General Approach for Monitoring Peptide–Protein Interactions Based on Graphene–Peptide Complex

Vertical Graphene-Based Biosensor for Tumor Cell Dielectric Signature Evaluation

The selective and rapid detection of tumor cells is of critical consequence for the theragnostic field of tumorigenesis; conventional methods, such as histopathological diagnostic methods, often require a long analysis time, excessive analytical costs, complex operations, qualified personnel and deliver many false-positive results. We are considering a new approach of an electrochemical biosensor based on graphene, which is evidenced to be a revolutionary nanomaterial enabling the specific and selective capture of tumor cells. In this paper, we report a biosensor fabricated by growing vertically aligned graphene nanosheets on the conductive surface of interdigitated electrodes which is functionalized with anti-EpCAM antibodies. The dielectric signature of the three types of tumor cells is determined by correlating the values from the Nyquist and Bode diagram: charge transfer resistance, electrical double layer capacity, Debye length, characteristic relaxation times of mobile charges, diffusion/adsorption coefficients, and variation in the electrical permittivity complex and of the phase shift with frequency. These characteristics are strongly dependent on the type of membrane molecules and the electromagnetic resonance frequency. We were able to use the fabricated sensor to differentiate between three types of tumor cell lines, HT-29, SW403 and MCF-7, by dielectric signature. The proposed evaluation method showed the permittivity at 1 MHz to be 3.63 nF for SW403 cells, 4.97 nF for HT 29 cells and 6.9 nF for MCF-7 cells.

Quenching Efficiency of Quantum Dots Conjugated to Lipid Bilayers on Graphene Oxide Evaluated by Fluorescence Single Particle Tracking

A single particle observation of quantum dots (QDs) was performed on lipid bilayers formed on graphene oxide (GO). The long-range fluorescence quenching of GO has been applied to biosensing for various biomolecules. We demonstrated the single particle observation of a QD on supported lipid bilayers in this study, aiming to detect the quenching efficiency of lipid and protein molecules in a lipid bilayer by fluorescence single particle tacking (SPT). A single lipid bilayer or double lipid bilayers were formed on GO flakes deposited on a thermally oxidized silicon substrate by the vesicle fusion method. The QDs were conjugated on the lipid bilayers, and single particle images of the QDs were obtained under the quenching effect of GO. The quenching efficiency of a single QD was evaluated from the fluorescence intensities on the regions with and without GO. The quenching efficiency reflecting the layer numbers of the lipid bilayers was obtained.

Terminal protection of peptides by interactions with proteins: A "signal-on" peptide-templated gold nanocluster beacon for label-free protein detection

Characterization of the protein-peptide interactions are a critical for understanding the functions and signal pathways of proteins. Herein, a new finding of universal terminal protection that protein bind specifically with peptide and provide a protective coating to prevent peptide hydrolysis in the presence of peptidase. On the basis of this mechanism, we first reported a novel label-free fluorescence biosensor strategy that utilizes the protection of specific terminal protein on peptide-templated gold nanocluster (AuNCs) beacon for the detection of proteins. The fluorescence quenching of peptide-templated AuNCs can be effectively inhibited with increasing concentration of the specific protein, exhibiting a satisfactory sensitivity and selectivity toward protein with the detection limit of MDM2 and gp120 are 0.0019 U/mL and 0.0012 U/mL, respectively. The developed label-free fluorescence biosensor strategy provides new ideas to detect and screen protein for analyzing protein-peptide interaction in biomedical applications.

Self-Assembled Pyrene Stacks and Peptide Monolayers Tune the Electronic Properties of Functionalized Electrolyte-Gated Graphene Field-Effect Transistors

Aromatic molecules such as pyrenes are a unique class of building units for graphene functionalization, forming highly ordered π-π stacks while peptides provide more complex, biocompatible linkers. Understanding the adsorption and stacking behavior of these molecules and their influence on material properties is an essential step in enabling highly repeatable 2D material-based applications, such as biosensors, gas sensors, and solar cells. In this work, we characterize pyrene and peptide self-assembly on graphene substrates using fluorescence microscopy, atomic force microscopy and electrolyte-gated field-effect measurements supported by quantum mechanical calculations. We find distinct binding and assembly modes for pyrenes versus peptides with corresponding distinct electronic signatures in their characteristic charge neutrality point and field-effect slope responses. Our data demonstrates that pyrene- and peptide-based self-assembly platforms can be highly beneficial for precisely customizing graphene electronic properties for desired device technologies such as transport-based biosensing graphene field-effect transistors.

Graphene, an Interesting Nanocarbon Allotrope for Biosensing Applications: Advances, Insights, and Prospects

Graphene, a relatively new two-dimensional (2D) nanomaterial, possesses unique structure (e.g. lighter, harder, and more flexible than steel) and tunable physicochemical (e.g. electronical, optical) properties with potentially wide eco-friendly and cost-effective usage in biosensing. Furthermore, graphene-related nanomaterials (e.g. graphene oxide, doped graphene, carbon nanotubes) have inculcated tremendous interest among scientists and industrials for the development of innovative biosensing platforms, such as arrays, sequencers and other nanooptical/biophotonic sensing systems (e.g. FET, FRET, CRET, GERS). Indeed, combinatorial functionalization approaches are constantly improving the overall properties of graphene, such as its sensitivity, stability, specificity, selectivity, and response for potential bioanalytical applications. These include real-time multiplex detection, tracking, qualitative, and quantitative characterization of molecules (i.e. analytes [H₂O₂, urea, nitrite, ATP or NADH]; ions [Hg²⁺, Pb²⁺, or Cu²⁺]; biomolecules (DNA, iRNA, peptides, proteins, vitamins or glucose; disease biomarkers such as genetic alterations in BRCA1, p53) and cells (cancer cells, stem cells, bacteria, or viruses). However, there is still a paucity of comparative reports that critically evaluate the relative toxicity of carbon nanoallotropes in humans. This manuscript comprehensively reviews the biosensing applications of graphene and its derivatives (i.e. GO and rGO). Prospects and challenges are also introduced.

Two-Dimensional Material-Based Biosensors for Virus Detection

Viral infections are one of the major causes of mortality and economic losses worldwide. Consequently, efficient virus detection methods are crucial to determine the infection prevalence. However, most detection methods face challenges related to false-negative or false-positive results, long response times, high costs, and/or the need for specialized equipment and staff. Such issues can be overcome by access to low-cost and fast response point-of-care detection systems, and two-dimensional materials (2DMs) can play a critical role in this regard. Indeed, the unique and tunable physicochemical properties of 2DMs provide many advantages for developing biosensors for viral infections with high sensitivity and selectivity. Fast, accurate, and reliable detection, even at early infection stages by the virus, can be potentially enabled by highly accessible surface interactions between the 2DMs and the analytes. High selectivity can be obtained by functionalization of the 2DMs with antibodies, nucleic acids, proteins, peptides, or aptamers, allowing for specific binding to a particular virus, viral fingerprints, or proteins released by the host organism. Multiplexed detection and discrimination between different virus strains are also feasible. In this Review, we present a comprehensive overview of the major advances of 2DM-based biosensors for the detection of viruses. We describe the main factors governing the efficient interactions between viruses and 2DMs, making them ideal candidates for the detection of viral infections. We also critically detail their advantages and drawbacks, providing insights for the development of future biosensors for virus detection. Lastly, we provide suggestions to stimulate research in the fast expanding field of 2DMs that could help in designing advanced systems for preventing virus-related pandemics.

Graphene biosensors for bacterial and viral pathogens

The infection and spread of pathogens (e.g., COVID-19) pose an enormous threat to the safety of human beings and animals all over the world. The rapid and accurate monitoring and determination of pathogens are of great significance to clinical diagnosis, food safety and environmental evaluation. In recent years, with the evolution of nanotechnology, nano-sized graphene and graphene derivatives have been frequently introduced into the construction of biosensors due to their unique physicochemical properties and biocompatibility. The combination of biomolecules with specific recognition capabilities and graphene materials provides a promising strategy to construct more stable and sensitive biosensors for the detection of pathogens. This review tracks the development of graphene biosensors for the detection of bacterial and viral pathogens, mainly including the preparation of graphene biosensors and their working mechanism. The challenges involved in this field have been discussed, and the perspective for further development has been put forward, aiming to promote the development of pathogens sensing and the contribution to epidemic prevention.

Janus Micromotors Coated with 2D Nanomaterials as Dynamic Interfaces for (Bio)-Sensing

In this work, we study the interaction of graphdiyne oxide (GDYO)-, graphene oxide (GO)-, or black phosphorous (BP)-wrapped Janus micromotors using a model system relying on a fluorescence-labeled affinity peptide, which is released upon specific interaction with a target Cholera Toxin B. Such ON-OFF-ON system allows mimicking similar processes occurring at (bio)-interfaces and to study the related sorption and desorption kinetics. The distinct surface properties of each nanomaterial play a critical role in the loading/release capacity of the peptide, greatly influencing the release profiles. Sorption obeys a second-order kinetic model using the two-dimensional (2D) nanomaterials in connection with micromotors, indicating a strong influence of chemisorption process for BP micromotors. Yet, release kinetics are faster for GDYO and GO nanomaterials, indicating a contribution of π and hydrophobic interactions in the probe sorption (Cholera Toxin B affinity peptide) and target probe release (in the presence of Cholera Toxin B). Micromotor movement also plays a critical role in such processes, allowing for efficient operation in low raw sample volumes, where the high protein content can diminish probe loading/release, affecting the overall performance. The loading/release capacity and feasibility of the (bio)-sensing protocol are illustrated in Vibrio cholerae and Vibrio parahaemolyticus bacteria cultures as realistic domains. The new concept described here holds considerable promise to understand the interaction of micromotor with biological counterparts in a myriad of biomedical and other practical applications, including the design of novel micromotor-based sensors.

A graphene oxide-aided triple helical aggregation-induced emission biosensor for highly specific detection of charged collagen peptides

Aggregation-induced emission (AIE) probes have emerged as promising "turn-on" sensing tools for DNA and proteins, and the AIE biosensors conjugated with graphene oxide (GO) have shown improved selectivity. Collagen is an essential structural protein in the human body, and its degraded products are involved in a plethora of severe diseases. Collagen has a high content of charged amino acids, while EOG represents one of the most abundant charged triplets in Type I collagen. We, herein, for the first time report the construction of a GO-aided AIE biosensor for the detection of charged collagen peptides. We have shown that an AIE fluorophore TPE conjugated with a triple helical peptide TPE-PRG possesses strong fluorescence due to the restriction of intramolecular rotation of TPE in the trimer state. The adsorption of the probe TPE-PRG by GO leads to efficient fluorescence quenching, while the addition of target collagen peptide EOG releases the probe peptide from the GO surface and recovers its fluorescence. We have demonstrated that the TPE-PRG/GO complex provides a highly specific "turn-on" sensing platform for the target collagen peptide with a typical charged amino acid-rich sequence. The assay has shown little interference from other biomolecules, and it can also effectively distinguish the target charged collagen peptide from its single amino acid mutant type. The development of robust analytical assays for charged collagen peptides could pronouncedly extend our capability to investigate the pathology of collagen diseases, showing great potential for their molecular diagnosis.

Study on Interaction Between TATA-Box Binding Protein (TBP), TATA-Box and Multiprotein Bridging Factor 1(MBF1) in Beauveria bassiana by Graphene-Based Electrochemical Biosensors

The regulation of transcription level is an important step in gene expression process. Beauveria bassiana is a broad-spectrum insecticidal fungi widely used in the biologic control of arthropod. The regulation of its transcription level is a multilevel complex process. Multiprotein bridging factor 1(MBF1) is a transcriptional co-activator that bridges sequence-specific activators and the TATA-box binding protein(TBP), Little is known about the interaction between MBF1, TBP, and TBP binding to DNA(TATA-sequences)in filamentous fungi of Beauveria bassiana, The binding of TBP to TATA-box and TBP to MBF1 was investigated via electrochemical biosensor. Graphene oxide has an electronic mobility that is unattainable for any metal, so it will be highly sensitive as a test electrode. Hence, we developed a simple, sensitive and specific sensor based on an TBP probe and graphene oxide that successfully detected the interaction of TBP and TATA-box or MBF1. From the electrochemical impedance spectroscopy (EIS), we find that the radius will increase when adding TATA-box or MBF1 buffer to the modified TBP protein electrode. When adding no TATA-box or no MBF1, the radius is relatively unchanged. The interaction between TBP and TATA-box or MBF1 was proved based on the results. These data confirmed the specificity of the interactions, (1) our developed graphene-based electrochemical biosensor can be used for monitoring the interaction between TBP and TATA-box or MBF1, (2) TBP can bind to TATA-box, (3) TBP can bind to MBF1, and (4) TBP mediates the interactions of MBF1 to DNA. Therefore, this work provided a label-free, low-cost and simple detection method for the complex process of eukaryotic gene transcription regulation.

Acceleration of chondrogenic differentiation of human mesenchymal stem cells by sustained growth factor release in 3D graphene oxide incorporated hydrogels

Damaged articular cartilage has limited self-healing capabilities, leading to degeneration that affects millions of people. Although cartilage tissue engineering is considered a promising approach for treatment, robust and long-term chondrogenesis within a 3-dimensional (3D) scaffold remains a major challenge for complete regeneration. Most current approaches involve incorporation of transforming growth factor-β (TGF-β) into the scaffold, but have limited utility owing to the short functional half-life and/or rapid clearance of TGF-β. In this study, we have tested the incorporation of graphene oxide nanosheets (GO) within a photopolymerizable poly-D, l-lactic acid/polyethylene glycol (PDLLA) hydrogel, for its applicability in sustained release of the chondroinductive growth factor TGF-β3. We found that with GO incorporation, the hydrogel scaffold (GO/PDLLA) exhibited enhanced initial mechanical strength, i.e., increased compressive modulus, and supported long-term, sustained release of TGF-β3 for up to 4 weeks. In addition, human bone marrow-derived mesenchymal stem cells (hBMSCs) seeded within TGF-β3 loaded GO/PDLLA hydrogels displayed high cell viability and improved chondrogenesis in a TGF-β3 concentration-dependent manner. hBMSCs cultured in GO/PDLLA also demonstrated significantly higher chondrogenic gene expression, including aggrecan, collagen type II and SOX9, and cartilage matrix production when compared to cultures maintained in GO-free scaffolds containing equivalent amounts of TGF-β3. Upon subcutaneous implantation in vivo, hBMSC-seeded TGF-β3-GO/PDLLA hydrogel constructs displayed considerably greater cartilage matrix than their TGF-β3/PDLLA counterparts without GO. Taken together, these findings support the potential application of GO in optimizing TGF-β3 induced hBMSC chondrogenesis for cartilage tissue engineering. STATEMENT OF SIGNIFICANCE: In this work, we have developed a graphene oxide (GO) incorporated, photocrosslinked PDLLA hybrid hydrogel for localized delivery and sustained release of loaded TGF-β3 to seeded cells. The incorporation of GO in PDLLA hydrogel suppressed the burst release of TGF-β3, and significantly prolonged the retention time of the TGF-β3 initially loaded in the hydrogel. Additionally, the GO improved the initial compressive strength of the hydrogel. Both in vitro analyses and in vivo implantation results showed that the GO/PDLLA constructs seeded with human mesenchymal stem cells (hMSCs) showed significantly higher cartilage formation, compared to GO-free scaffolds containing equivalent amount of TGF-β3. Findings from this work suggest the potential application of the GO-TGF/PDLLA hydrogel as a functional scaffold for hMSC-based cartilage tissue engineering.

Interactions, electronic and optical properties of nanographene–peptide complexes: a theoretical study

We studied the interaction of planar phenylalanine (phe), tryptophan (try), tyrosine (tyr); amide asparagine (asn) and glutamine (gln); arginine (arg) side-chains, charged histidine (his-c) and charged lysine (lys-c) side-chains on a nanographene (g) surface by Density Functional theory (DFT) and Time Dependent Density Functional Theory (TDDFT). The occupied number of states by the system at each energy level and relative contribution of a particular atom/orbital has been studied by Density of States (DOS) and Partial Density of States (PDOS) respectively. Atom-in Molecules (AIM) analysis and non-covalent interaction (NCI) PLOT are used to study the interactions in these complexes. The absorption spectra and HOMO–LUMO (HL) gaps are quantitatively analysed to study the correlation between the optical properties of the studied complexes. The HL gap of peptides is larger than the HL gap of graphene–peptide complexes, indicating strong interactions. All the peptides interact from the above the nanographene surfaces. garg, glys-c, gtry and gtyr complexes have smaller bond distance as compared to gasn, ggln, ghis-c and gphe complexes. AIM analysis and (NCI) PLOT showed noncovalent interactions for these complexes. TDDFT calculations indicated the applicability of these complexes as biosensors.

We studied interactions of planar phenylalanine, tryptophan, tyrosine; amide asparagine and glutamine; arginine side-chains, charged histidine and charged lysine side-chains on a nanographene surface by density functional theory and time dependent density functional theory.

A review on peptide functionalized graphene derivatives as nanotools for biosensing

Peptides exhibit unique binding behavior with graphene and its derivatives by forming bonds on its edges and planes. This makes them useful for sensing and imaging applications. This review with (155 refs.) summarizes the advances made in the last decade in the field of peptide-GO bioconjugation, and the use of these conjugates in analytical sciences and imaging. The introduction emphasizes the need for understanding the biotic-abiotic interactions in order to construct controllable peptide-functionalized graphitic material-based nanotools. The next section covers covalent and non-covalent interactions between peptide and oxidized graphene derivatives along with a discussion of the adsorption events during interfacing. We then describe applications of peptide-graphene conjugates in bioassays, with subsections on (a) detection of cancer cells, (b) monitoring protease activity, (c) determination of environmental pollutants and (d) determination of pathogenic microorganisms. The concluding section describes the current status of peptide functionalized graphitic bioconjugates and addresses future perspectives. Graphical abstractSchematic representation depicting biosensing applications of peptide functionalized graphene oxide.

Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review

Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π⁻π stacking, DNA base pairing, and ligand⁻receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

Label-free sensitive luminescence biosensor for immunoglobulin G based on Ag6Au6 ethisterone cluster-estrogen receptor α aggregation and graphene

A specific and label-free "on-off-on" luminescence biosensor based on a novel heterometallic cluster [Ag₆Au₆(ethisterone)₁₂]-estrogen receptor α (Ag₆Au₆Eth-ERα) aggregation utilizing graphene oxide (GO) as a quencher to lead a small background signal was firstly constructed to detect immunoglobulin G (IgG) with a simple process and high selectivity. The efficient photoluminescent (PL) Ag₆Au₆Eth-ERα aggregation is strongly quenched by GO. In the presence of IgG, the PL of this system will be restored, and perceivable by human eyes under UV lamp excitation (365 nm). The quenching mechanism of GO on Ag₆Au₆Eth-ERα and enhancement mechanism of IgG on Ag₆Au₆Eth-ERα-GO were investigated in detail. Under the optimum conditions, the biosensor for high sensitive IgG detection expressed a wider linear range of 0.0078-10 ng/mL and a lower detection limit of 0.65 pg/mL with good stability and repeatability, which provided a new approach for label-free IgG detection.

A peptide–WS2 nanosheet based biosensing platform for determination of β-secretase and screening of its inhibitors

β-Secretase (BACE1) is an important drug target in the treatment of Alzheimer's disease (AD).

WS2 and MoS2 biosensing platforms using peptides as probe biomolecules

Biosensors based on the two-dimensional layered nanomaterials transition metal dichalcogenides such as WS2 and MoS2 have shown broad applications, while they largely rely on the utilization of single stranded DNA as probe biomolecules. Herein we have constructed novel WS2- and MoS2- based biosensing platforms using peptides as probe biomolecules. We have revealed for the first time that the WS2 and MoS2 nanosheets display a distinct adsorption for Arg amino acid and particularly, Arg-rich peptdies. We have demonstrated that the WS2 and MoS2 dramatically quench the fluorescence of our constructed Arg-rich probe peptide, while the hybridization of the probe peptide with its target collagen sequence leads to the fluorescence recovery. The WS2-based platform provides a sensitive fluorescence-enhanced assay that is highly specific to the target collagen peptide with little interferences from other proteins. This assay can be applied for quantitative detection of collagen biomarkers in complex biological fluids. The successful development of WS2- and MoS2- based biosensors using non-ssDNA probes opens great opportunities for the construction of novel multifunctional biosensing platforms, which may have great potential in a wide range of biomedical field.

Designed graphene-peptide nanocomposites for biosensor applications: A review

The modification of graphene with biomacromolecules like DNA, protein, peptide, and others extends the potential applications of graphene materials in various fields. The bound biomacromolecules could improve the biocompatibility and bio-recognition ability of graphene-based nanocomposites, therefore could greatly enhance their biosensing performances on both selectivity and sensitivity. In this review, we presented a comprehensive introduction and discussion on recent advance in the synthesis and biosensor applications of graphene-peptide nanocomposites. The biofunctionalization of graphene with specifically designed peptides, and the synthesis strategies of graphene-peptide (monomer, nanofibrils, and nanotubes) nanocomposites were demonstrated. On the other hand, the fabrication of graphene-peptide nanocomposite based biosensor architectures for electrochemical, fluorescent, electronic, and spectroscopic biosensing were further presented. This review includes nearly all the studies on the fabrication and applications of graphene-peptide based biosensors recently, which will promote the future developments of graphene-based biosensors in biomedical detection and environmental analysis.

A Graphene Oxide-Based Fluorescent Method for the Detection of Human Chorionic Gonadotropin

Human chorionic gonadotropin (hCG) has been regarded as a biomarker for the diagnosis of pregnancy and some cancers. Because the currently used methods (e.g., disposable Point of Care Testing (POCT) device) for hCG detection require the use of many less stable antibodies, simple and cost-effective methods for the sensitive and selective detection of hCG have always been desired. In this work, we have developed a graphene oxide (GO)-based fluorescent platform for the detection of hCG using a fluorescein isothiocyanate (FITC)-labeled hCG-specific binding peptide aptamer (denoted as FITC-PPLRINRHILTR) as the probe, which can be manufactured cheaply and consistently. Specifically, FITC-PPLRINRHILTR adsorbed onto the surface of GO via electrostatic interaction showed a poor fluorescence signal. The specific binding of hCG to FITC-PPLRINRHILTR resulted in the release of the peptide from the GO surface. As a result, an enhanced fluorescence signal was observed. The fluorescence intensity was directly proportional to the hCG concentration in the range of 0.05–20 IU/mL. The detection limit was found to be 20 mIU/mL. The amenability of the strategy to hCG analysis in biological fluids was demonstrated by assaying hCG in the urine samples.

Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide

Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to investigate the dynamic process of the adsorption of Vpr13-33 onto GO and the conformation change after aggregating on GO surface. We found that Vpr13-33 was adsorbed on GO surface very quickly and lost its secondary structure. The conformation of peptides-GO complex was highly stable because of π-π stacking and electrostatic interactions. When two peptides aggregated on GO, they did not dimerize, since the interactions between the two peptides were much weaker than those between each peptide and GO.

A Graphene Oxide-Based Fluorescent Platform for Probing of Phosphatase Activity

We presented a strategy for fabricating graphene oxide (GO)-based fluorescent biosensors to monitor the change of phosphorylation state and detect phosphatase activity. By regulating the interaction between the negatively charged phosphate group and the positively charged amino residue, we found that GO showed different quenching efficiency toward the phosphorylated and dephosphorylated dye-labeled peptides. To demonstrate the application of our method, alkaline phosphatase (ALP) was tested as a model enzyme with phosphorylated fluorescein isothiocyanate (FITC)-labeled short peptide FITC-Gly-Gly-Gly-Tyr(PO₃^2-)-Arg as the probe. When the negatively charged phosphate group in the Tyr residue was removed from the peptide substrate by enzymatic hydrolysis, the resulting FITC-Gly-Gly-Gly-Tyr-Arg was readily adsorbed onto the GO surface through electrostatic interaction. As a result, fluorescence quenching was observed. Furthermore, the method was applied for the screening of phosphatase inhibitors.

Trichromophoric pentapeptide: impact of β-sheet conformation on dual path to excimer emission and sensing of BSA

We established dual mechanisms for excimer emission-either via FRET or direct excitation of a FRET acceptor- in a conceptually novel trichromophoric pentapeptide which serves as an effective fluorescence light-up probe for protein–peptide interaction.

The effects of a series of carbon dots on fibrillation and cytotoxicity of human islet amyloid polypeptide

Carbon dots can change hIAPP aggregation kinetics and have a potential to reduce the cytotoxicity of the polypeptide.

A highly specific graphene platform for sensing collagen triple helix

We have designed a dye-labeled, highly positively charged single stranded collagen (ssCOL) peptide probe whose adsorption into GO quenches its fluorescence. The hybridization of the ssCOL probe with a complementary target sequence forms a triple stranded collagen (tsCOL) peptide, resulting in the retention of the fluorescence of the probe.

Interaction of nucleobases with silicon doped and defective silicon doped graphene and optical properties

The interaction of nucleobases (NBs) with the surface of silicon doped graphene (SiGr) and defective silicon doped graphene (dSiGr) has been studied using electronic structure methods.

A sedimentation study of graphene oxide in aqueous solution using gradient differential centrifugation

This work involved the study of sedimentation of graphene oxide (GO) in aqueous solution by gradient differential centrifugation.

Paper-based FRET for the direct detection of collagen triple helix

The integration of the GO-based FRET assay with a patterned paper provides a powerful new tool for the detection of collagen molecules with many superior features: tiny volumes of samples, multichannel detection mode, easy operation and low-cost equipment.

A graphene oxide-based FRET sensor for rapid and specific detection of unfolded collagen fragments

The unstructured collagen species plays a critical role in a variety of important biological processes as well as pathological conditions. In order to develop novel diagnosis and therapies for collagen-related diseases, it is essential to construct simple and efficient methods to detect unfolded collagen fragments. We therefore have designed a FITC-labeled collagen mimic triple helical peptide, whose adsorption on the surface of GO effectively quenches its fluorescence. The newly constructed GO/FITC-GPO complex specifically detects unstructured collagen fragments, but not fully folded triple helix species. The detection shows a clear preference for the collagen targets with complementary GPO-rich sequences. The conformation-sensitive, sequence-specific GO-based approach can be applied as an efficient biosensor for rapid detection of unfolded collagen fragments at nM level, and may have great potential in drug screening for inhibitors of unfolded collagen. It may provide a prototype to develop GO-based assays to detect other important unstructured proteins involved in diseases.

N-butylamine functionalized graphene oxide for detection of iron(III) by photoluminescence quenching

An N-butylamine functionalized graphene oxide nanolayer was synthesized and characterized by ultraviolet (UV)-visible spectrometry, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and transmission electron microscopy. Detection of iron(III) based on photoluminescence spectroscopy was investigated. The N-butylamine functionalized graphene oxide was shown to specifically interact with iron (III), compared with other cationic trace elements including potassium (I), sodium (I), calcium (II), chromium (III), zinc (II), cobalt (II), copper (II), magnesium (II), manganese (II), and molybdenum (VI). The quenching effect of iron (III) on the luminescence emission of N-butylamine functionalized graphene oxide layer was used to detect iron (III). The limit of detection (2.8 × 10(-6)  M) and limit of quantitation (2.9 × 10(-5)  M) were obtained under optimal conditions.

Fluorescent nanosensor for probing histone acetyltransferase activity based on acetylation protection and magnetic graphitic nanocapsules

Protein acetylation catalyzed by histone acetyltransferases (HATs) is significant in biochemistry and pharmacology because of its crucial role in epigenetic gene regulations. Herein, an antibody-free fluorescent nanosensor is developed for the facile detection of HAT activity based on acetylation protection against exopeptidase cleavage and super-quenching ability of nanomaterials. It is shown for the first time that HAT-catalyzed acetylation could protect the peptide against exopeptidase digestion. FITC-tagged acetylated peptide causes the formation of a nano-quenchers/peptide nano-complex resulting in fluorescence quenching, while the unacetylated peptide is fully degraded by exopeptidase to release the fluorophore and restore fluorescence. Four kinds of nano-quenchers, including core-shell magnetic graphitic nanocapsules (MGN), graphene oxide (GO), single-walled carbon nanotubes (SWCNTs), and gold nanoparticles (AuNPs), are comprehensively compared. MGN shows the best selectivity to recognize the acetylated peptide and the lowest detection limit because of its excellent quenching efficiency and magnetic enrichment property. With this MGN-based nanosensor, HAT p300 is detected down to 0.1 nM with wide linear range from 0.5 to 100 nM. This sensor is feasible to assess HAT inhibition and detect p300 activity in cell lysate. The proposed nanosensor is simple, sensitive, and cost-effective for HAT assay, presenting a promising toolkit for epigenetic research and HAT-targeted drug discovery.

Probing disease-related proteins with fluorogenic composite materials

Construction of composite materials based on the self-assembly of fluorescently labeled biomolecules with a variety of micro- or nano-quenching materials (by the Förster Resonance Energy Transfer mechanism) for the fluorogenic recognition of disease-related proteins has become a dynamic research topic in the field of fluorescence recognition. Here we summarize the recent progress on the composition of fluorescence dye-labeled biomolecules including sugars, peptides and nucleotides with organic (graphene and carbon nanotubes) and inorganic (gold nanoparticles) materials. Their application in the fluorescence detection of proteins and enzymes on both the molecular and cellular levels is discussed. Perspectives are proposed with respect to the future directions of employing these composite materials in the recognition of pathological proteins.

Self-assembly-induced far-red/near-infrared fluorescence light-up for detecting and visualizing specific protein-Peptide interactions

Understanding specific protein-peptide interactions could offer a deep insight into the development of therapeutics for many human diseases. In this work, we designed and synthesized a far-red/near-infrared (FR/NIR) fluorescence light-up probe (DBT-2EEGWRESAI) by simply integrating two tax-interacting protein-1 (TIP-1)-specific peptide ligands (EEGWRESAI) with one 4,7-di(thiophen-2-yl)-2,1,3-benzothiadiazole (DBT) unit. We first demonstrated that DBT is an environment-sensitive fluorophore with FR/NIR fluorescence due to its strong charge transfer character in the excited state. Thanks to the environmental sensitivity of DBT, the probe DBT-2EEGWRESAI is very weakly fluorescent in aqueous solution but lights up its fluorescence when the probe specifically binds to TIP-1 protein or polyprotein (ULD-TIP-1 tetramer). It is found that the DBT-2EEGWRESAI/TIP-1 protein and the DBT-2EEGWRESAI/ULD-TIP-1 tetramer could self-assemble into spherical nanocomplexes and a nanofiber network, respectively, which lead to probe fluorescence turn-on through providing DBT with a hydrophobic microenvironment. By virtue of the self-assembly-induced FR/NIR fluorescence turn-on, DBT-2EEGWRESAI can detect and visualize specific protein/polyprotein-peptide interactions in both solution and live bacteria in a high contrast and selective manner.

Upconversion fluorescence resonance energy transfer biosensor for sensitive detection of human immunodeficiency virus antibodies in human serum

An upconversion FRET-based biosensor has been developed for the sensitive and selective determination of HIV antibodies in human serum.

Functional nanoprobes for ultrasensitive detection of biomolecules: an update

With the rapidly increasing demands for ultrasensitive biodetection, the design and applications of functional nanoprobes have attracted substantial interest for biosensing with optical, electrochemical, and various other means. In particular, given the comparable sizes of nanomaterials and biomolecules, there exists plenty of opportunities to develop functional nanoprobes with biomolecules for highly sensitive and selective biosensing. Over the past decade, numerous nanoprobes have been developed for ultrasensitive bioaffinity sensing of proteins and nucleic acids in both laboratory and clinical applications. In this review, we provide an update on the recent advances in this direction, particularly in the past two years, which reflects new progress since the publication of our last review on the same topic in Chem. Soc. Rev. The types of probes under discussion include: (i) nanoamplifier probes: one nanomaterial loaded with multiple biomolecules; (ii) quantum dots probes: fluorescent nanomaterials with high brightness; (iii) superquenching nanoprobes: fluorescent background suppression; (iv) nanoscale Raman probes: nanoscale surface-enhanced Raman resonance scattering; (v) nanoFETs: nanomaterial-based electrical detection; and (vi) nanoscale enhancers: nanomaterial-induced metal deposition.

Highly tunable aptasensing microarrays with graphene oxide multilayers

A highly tunable layer-by-layer (LbL)-assembled graphene oxide (GO) array has been devised for high-throughput multiplex protein sensing. In this array, the fluorescence of different target-bound aptamers labeled with dye is efficiently quenched by GO through fluorescence resonance energy transfer (FRET), and simultaneous multiplex target detection is performed by recovering the quenched fluorescence caused by specific binding between an aptamer and a protein. Thin GO films consisting of 10 bilayers displayed a high quenching ability, yielding over 85% fluorescence quenching with the addition of a 2 μM dye-labeled aptamer. The limit for human thrombin detection in the 6- and 10-bilayered GO array is estimated to be 0.1 and 0.001 nM, respectively, indicating highly tunable nature of LbL assembled GO multilayers in controlling the sensitivity of graphene-based FRET aptasensor. Furthermore, the GO chip could be reused up to four times simply by cleaning it with distilled water.