 6 × 104 particles mL-1 . The sensitivity and compact electronics of the EV-chip improves upon previously published electronic biosensors, making it ideal for a physician's office or a simple biological laboratory. The sensitivity, selectivity, and portability of the EV-chip demonstrate the potential of the biosensor as a powerful point-of-care diagnostic and prognostic tool for age-related diseases.

Protein Detection using Quadratic Fit Analysis Near Dirac Point of Graphene Field Effect Biosensors.

Although graphene-based biosensors provid extreme sensitivity for the detection of atoms, gases, and biomolecules, the specificity of graphene biosensors to the target molecules requires surface decoration of graphene with bifunctional linkers such pyrene derivatives. Here, we demonstrate that the pyrene functionalization influences graphene's electrical properties by yielding partial formation of bilayer graphene which was confirmed by Raman 2D spectrum. Based on this observation, we introduce quadratic fit analysis of the nonlinear electrical behavior of pyrene-functionalized graphene near the Dirac point. Compared to the conventional linear fit analysis of the transconductance at a distance from the Dirac point, the quadratic fit analysis of the nonlinear transconductance near the Dirac point increased the overall protein detection sensitivity by a factor of 5. Furthermore, we show that both pyrene linkers and gating voltage near the Dirac point play critical roles in sensitive and reliable detection of proteins' biological activities with the graphene biosensors.

Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor.

Most methods for the detection of nucleic acids require many reagents and expensive and bulky instrumentation. Here, we report the development and testing of a graphene-based field-effect transistor that uses clustered regularly interspaced short palindromic repeats (CRISPR) technology to enable the digital detection of a target sequence within intact genomic material. Termed CRISPR-Chip, the biosensor uses the gene-targeting capacity of catalytically deactivated CRISPR-associated protein 9 (Cas9) complexed with a specific single-guide RNA and immobilized on the transistor to yield a label-free nucleic-acid-testing device whose output signal can be measured with a simple handheld reader. We used CRISPR-Chip to analyse DNA samples collected from HEK293T cell lines expressing blue fluorescent protein, and clinical samples of DNA with two distinct mutations at exons commonly deleted in individuals with Duchenne muscular dystrophy. In the presence of genomic DNA containing the target gene, CRISPR-Chip generates, within 15 min, with a sensitivity of 1.7 fM and without the need for amplification, a significant enhancement in output signal relative to samples lacking the target sequence. CRISPR-Chip expands the applications of CRISPR-Cas9 technology to the on-chip electrical detection of nucleic acids.

Digital Biosensing by Foundry-Fabricated Graphene Sensors.

The prevailing philosophy in biological testing has been to focus on simple tests with easy to interpret information such as ELISA or lateral flow assays. At the same time, there has been a decades long understanding in device physics and nanotechnology that electrical approaches have the potential to drastically improve the quality, speed, and cost of biological testing provided that computational resources are available to analyze the resulting complex data. This concept can be conceived of as "the internet of biology" in the same way miniaturized electronic sensors have enabled "the internet of things." It is well established in the nanotechnology literature that techniques such as field effect biosensing are capable of rapid and flexible biological testing. Until now, access to this new technology has been limited to academic researchers focused on bioelectronic devices and their collaborators. Here we show that this capability is retained in an industrially manufactured device, opening access to this technology generally. Access to this type of production opens the door for rapid deployment of nanoelectronic sensors outside the research space. The low power and resource usage of these biosensors enables biotech engineers to gain immediate control over precise biological and environmental data.

Novel graphene-based biosensor for early detection of Zika virus infection.

We have developed a cost-effective and portable graphene-enabled biosensor to detect Zika virus with a highly specific immobilized monoclonal antibody. Field Effect Biosensing (FEB) with monoclonal antibodies covalently linked to graphene enables real-time, quantitative detection of native Zika viral (ZIKV) antigens. The percent change in capacitance in response to doses of antigen (ZIKV NS1) coincides with levels of clinical significance with detection of antigen in buffer at concentrations as low as 450pM. Potential diagnostic applications were demonstrated by measuring Zika antigen in a simulated human serum. Selectivity was validated using Japanese Encephalitis NS1, a homologous and potentially cross-reactive viral antigen. Further, the graphene platform can simultaneously provide the advanced quantitative data of nonclinical biophysical kinetics tools, making it adaptable to both clinical research and possible diagnostic applications. The speed, sensitivity, and selectivity of this first-of-its-kind graphene-enabled Zika biosensor make it an ideal candidate for development as a medical diagnostic test.

Detecting cancer by breath volatile organic compound analysis: a review of array-based sensors.

Cancer diagnosis is typically delayed to the late stages of disease due to the asymptomatic nature of cancer in its early stages. Cancer screening offers the promise of early cancer detection, but most conventional diagnostic methods are invasive and remain ineffective at early detection. Breath analysis is, however, non-invasive and has the potential to detect cancer at an earlier stage by analyzing volatile biomarkers in exhaled breath. This paper summarizes breath sampling techniques and recent developments of various array-based sensor technologies for breath analysis. Significant advancements were made by a number of different research groups in the development of nanomaterial-based sensor arrays, and the ability to accurately distinguish cancer patients from healthy controls based on the volatile organic compounds (VOCs) in exhaled breath has been demonstrated. Optical sensors based on colorimetric sensor array technology are also discussed, where preliminary clinical studies suggest that metabolic VOC profiles could be used to accurately diagnose various forms of lung cancer. Recent studies have demonstrated the potential of using metabolic VOCs for cancer detection, but further standardization and validation is needed before breath analysis can be widely adopted as a clinically useful tool.

Volatile biomarkers from human melanoma cells.

Dogs can identify, by olfaction, melanoma on the skin of patients or melanoma samples hidden on healthy subjects, suggesting that volatile organic compounds (VOCs) from melanoma differ from those of normal skin. Studies employing gas chromatography-mass spectrometry (GC-MS) and gas sensors reported that melanoma-related VOCs differed from VOCs from normal skin sources. However, the identities of the VOCs that discriminate melanoma from normal skin were either unknown or likely derived from exogenous sources. We employed solid-phase micro-extraction, GC-MS and single-stranded DNA-coated nanotube (DNACNT) sensors to examine VOCs from melanoma and normal melanocytes. GC-MS revealed dozens of VOCs, but further analyses focused on compounds most likely of endogenous origin. Several compounds differed between cancer and normal cells, e.g., isoamyl alcohol was higher in melanoma cells than in normal melanocytes but isovaleric acid was lower in melanoma cells. These two compounds share the same precursor, viz., leucine. Melanoma cells produce dimethyldi- and trisulfide, compounds not detected in VOCs from normal melanocytes. Furthermore, analyses of the total volatile metabolome from both melanoma cells and normal melanocytes by DNACNT sensors, coupled with the GC-MS results, demonstrate clear differences between these cell systems. Consequently, monitoring of melanoma VOCs has potential as a useful screening methodology.

Detecting Lyme disease using antibody-functionalized single-walled carbon nanotube transistors.

We examined the potential of antibody-functionalized single-walled carbon nanotube (SWNT) field-effect transistors (FETs) to use as a fast and accurate sensor for a Lyme disease antigen. Biosensors were fabricated on oxidized silicon wafers using chemical vapor deposition grown carbon nanotubes that were functionalized using diazonium salts. Attachment of Borrelia burgdorferi (Lyme) flagellar antibodies to the nanotubes was verified by atomic force microscopy and electronic measurements. A reproducible shift in the turn-off voltage of the semiconducting SWNT FETs was seen upon incubation with B. burgdorferi flagellar antigen, indicative of the nanotube FET being locally gated by the residues of flagellar protein bound to the antibody. This sensor effectively detected antigen in buffer at concentrations as low as 1 ng/ml, and the response varied strongly over a concentration range coinciding with levels of clinical interest. Generalizable binding chemistry gives this biosensing platform the potential to be expanded to monitor other relevant antigens, enabling a multiple vector sensor for Lyme disease. The speed and sensitivity of this biosensor make it an ideal candidate for development as a medical diagnostic test.

Hybrids of a genetically engineered antibody and a carbon nanotube transistor for detection of prostate cancer biomarkers.

We developed a novel detection method for osteopontin (OPN), a new biomarker for prostate cancer, by attaching a genetically engineered single-chain variable fragment (scFv) protein with high binding affinity for OPN to a carbon nanotube field-effect transistor (NT-FET). Chemical functionalization using diazonium salts is used to covalently attach scFv to NT-FETs, as confirmed by atomic force microscopy, while preserving the activity of the biological binding site for OPN. Electron transport measurements indicate that functionalized NT-FET may be used to detect the binding of OPN to the complementary scFv protein. A concentration-dependent increase in the source-drain current is observed in the regime of clinical significance, with a detection limit of approximately 30 fM. The scFv-NT hybrid devices exhibit selectivity for OPN over other control proteins. These devices respond to the presence of OPN in a background of concentrated bovine serum albumin, without loss of signal. On the basis of these observations, the detection mechanism is attributed to changes in scattering at scFv protein-occupied defect sites on the carbon nanotube sidewall. The functionalization procedure described here is expected to be generalizable to any antibody containing an accessible amine group and to result in biosensors appropriate for detection of corresponding complementary proteins at fM concentrations.

Biomimetic chemical sensors using nanoelectronic readout of olfactory receptor proteins.

We have designed and implemented a practical nanoelectronic interface to G-protein coupled receptors (GPCRs), a large family of membrane proteins whose roles in the detection of molecules outside eukaryotic cells make them important pharmaceutical targets. Specifically, we have coupled olfactory receptor proteins (ORs) with carbon nanotube transistors. The resulting devices transduce signals associated with odorant binding to ORs in the gas phase under ambient conditions and show responses that are in excellent agreement with results from established assays for OR-ligand binding. The work represents significant progress on a path toward a bioelectronic nose that can be directly compared to biological olfactory systems as well as a general method for the study of GPCR function in multiple domains using electronic readout.

High-on/off-ratio graphene nanoconstriction field-effect transistor.

A method is reported to pattern monolayer graphene nanoconstriction field-effect transistors (NCFETs) with critical dimensions below 10 nm. NCFET fabrication is enabled by the use of feedback-controlled electromigration (FCE) to form a constriction in a gold etch mask that is first patterned using conventional lithographic techniques. The use of FCE allows the etch mask to be patterned on size scales below the limit of conventional nanolithography. The opening of a confinement-induced energy gap is observed as the NCFET width is reduced, as evidenced by a sharp increase in the NCFET on/off ratio. The on/off ratios obtained with this procedure can be larger than 1000 at room temperature for the narrowest devices; this is the first report of such large room-temperature on/off ratios for patterned graphene FETs.

Mechanism-guided improvements to the single molecule oxidation of carbon nanotube sidewalls.

Real-time monitoring of carbon nanotube conductance during electrochemical and chemical etching reveals the electronic signatures of individual bond alteration events on the nanotube sidewall. Tracking the conductance of multiple single-molecule experiments through different synthetic protocols supports putative mechanisms for sidewall derivatization. Insights gained from these mechanistic observations imply the formation of sidewall carboxylates, which are useful as handles for bioconjugation. We describe an electronic state required for efficacious chemical treatment. Such real-time monitoring can improve carboxylate yields to 45 % or more. The experiments illustrate the power of molecular nanocircuits to uncover and direct the mechanisms of chemical reactions.

Monitoring single-molecule reactivity on a carbon nanotube.

Using point-functionalized carbon nanotube devices, we demonstrate continuous, multihour monitoring of a single carboxylate group interacting with its immediate environment. The conductance of the nanotube device directly transduces single-molecule attachments and detachments in the presence of the carboxylate-selective reagent 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC). Because only one carboxylate is present in the device, it can be studied through hundreds of reactions, providing the statistical accuracy to directly determine a 12 s lifetime of the carboxy-EDC complex. An additional instability of the complex is transduced in real time and observed to have a median lifetime of 2 ms. By determining a turnover time in good agreement with bulk measurements and simultaneously illuminating additional dynamics, these results demonstrate this platform's potential for complementing optical methods in single-molecule research.

Conductance-controlled point functionalization of single-walled carbon nanotubes.

We used covalent attachments to single-walled carbon nanotubes (SWNTs) to fabricate single-molecule electronic devices. The technique does not rely on submicrometer lithography or precision mechanical manipulation, but instead uses circuit conductance to monitor and control covalent attachment to an electrically connected SWNT. Discrete changes in the circuit conductance revealed chemical processes happening in real time and allowed the SWNT sidewalls to be deterministically broken, reformed, and conjugated to target species. By controlling the chemistry through electronically controlled electrochemical potentials, we were able to achieve single chemical attachments. We routinely functionalized pristine, defect-free SWNTs at one, two, or more sites and demonstrated three-terminal devices in which a single attachment controls the electronic response.

Chemically induced conductance switching in carbon nanotube circuits.

The chemical reactivity of carbon nanotubes in H2SO4 is investigated using individual, single-walled carbon nanotubes (SWNTs) incorporated into electronic devices. Exploiting the device conductance as a sensitive indicator of chemical reactions, discrete oxidation and reduction events can be clearly observed. During oxidation, a SWNT opens circuits to a nanometer-scale tunnel junction with residual conduction similar to Frenkel-Poole charge emission. When electrochemically reduced, a SWNT returns to its original conductance. This redox cycle can be repeated many times, suggesting a novel chemical method of reversibly switching SWNT conductivity.

Identifying and counting point defects in carbon nanotubes.

The prevailing conception of carbon nanotubes and particularly single-walled carbon nanotubes (SWNTs) continues to be one of perfectly crystalline wires. Here, we demonstrate a selective electrochemical method that labels point defects and makes them easily visible for quantitative analysis. High-quality SWNTs are confirmed to contain one defect per 4 microm on average, with a distribution weighted towards areas of SWNT curvature. Although this defect density compares favourably to high-quality, silicon single-crystals, the presence of a single defect can have tremendous electronic effects in one-dimensional conductors such as SWNTs. We demonstrate a one-to-one correspondence between chemically active point defects and sites of local electronic sensitivity in SWNT circuits, confirming the expectation that individual defects may be critical to understanding and controlling variability, noise and chemical sensitivity in SWNT electronic devices. By varying the SWNT synthesis technique, we further show that the defect spacing can be varied over orders of magnitude. The ability to detect and analyse point defects, especially at very low concentrations, indicates the promise of this technique for quantitative process analysis, especially in nanoelectronics development.