An all-graphene quantum dot Förster resonance energy transfer (FRET) probe for ratiometric detection of HE4 ovarian cancer biomarker

Finding the partner: FRET and beyond

Given the importance of aberrant protein-protein interactions (PPIs) in disease, the recent drug discovery focuses on targeting the altered PPIs to treat the disease. In this context, identifying the atypical PPIs underlying the disease is critical for the development of diagnostics and therapeutics. Various biochemical, biophysical, and genetic methods have been reported to study PPIs. Here, we are giving a short account of those techniques with more emphasis on Förster resonance energy transfer (FRET), which can be used to monitor macromolecular interactions in live cells. Besides the basics of FRET, we explain the modifications of its application, like Single molecule FRET (smFRET), Fluorescence Lifetime Imaging Microscopy-FRET (FLIM-FRET), and photoswitching FRET. While smFRET is extensively used for evaluating the biology of nucleic acids and also to develop diagnostics, FLIM-FRET is widely exploited to study the PPIs underlying neurological disorders and cancer. Photoswitching FRET is a relatively newer technique and it has tremendous potential to unravel the significance of different PPIs. Besides these modifications, there are several advancements in the field by introducing new fluorophores. Identification of lanthanide chelates, quantum dots, and other nanoparticle fluorophores has revolutionized the applications of FRET in diagnostics and basic biology. Yet, these methods can be employed to study the interactions of only two molecules. Since the majority of the PPIs are multimeric complexes, we still need to improve our technologies to study these interactions in live cells in real-time.

One-step detection of procollagen type III N-terminal peptide as a fibrosis biomarker using fluorescent immunosensor (quenchbody)

BACKGROUND

Procollagen type III N-terminal peptide (P-III-NP) is a fibrosis biomarker associated with liver and cardiac fibrosis. Despite the value of P-III-NP as a biomarker, its analysis currently relies on enzyme-linked immunosorbent assays (ELISA) and radioimmunoassays (RIA), which require more than 3 h. To facilitate early diagnosis and treatment through rapid biomarker testing, we developed a one-step immunoassay for P-III-NP using a quenchbody, which is a fluorescence-labeled immunosensor for immediate signal generation.

RESULTS

To create quenchbodies, the total mRNA of P-III-NP antibodies was extracted from early-developed hybridoma cells, and genes of variable regions were obtained through cDNA synthesis, inverse PCR, and sequencing. A single-chain variable fragment (scFv) with an N-terminal Cys-tag was expressed in E. coli Shuffle T7, resulting in a final yield of 9.8 mg L-1. The fluorescent dye was labeled on the Cys-tag of the anti-P-III-NP scFv using maleimide-thiol click chemistry, and the spacer arm lengths between the maleimide-fluorescent dyes were compared. Consequently, a TAMRA-C6-labeled quenchbody exhibited antigen-dependent fluorescence signals and demonstrated its ability to detect P-III-NP at concentrations as low as 0.46 ng mL-1 for buffer samples, 1.0 ng mL-1 for 2 % human serum samples.

SIGNIFICANCE

This one-step P-III-NP detection method provides both qualitative and quantitative outcomes within a concise 5-min timeframe. Furthermore, its application can be expanded using a 96-well platform and human serum, making it a high-throughput and sensitive method for testing fibrotic biomarkers.

A review on synthesis, properties, and biomedical applications of graphene quantum dots (GQDs)

A new type of 0-dimensional carbon-based materials called graphene quantum dots (GQDs) is gaining significant attention as a non-toxic and eco-friendly nanomaterial. GQDs are nanomaterials composed of sp2hybridized carbon domains and functional groups, with their lateral size less than 10 nm. The unique and exceptional physical, chemical, and optical properties arising from the combination of graphene structure and quantum confinement effect due to their nano-size make GQDs more intriguing than other nanomaterials. Particularly, the low toxicity and high solubility derived from the carbon core and abundant edge functional groups offer significant advantages for the application of GQDs in the biomedical field. In this review, we summarize various synthetic methods for preparing GQDs and important factors influencing the physical, chemical, optical, and biological properties of GQDs. Furthermore, the recent application of GQDs in the biomedical field, including biosensor, bioimaging, drug delivery, and therapeutics are discussed. Through this, we provide a brief insight on the tremendous potential of GQDs in biomedical applications and the challenges that need to be overcome in the future.

Freeze-Dryable, Stable, and Click-Reactive Nanoparticles Composed of Cello-oligosaccharides for Biomolecular Sensing

Nanoparticles have been widely used as platforms for biomolecular sensing because of their high specific surface area and attractive properties depending on their constituents and structures. Nevertheless, it remains challenging to develop nanoparticulate sensing platforms that are easily storable without aggregation and conjugatable with various ligands in a simple manner. Herein, we demonstrate that nanoparticulate assemblies of cello-oligosaccharides with terminal azido groups are promising candidates. Azidated cello-oligosaccharides can be readily synthesized via the enzyme-catalyzed oligomerization reaction. This study characterized the assembled structures of azidated cello-oligosaccharides produced during the enzymatic synthesis and revealed that the terminal azidated cello-oligosaccharides formed rectangular nanosheet-shaped lamellar crystals. The azido groups located on the nanosheet surfaces were successfully exploited for antigen conjugation via the click chemistry. The resultant antigen-conjugated nanosheets allowed for the quantitative and specific detection of a corresponding antibody, even in 10% serum, owing to the antifouling properties of cello-oligosaccharide assemblies against proteins. It was found that the functionalized nanosheets were redispersible in water after freeze-drying. This remarkable characteristic is attributed to the well-hydrated saccharide residues on the nanosheet surfaces. Moreover, the antibody detection capability did not decline after the thermal treatment of the functionalized nanosheets in a freeze-dried state. Our findings contribute to developing convenient nanoparticulate biomolecular sensing platforms.

Quantum Material-Based Self-Propelled Microrobots for the Optical "On-the-Fly" Monitoring of DNA

Quantum dot-based materials have been found to be excellent platforms for biosensing and bioimaging applications. Herein, self-propelled microrobots made of graphene quantum dots (GQD-MRs) have been synthesized and explored as unconventional dynamic biocarriers toward the optical "on-the-fly" monitoring of DNA. As a first demonstration of applicability, GQD-MRs have been first biofunctionalized with a DNA biomarker (i.e., fluorescein amidite-labeled, FAM-L) via hydrophobic π-stacking interactions and subsequently exposed toward different concentrations of a DNA target. The biomarker-target hybridization process leads to a biomarker release from the GQD-MR surface, resulting in a linear alteration in the fluorescence intensity of the dynamic biocarrier at the nM range (1-100 nM, R2 = 0.99), also demonstrating excellent selectivity and sensitivity, with a detection limit as low as 0.05 nM. Consequently, the developed dynamic biocarriers, which combine the appealing features of GQDs (e.g., water solubility, fluorescent activity, and supramolecular π-stacking interactions) with the autonomous mobility of MRs, present themselves as potential autonomous micromachines to be exploited as highly efficient and sensitive "on-the-fly" biosensing systems. This method is general and can be simply customized by tailoring the biomarker anchored to the GQD-MR's surface.

Functionalized Graphene Quantum Dots (GQDs) based Label-Free Optical Fluorescence Sensor for CD59 Antigen Detection and Cellular Bioimaging

Cluster of differentiation (CD59), a cell surface glycoprotein, regulates the complement system to prevent immune damage. In cancer, altered CD59 expression allows tumors to evade immune surveillance, promote growth, and resist certain immunotherapies. Targeting CD59 could enhance cancer treatment strategies by boosting the immune response against tumors. Herein, we present a one-step synthesis of Polyethyleneimine (PEI) functionalized graphene quantum dots (Lf-GQDs) from weathered lemon leaf extract. The fabricated Lf-GQDs were successfully used for the quantitative detection of the cluster of CD59 antigen that is reported for its expression in different types of cancer. In this work, we utilized orientation-based attachment of CD59 antibody (Anti-CD59). Our findings reveal that, instead of using random serial addition of antigen or antibody, oriented conjugation saves accumulated concentration offering greater sensitivity and selectivity. The Anti-CD59@Lf-GQDs immunosensor was fabricated using the oriented conjugation of antibodies onto the Lf-GQDs surface. Besides, the fabricated immunosensor demonstrated detection of CD59 in the range of 0.01 to 40.0 ng mL-1 with a low detection limit of 5.3 pg mL-1. Besides, the cellular uptake potential of the synthesized Lf-GQDs was also performed in A549 cells using a bioimaging study. The present approach represents the optimal utilization of Anti-CD59 and CD59 antigen. This approach could afford a pathway for constructing oriented conjugation of antibodies on the nanomaterials-based immunosensor for different biomarkers detection.

Detection of SARS-CoV-2 S protein based on FRET between carbon quantum dots and gold nanoparticles

The COVID-19 pandemic caused by SARS-CoV-2 virus brings nasty crisis for public health in the world. Until now, the virus has caused multiple infections in many people. Detecting antigen to SARS-CoV-2 is a powerful method for the diagnosis of COVID-19 and is helpful for controlling and stopping the pandemic. Herein, a rapid and quantitative detection method of SARS-CoV-2 spike(S) protein was built based on the fluorescence resonance energy transfer (FRET) phenomenon without complicated steps. In the process of detecting, the carbon quantum dots (CQDs) and gold nanoparticles (AuNPs) act as donor and acceptor. By modifying the SARS-CoV-2 antibodies on the surface of CQDs and AuNPs, we achieved S protein specific detection using the distance-based FRET phenomenon. Through the electric charge regulation, the limit of detection (LOD) is 0.05 ng/mL, the linear range is 0.1-100 ng/mL, and the detection process only takes 12 min. The proposed method exhibits several advantages such as be available for variants (B.1.1.529 and B.1.617.2) and be suitable for human serum, which is of significance for detecting viral in time and prevention the viral transmission.

A novel fluorescent strategy for Golgi protein 73 determination based on aptamer/nitrogen-doped graphene quantum dots/molybdenum disulfide @ reduced graphene oxide nanosheets

The effective detection of biomarkers associated with hepatocellular carcinoma (HCC) is of great importance. Golgi protein 73 (GP73), a serum biomarker of HCC, has better diagnostic value than Alpha-fetoprotein (AFP) has been reported. In this paper, highly accurate fluorescence sensing platform for detecting GP73 was constructed based on fluorescence resonance energy transfer (FRET), in which nitrogen-doped graphene quantum dots (NGQDs) labelling with GP73 aptamer (GP73_Apt) was used as fluorescence probe, and molybdenum disulfide @ reduced graphene oxide (MoS₂@RGO) nanosheets was used as fluorescent receptors. MoS₂@RGO nanosheets can quench the fluorescence of NGQDs-GP73_Apt owing to FRET mechanisms. In the presence of GP73, the NGQDs-GP73_Apt specifically bound with GP73 to from the deployable structures, making NGQDs-GP73_Apt far away from MoS₂@RGO nanosheets, blocking the FRET process, resulting in fluorescence recovery of NGQDs-GP73_Apt. Under optimal conditions, the recovery intensity of fluorescence in the detection system is linearly related to the concentration of GP73 in the range of 5 ng/mL - 100 ng/mL and the limit of detection is 4.54 ng/mL (S/N = 3). Moreover, detection of GP73 was performed in human serum samples with good recovery (97.21-100.83%). This platform provides a feasible method for the early diagnosis of HCC, and can be easily extended to the detection of other biomarkers.

Co-Immobilization of GOD & HRP on Y-Shaped DNA Scaffold and the Regulation of Inter-Enzyme Distance

In multienzymes cascade reaction, the inter-enzyme spacing is supposed to be a factor affecting the cascade activity. Here, a simple and efficient Y-shaped DNA scaffold is assembled using two partially complementary DNA single strands on magnetic microspheres, which is used to coimmobilize glucose oxidase (GOD) and horseradish peroxidase (HRP). As a result, on poly(vinyl acetate) magnetic microspheres (PVAC), GOD/HRP-DNA@PVAC multienzyme system is obtained, which can locate GOD and HRP accurately and control the inter-enzyme distance precisely. The distance between GOD and HRP is regulated by changing the length of DNA strand. It showed that the cascade activity is significantly distance-dependent. Moreover, the inter-enzyme spacing is not the closer the better, and too short distance would generate steric hindrance between enzymes. The cascade activity reached the maximum value of 967 U mg^-1 at 13.6 nm, which is 3.5 times higher than that of free enzymes. This is ascribed to the formation of substrate channeling.

Prospects of microbial-engineering for the production of graphene and its derivatives: Application to design nanosystms for cancer theranostics

Cancer is known as one of the leading causes of morbidity and fatality, currently faced by our society. The prevalence of cancer related dieses is rapidly increasing around the world. To reduce the mortality rates, early diagnosis and subsequent treatment of cancer in timely manner is quite essential. Advancements have been made to achieve effective theranostics strategies to tackle cancerous dieses, yet very challenging to overcome this issue. Recently, advances made in the field of nanotechnology have shown tremendous potential for cancer theranostics. Different types of nanomaterials have been successfully employed to develop sophisticated diagnosis and therapy techniques. In this context, graphene and its derivatives e.g. graphene oxide (GO) and reduced graphene oxide (RGO) have been investigated as promising candidates to design graphene-based nanosystems for the diagnosis and therapeutic purpose. Further, to synthesize graphene and its derivatives different types of physicochemical methods are being adopted. However, each method has its own advantage and disadvantages. In this reference, among diverse biological methods, microbial technique can be one of the most promising and eco-friendly approach for the preparation of graphene and its derivatives, particularly GO and RGO. In this review, we summarize studies performed on the preparation of graphene and its derivatives following microbial routes meanwhile focus has been made on the preparation method and the possible mechanism involved therein. Thereafter, we have discussed applications of graphene and its derivatives to developed advanced nanosystem that can be imperative for the cancer theranostics. Results of recent studies exploring applications graphene based nanosystem for the preparation of different types of biosensors for early diagnosis; advanced therapeutic approaches by designing drug delivery nanosystems along with multifunctionality (e.g cancer imaging, drug delivery, photodynamic and photo thermal therapy) in cancer theranostics have been discussed. Particularly, emphasis has been given on the preparation techniques of graphene based nanosystems, being employed in designing of biosensing platforms, drug delivery and multifunctional nanosystems. Moreover, issues have been discussed on the preparation of graphene and its derivatives following microbial technique and the implementation of graphene based nanosystems in cancer theranostics.

Role of Förster Resonance Energy Transfer in Graphene-Based Nanomaterials for Sensing

Förster resonance energy transfer (FRET)-based fluorescence sensing of various target analytes has been of growing interest in the environmental, bioimaging, and diagnosis fields. Graphene-based zero- (0D) to two-dimensional (2D) nanomaterials, such as graphene quantum dots (GQDs), graphene oxide (GO), reduced graphene oxide (rGO), and graphdiyne (GD), can potentially be employed as donors/acceptors in FRET-based sensing approaches because of their unique electronic and photoluminescent properties. In this review, we discuss the basics of FRET, as well as the role of graphene-based nanomaterials (GQDs, GO, rGO, and GD) for sensing various analytes, including cations, amino acids, explosives, pesticides, biomolecules, bacteria, and viruses. In addition, the graphene-based nanomaterial sensing strategy could be applied in environmental sample analyses, and the reason for the lower detection ranges (micro- to pico-molar concentration) could also be explained in detail. Challenges and future directions for designing nanomaterials with a new sensing approach and better sensing performance will also be highlighted.

Graphene quantum dots: A review on the effect of synthesis parameters and theranostic applications

The rising demand for early-stage diagnosis of diseases such as cancer, diabetes, neurodegenerative can be met with the development of materials offering high sensitivity and specificity. Graphene quantum dots (GQDs) have been investigated extensively for theranostic applications owing to their superior photostability and high aqueous dispersibility. These are attractive for a range of biomedical applications as their physicochemical and optoelectronic properties can be tuned precisely. However, many aspects of these properties remain to be explored. In the present review, we have discussed the effect of synthetic parameters upon their physicochemical characteristics relevant to bioimaging. We have highlighted the effect of particle properties upon sensing of biological molecules through 'turn-on' and 'turn-off' fluorescence and generation of electrochemical signals. After describing the effect of surface chemistry and solution pH on optical properties, an inclusive view on application of GQDs in drug delivery and radiation therapy has been given. Finally, a brief overview on their application in gene therapy has also been included.

Properties and Applications of Graphene and Its Derivatives in Biosensors for Cancer Detection: A Comprehensive Review

Cancer is one of the deadliest diseases worldwide, and there is a critical need for diagnostic platforms for applications in early cancer detection. The diagnosis of cancer can be made by identifying abnormal cell characteristics such as functional changes, a number of vital proteins in the body, abnormal genetic mutations and structural changes, and so on. Identifying biomarker candidates such as DNA, RNA, mRNA, aptamers, metabolomic biomolecules, enzymes, and proteins is one of the most important challenges. In order to eliminate such challenges, emerging biomarkers can be identified by designing a suitable biosensor. One of the most powerful technologies in development is biosensor technology based on nanostructures. Recently, graphene and its derivatives have been used for diverse diagnostic and therapeutic approaches. Graphene-based biosensors have exhibited significant performance with excellent sensitivity, selectivity, stability, and a wide detection range. In this review, the principle of technology, advances, and challenges in graphene-based biosensors such as field-effect transistors (FET), fluorescence sensors, SPR biosensors, and electrochemical biosensors to detect different cancer cells is systematically discussed. Additionally, we provide an outlook on the properties, applications, and challenges of graphene and its derivatives, such as Graphene Oxide (GO), Reduced Graphene Oxide (RGO), and Graphene Quantum Dots (GQDs), in early cancer detection by nanobiosensors.

A fluorescence aptasensor based on GSH@GQDs and RGO for the detection of Glypican-3

Glypican-3 (GPC3), a heparin sulfate proteoglycan, is a potential diagnostic and therapeutic target for hepatocellular carcinoma. In this paper, a novel fluorescent aptasensor for GPC3 detection is constructed via glutathione@graphene quantum dots-labeled GPC3 aptamer (GSH@GQDs-GPC3_Apt) as a fluorescence probe. First, GSH@GQDs is screened out with higher fluorescence intensity, which emits bright blue fluorescence under ultraviolet light. Then, the fluorescence-labeled GSH@GQDs-GPC3_Apt probe is formed by the combination of amination GPC3_Apt and GSH@GQDs using EDC/NHS coupled reaction. Under hydrogen bond and π-π interaction/stacking, the fluorescence of GSH@GQDs-GPC3_Apt could be quenched by reductive graphene oxide (RGO) with the help of the photoinduced electron transfer and the fluorescence resonance energy transfer mechanism. In the presence of GPC3, the GSH@GQDs-GPC3_Apt specifically recognizes and binds to GPC3, giving rise to the change of secondary structure of GPC3_Apt to form the GPC3/GPC3_Apt-GSH@GQDs complex, which would lead to the disintegration of the GSH@GQDs-GPC3_Apt-RGO compound. Therefore, the energy transfer process is blocked and the fluorescence intensity is restored, enabling a highly sensitive response to GPC3. When the concentration of GPC3 is from 5.0 ng/mL to 150.0 ng/mL, the fluorescence recovery rate is well linearly related to GPC3 concentration with the limit of detection of 2.395 ng/mL (S/N = 3). This strategy shows recoveries from 98.31% to 101.89% in human serum samples and provides simple, fast and cheap analysis of GPC3, which suggests that it has great potential applications in clinical diagnosis for hepatocellular carcinoma.

Measuring calibration factors by imaging a dish of cells expressing different tandem constructs plasmids

Three-cube Förster resonance energy transfer (FRET) method is the most extensively applied approach for live-cell FRET quantification. Reliable measurements of calibration factors are crucial for quantitative FRET measurement. We here proposed a modified TA-G method (termed as mTA-G) to simultaneously obtain the FRET-sensitized quenching transition factor (G) and extinction coefficients ratio (γ) between donor and acceptor. mTA-G method includes four steps: (1) predetermining the ratio ranges of the sensitized emission of acceptor (F_C ) to the donor excitation and donor channel image (I_DD [(DA])) for all FRET plasmids; (2) culturing the cells which express every FRET plasmid in one dish respectively; (3) distinguishing and marking the cells expressing different FRET plasmids by detecting their F_C /I_DD (DA) values; (4) linearly fitting F_C /I_AA (DA) (acceptor excitation and acceptor channel image) to I_DD (DA)/I_AA (DA) for different kinds of cells. We implemented mTA-G method by imaging tandem constructs cells with different FRET efficiency cultured in one dish on different days, and obtained consistent G and γ values. mTA-G method not only circumvents switchover of different culture dishes but also keep the constant imaging conditions, exhibiting excellent robustness, and thus will expands the biological applications of quantitative FRET analysis in living cells.