Sensing Reversible Protein-Ligand Interactions with Single-Walled Carbon Nanotube Field-Effect Transistors

Protein-structure-dependent spectral shifts of near-infrared photoluminescence from locally functionalized single-walled carbon nanotubes based on avidin-biotin interactions

Single-walled carbon nanotubes (SWCNTs) emit photoluminescence (PL) in the near-infrared (NIR) region (>900 nm). To enhance their PL properties, defect doping via local chemical functionalization has been developed. The locally functionalized SWCNTs (lf-SWCNTs) emit red-shifted and bright E₁₁* PL originating from the excitons localized at the defect-doped sites. Here, we observe the E₁₁* PL energy shifts induced by protein adsorption via the avidin-biotin interactions at the doped sites of lf-SWCNTs. We establish that the difference in the structures of the avidin derivatives notably influences the energy shifts. First, lf-SWCNT-tethering biotin groups (lf-SWCNTs-b) are synthesized based on diazonium chemistry, followed by post-modification. The responsiveness of the lf-SWCNTs-b to different microenvironments is investigated, and a correlation between the E₁₁* PL energy shift and the induction-polarity parameters of surrounding solvents is established. The adsorption of neutravidin onto the lf-SWCNTs-b induces an increase in the induction-polarity parameters around the biotin-doped sites, resulting in the red-shift of the E₁₁* PL peak. The E₁₁* PL shift behaviors of the lf-SWCNTs-b change noticeably when avidin and streptavidin are introduced compared to the case with neutravidin. This is due to the different microenvironments formed at the biotin-doped sites, attributed to the difference in the structural features of the introduced avidin derivatives. Moreover, we successfully enhance the detection signals of lf-SWCNTs-b (>three fold) for streptavidin detection using a fabricated film device. Therefore, lf-SWCNTs exhibit significant promise for application in advanced protein detection/recognition devices based on NIR PL.

Sensors Based on the Carbon Nanotube Field-Effect Transistors for Chemical and Biological Analyses

Nano biochemical sensors play an important role in detecting the biomarkers related to human diseases, and carbon nanotubes (CNTs) have become an important factor in promoting the vigorous development of this field due to their special structure and excellent electronic properties. This paper focuses on applying carbon nanotube field-effect transistor (CNT-FET) biochemical sensors to detect biomarkers. Firstly, the preparation method, physical and electronic properties and functional modification of CNTs are introduced. Then, the configuration and sensing mechanism of CNT-FETs are introduced. Finally, the latest progress in detecting nucleic acids, proteins, cells, gases and ions based on CNT-FET sensors is summarized.

Ultrasensitive and Regenerative Transistor Sensor Based on Dynamic Covalent Chemistry

Field-effect transistor (FET) sensors require not only high sensitivity but also excellent regeneration ability before widespread applications are possible. Although some regenerative FETs have been reported, their lowest limit of detection (LoD) barely achieves 10-15 mol L-1. Here, we develop a graphene FET with a regenerative sensing interface based on dynamic covalent chemistry (DCvC). The LoD down to 5.0 × 10-20 mol L-1 remains even after 10 regenerative cycles, around 4-5 orders of magnitude lower than existing transistor sensors. Owing to its ultra-sensitivity, regeneration ability, and advantages such as simplicity, low cost, label-free and real-time response, the FET sensor based on DCvC is valuable in applications such as medical diagnosis, environment monitoring, etc.

The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations

Field-effect biosensors (bioFETs) offer a novel way to measure the kinetics of biomolecular events such as protein function and DNA hybridization at the single-molecule level on a wide range of time scales. These devices generate an electrical current whose fluctuations are correlated to the kinetics of the biomolecule under study. BioFETs are indeed highly sensitive to changes in the electrostatic potential (ESP) generated by the biomolecule. Here, using all-atom solvent explicit molecular dynamics simulations, we further investigate the molecular origin of the variation of this ESP for two prototypical cases of proteins or nucleic acids attached to a carbon nanotube bioFET: the function of the lysozyme protein and the hybridization of a 10-nt DNA sequence, as previously done experimentally. Our results show that the ESP changes significantly on the surface of the carbon nanotube as the state of these two biomolecules changes. More precisely, the ESP distributions calculated for these molecular states explain well the magnitude of the conductance fluctuations measured experimentally. The dependence of the ESP with salt concentration is found to agree with the reduced conductance fluctuations observed experimentally for the lysozyme, but to differ for the case of DNA, suggesting that other mechanisms might be at play in this case. Furthermore, we show that the carbon nanotube does not impact significantly the structural stability of the lysozyme, corroborating that the kinetic rates measured using bioFETs are similar to those measured by other techniques. For DNA, we find that the structural ensemble of the single-stranded DNA is significantly impacted by the presence of the nanotube, which, combined with the ESP analysis, suggests a stronger DNA-device interplay. Overall, our simulations strengthen the comprehension of the inner working of field-effect biosensors used for single-molecule kinetics measurements on proteins and nucleic acids.

Imparting Immunomodulatory Activity to Scaffolds via Biotin-Avidin Interactions

Biotin-avidin interactions have been explored for decades as a technique to functionalize biomaterials, as well as for in vivo targeting, but whether changes in these interactions can be leveraged for immunomodulation remain unknown. The goal of this study was to investigate how biotin density and avidin variant can be used to deliver the immunomodulatory cytokine, interleukin 4 (IL4), from a porous gelatin scaffold, Gelfoam, to primary human macrophages in vitro. Here, we demonstrate that the degree of scaffold biotinylation controlled the binding of two different avidin variants, streptavidin and CaptAvidin. Biotinylated scaffolds were also loaded with streptavidin and biotinylated IL4 under flow, suggesting a potential use for targeting this biomaterial in vivo. While biotin-avidin interactions did not appear to influence the protein release in this system, increasing degrees of biotinylation did lead to increased M2-like polarization of primary human macrophages over time in vitro, highlighting the capability to leverage biotin-avidin interactions to modulate the macrophage phenotype. These results demonstrate a versatile and modular strategy to impart immunomodulatory activity to biomaterials.

Addressing the Theoretical and Experimental Aspects of Low-Dimensional-Materials-Based FET Immunosensors: A Review

Electrochemical immunosensors (EI) have been widely investigated in the last several years. Among them, immunosensors based on low-dimensional materials (LDM) stand out, as they could provide a substantial gain in fabricating point-of-care devices, paving the way for fast, precise, and sensitive diagnosis of numerous severe illnesses. The high surface area available in LDMs makes it possible to immobilize a high density of bioreceptors, improving the sensitivity in biorecognition events between antibodies and antigens. If on the one hand, many works present promising results in using LDMs as a sensing material in EIs, on the other hand, very few of them discuss the fundamental interactions involved at the interfaces. Understanding the fundamental Chemistry and Physics of the interactions between the surface of LDMs and the bioreceptors, and how the operating conditions and biorecognition events affect those interactions, is vital when proposing new devices. Here, we present a review of recent works on EIs, focusing on devices that use LDMs (1D and 2D) as the sensing substrate. To do so, we highlight both experimental and theoretical aspects, bringing to light the fundamental aspects of the main interactions occurring at the interfaces and the operating mechanisms in which the detections are based.

Detecting Protein-Ligand Interaction from Integrated Transient Induced Molecular Electronic Signal (i-TIMES)

Quantitative information about protein-ligand interactions is central to drug discovery. To obtain the quintessential reaction dissociation constant, ideally measurements of reactions should be performed without perturbations by molecular labeling or immobilization. The technique of transient induced molecular electrical signal (TIMES) has provided a promising technique to meet such requirements, and its performance in a microfluidic environment further offers the potential for high throughput and reduced consumption of reagents. In this work, we further the development by using integrated TIMES signal (i-TIMES) to greatly enhance the accuracy and reproducibility of the measurement. While the transient response may be of interest, the integrated signal directly measures the total amount of surface charge density resulted from molecules near the surface of electrode. The signals enable quantitative characterization of protein-ligand interactions. We have demonstrated the feasibility of i-TIMES technique using different biomolecules including lysozyme, N,N',N″-triacetylchitotriose (TriNAG), aptamer, p-aminobenzamidine (pABA), bovine pancreatic ribonuclease A (RNaseA), and uridine-3'-phosphate (3'UMP). The results show i-TIMES is a simple and accurate technique that can bring tremendous value to drug discovery and research of intermolecular interactions.

Probing Ca2+-induced conformational change of calmodulin with gold nanoparticle-decorated single-walled carbon nanotube field-effect transistors

Nanomaterials are ideal for electrochemical biosensors, with their nanoscale dimensions enabling the sensitive probing of biomolecular interactions. In this study, we compare field-effect transistors (FET) comprised of unsorted (un-) and semiconducting-enriched (sc-) single-walled carbon nanotubes (SWCNTs). un-SWCNTs have both metallic and semiconducting SWCNTs in the ensemble, while sc-SWCNTs have a >99.9% purity of semiconducting nanotubes. Both SWCNT FET devices were decorated with gold nanoparticles (AuNPs) and were then employed in investigating the Ca²⁺-induced conformational change of calmodulin (CaM) - a vital process in calcium signal transduction in the human body. Different biosensing behavior was observed from FET characteristics of the two types of SWCNTs, with sc-SWCNT FET devices displaying better sensing performance with a dynamic range from 10^-15 M to 10^-13 M Ca²⁺, and a lower limit of detection at 10^-15 M Ca²⁺.

Design and Demonstration of Tunable Amplified Sensitivity of AlGaN/GaN High Electron Mobility Transistor (HEMT)-Based Biosensors in Human Serum

We have developed a swift and simplistic protein immunoassay using aptamer functionalized AlGaN/GaN high electron mobility transistors (HEMTs). The unique design of the sensor facilitates protein detection in a physiological salt environment overcoming charge screening effects, without requiring sample preprocessing. This study reports a tunable and amplified sensitivity of solution-gated electric double layer (EDL) HEMT-based biosensors, which demonstrates significantly enhanced sensitivity by designing a smaller gap between the gate electrode and the detection, and by operating at higher gate voltage. Sensitivity is calculated by quantifying NT-proBNP, a clinical biomarker of heart failure, in buffer and untreated human serum samples. The biosensor depicts elevated sensitivity and high selectivity. Furthermore, detailed investigation of the amplified sensitivity in an increased ionic strength environment is conducted, and it is revealed that a high sensitivity of 80.54 mV/decade protein concentration can be achieved, which is much higher than that of previously reported FET biosensors. This sensor technology demonstrates immense potential in developing surface affinity sensors for clinical diagnostics.

Dielectrophoresis-Assisted Integration of 1024 Carbon Nanotube Sensors into a CMOS Microsystem

Carbon-nanotube (CNT)-based sensors offer the potential to detect single-molecule events and picomolar analyte concentrations. An important step toward applications of such nanosensors is their integration in large arrays. The availability of large arrays would enable multiplexed and parallel sensing, and the simultaneously obtained sensor signals would facilitate statistical analysis. A reliable method to fabricate an array of 1024 CNT-based sensors on a fully processed complementary-metal-oxide-semiconductor microsystem is presented. A high-yield process for the deposition of CNTs from a suspension by means of liquid-coupled floating-electrode dielectrophoresis (DEP), which yielded 80% of the sensor devices featuring between one and five CNTs, is developed. The mechanism of floating-electrode DEP on full arrays and individual devices to understand its self-limiting behavior is studied. The resistance distributions across the array of CNT devices with respect to different DEP parameters are characterized. The CNT devices are then operated as liquid-gated CNT field-effect-transistors (LG-CNTFET) in liquid environment. Current dependency to the gate voltage of up to two orders of magnitude is recorded. Finally, the sensors are validated by studying the pH dependency of the LG-CNTFET conductance and it is demonstrated that 73% of the CNT sensors of a given microsystem show a resistance decrease upon increasing the pH value.

Nano-Bioelectronics

Nano-bioelectronics represents a rapidly expanding interdisciplinary field that combines nanomaterials with biology and electronics and, in so doing, offers the potential to overcome existing challenges in bioelectronics. In particular, shrinking electronic transducer dimensions to the nanoscale and making their properties appear more biological can yield significant improvements in the sensitivity and biocompatibility and thereby open up opportunities in fundamental biology and healthcare. This review emphasizes recent advances in nano-bioelectronics enabled with semiconductor nanostructures, including silicon nanowires, carbon nanotubes, and graphene. First, the synthesis and electrical properties of these nanomaterials are discussed in the context of bioelectronics. Second, affinity-based nano-bioelectronic sensors for highly sensitive analysis of biomolecules are reviewed. In these studies, semiconductor nanostructures as transistor-based biosensors are discussed from fundamental device behavior through sensing applications and future challenges. Third, the complex interface between nanoelectronics and living biological systems, from single cells to live animals, is reviewed. This discussion focuses on representative advances in electrophysiology enabled using semiconductor nanostructures and their nanoelectronic devices for cellular measurements through emerging work where arrays of nanoelectronic devices are incorporated within three-dimensional cell networks that define synthetic and natural tissues. Last, some challenges and exciting future opportunities are discussed.

Tuning the isoelectric point of graphene by electrochemical functionalization

The ability to control the charge-potential landscape at solid-liquid interfaces is pivotal to engineer novel devices for applications in sensing, catalysis and energy conversion. The isoelectric point (pI)/point of zero charge (pzc) of graphene plays a key role in a number of physico-chemical phenomena occurring at the graphene-liquid interface. Supported by theory, we present here a methodology to identify the pI/pzc of (functionalized) graphene, which also allows for estimating the nature and extent of ion adsorption. The pI of bare graphene (as-prepared, chemical vapor deposition (CVD)-grown) is found to be less than 3.3, which we can continuously modify up to 7.5 by non-covalent electrochemical attachment of aromatic amino groups, preserving the favorable electronic properties of graphene throughout. Modelling all the observed results with detailed theory, we also show that specific adsorption of ions and the substrate play only an ancillary role in our capability to tune the pI of graphene.

LDL-R promoting activity of peptides derived from human PCSK9 catalytic domain (153-421): design, synthesis and biochemical evaluation

BACKGROUND

High level of Low Density Lipoprotein-Cholesterol (LDL-C) in circulation in the blood is associated with an elevated risk of cardiovascular disease (CVD) and stroke. Currently the statin drugs which inhibit the enzyme HMG-CoA reductase responsible for cholesterol synthesis in the liver are very effective in lowering LDL-cholesterol. However these drugs are often associated with serious side effects particularly for ∼10-12% of cases. Therefore there is a need to develop non-statin based cholesterol reducing agents. Recently it was revealed that the secreted Proprotein Convertase Subtilisin Kexin 9 (PCSK9) binds with LDL-receptor (LDL-R) causing its degradation in the lysosome with the result of LDL-C accumulating in the blood. Thus PCSK9 has become an alternative target for development of non-statin cholesterol reducing agents. It is established that the catalytic domain of PCSK9 (aa153-421) and the EGF-A domain of LDL-R (aa314-355) are involved in the above bind leading to the reduction of LDL-R level and accumulation of LDL-C.

OBJECTIVE

The major goal of this study is to identify peptide/s from the catalytic domain of hPCSK9 that can block the binding of hPCSK9 and LDL-R and therefore can reduce LDL-R degradation leading to the clearance of LDL-C from the plasma.

RESULTS

Using 51 synthetic linear peptides (P1-P51) of 15aa long with 10 amino acids overlapping sequences spanning the entire catalytic segment of hPCSK9 (aa153-421), we identified two domains of hPCSK9 namely (aa323-358) and (aa365-384) that exhibited strong binding affinity towards synthetic EGF-A peptide. The results were based on mass spectrometry, fluorescence spectroscopy and native gel electrophoresis. Thus peptides containing the above segments in part (P35-P39 and P42-P47) exhibited LDL-R promoting activity when added exogenously to culture medium of growing human hepatic cells like HepG2 and HuH7. The effects were particularly significant with peptides P36, P37, P46 and P47. Interestingly, the first two peptides are present within the disulphide loop Cys(323)-Cys(358) and contain the key gain of function mutation D(374)/Y site while the last two peptides contain another disulphide bridge loop Cys(375)-Cys(378) and the second most potent gain of function mutation R(357)/H. Further studies revealed that S-S bridged cyclic loop peptide hPCSK9(365-384) exhibited the highest (∼3.5-fold) LDL-R promoting activity in both HepG2 and HuH7 when applied at 5 μM concentration level. This effect is completely abrogated when one of the Cys residues is substituted by Ala thereby preventing any S-S bond formation. This suggested its critical role in the bioactivity. It is proposed that LDL-R promoting activity of this and other selected PCSK9 catalytic peptides such as P36, P37, P46 and P47 are most likely mediated via intervention of PCSK9:LDL-R complex formation. Our findings may find useful application in future development of small molecule PCSK9 inhibitors for intervention of hypercholesterolemia and associated cardiovascular disease.