A graphene-based platform for the assay of duplex-DNA unwinding by helicase

Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair

DNA helicase activity is essential for the vital DNA metabolic processes of recombination, replication, transcription, translation, and repair. Recently, an unexpected, rapid exponential ATP-stimulated DNA unwinding rate was observed from an Archaeoglobus fulgidus helicase (AfXPB) as compared to the slower conventional helicases from Sulfolobus tokodaii, StXPB1 and StXPB2. This unusual rapid activity suggests a "molecular wrench" mechanism arising from the torque applied by AfXPB on the duplex structure in transitioning from open to closed conformations. However, much remains to be understood. Here, we investigate the concentration dependence of DNA helicase binding and ATP-stimulated kinetics of StXPB2 and AfXPB, as well as their binding and activity in Bax1 complexes, via an electrochemical assay with redox-active DNA monolayers. StXPB2 ATP-stimulated activity is concentration-independent from 8 to 200 nM. Unexpectedly, AfXPB activity is concentration-dependent in this range, with exponential rate constants varying from seconds at concentrations greater than 20 nM to thousands of seconds at lower concentrations. At 20 nM, rapid exponential signal decay ensues, linearly reverses, and resumes with a slower exponential decay. This change in AfXPB activity as a function of its concentration is rationalized as the crossover between the fast molecular wrench and slower conventional helicase modes. AfXPB-Bax1 inhibits rapid activity, whereas the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations. This activity is rationalized with the crystal structures of these complexes. These findings illuminate the different physical models governing molecular wrench activity for improved biological insight into a key factor in DNA repair.

Facilitation of Dye-Based Quantitative Real-Time Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide

Quantitative real-time polymerase chain reaction (qPCR) is an important and extensively utilized technique in medical and biotechnological applications. qPCR enables the real-time detection of nucleic acid during amplification, thus surpassing the necessity of post-amplification gel electrophoresis for amplicon detection. Despite being widely employed in molecular diagnostics, qPCR exhibits limitations attributed to nonspecific DNA amplification that compromises the efficiency and fidelity of qPCR. Herein, we demonstrate that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the efficiency and specificity of qPCR by adsorbing single-stranded DNA (ssDNA) without affecting the fluorescence of double-stranded DNA binding dye during DNA amplification. PEG-nGO adsorbs surplus ssDNA primers in the initial phase of PCR, having lower concentrations of DNA amplicons and thus minimizing the nonspecific annealing of ssDNA and false amplification due to primer dimerization and erroneous priming. As compared to conventional qPCR, the addition of PEG-nGO and the DNA binding dye, EvaGreen, in the qPCR setup (dubbed as PENGO-qPCR) significantly enhances the specificity and sensitivity of DNA amplification by preferential adsorption of ssDNA without inhibiting DNA polymerase activity. The PENGO-qPCR system for detection of influenza viral RNA exhibited a 67-fold higher sensitivity than the conventional qPCR setup. Thus, the performance of a qPCR can be greatly enhanced by adding PEG-nGO as a PCR enhancer as well as EvaGreen as a DNA binding dye to the qPCR mixture, which exhibits a significantly improved sensitivity of the qPCR.

Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study

Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.

Label-free bioassay with graphene oxide-based fluorescent aptasensors: A review

Bioassays using a fluorophore and DNA aptamer have been extensively developed due to the ultrasensitivity of fluorophores and recognition ability of DNA aptamers. Conventional fluorescent aptamer-based sensors (aptasensors) require chemical labeling between the fluorophore and aptamer and is technologically impracical for various sensing and assay applications. A simple "mix and go" strategy has been introduced that uses label-free technology as a platform for sensor development. The biosensors comprise a fluorophore, a ssDNA aptamer, and eco-friendly graphene oxide (GO). In the absence of the sensor target, GO quenches the fluorescence of the fluorophore and single-strand DNA aptamer complex. When the target is added, the DNA aptamer conformationally turns into a duplex, G-quadruplexe, or other secondary structure. This structure change leads to release of GO by the fluorophore-aptamer-target complex, generating dramatic fluorescence recovery and amplification. With this sensing method, the DNA aptamer does not need to be chemically labeled. Therefore, flexible fluorophore indicators and ssDNA aptamers can be used in this label-free aptasensing strategy. In this review, we discuss various unlabeled fluorophores, including synthetic small molecular fluorophores and genetically encoded fluorescent proteins, as indicators for generating GO-based fluorescent DNA aptasensors for label-free bioassay.

Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery

Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.

Graphene and graphene oxide for bio-sensing: General properties and the effects of graphene ripples

The use of Graphene based materials, such as graphene oxide (GO), in biosensing applications is gaining significant interest, due to high signal output, with strong potential for high industrial growth rate. Graphene's excellent conduction and mechanical properties (such as toughness and elasticity) coupled with high reactivity to chemical molecules are some of its appealing properties. The presence of ripples on the surface (whether indigenous or induced) represents another property/variable that provide enormous potential if harnessed properly. In this article, we review the current knowledge regarding the use of graphene for biosensing. We discuss briefly the general topic of using graphene for biosensing applications with special emphasis on wearable graphene-based biosensors. The intrinsic ripples of graphene and their effect on graphene biosensing capabilities are thoroughly discussed. We dedicate a section also for the manipulation of intrinsic ripples. Then we review the use of Graphene oxide (GO) in biosensing and discuss the effect of ripples on its properties. We present a review of the current biosensor devices made out of GO for detection of different molecular targets. Finally, we present some thoughts for future perspectives and opportunities of this field. STATEMENT OF SIGNIFICANCE: Biosensors are tools that detect the presence and amount of a chemical substance, such as pregnancy tests and glucose monitoring devices. They are general portable, have short response times and are sensitive, making them highly effective. Gold and silver are used in biosensors and more recently, graphene.  Graphene is sheets of carbon atoms and is the only two-dimensional crystal in nature. It has unique features allowing its effective use in biosensing applications, including the presence of ripples (non-flat areas that give it its electronic properties). The last comprehensive review of this topic was published in 2016. This paper reviews the current knowledge of graphene based biosensors, with a focus on ripples and their effect on graphene biosensing capabilities.

Identification of a Direct-Acting Antiviral Agent Targeting RNA Helicase via a Graphene Oxide Nanobiosensor

Dengue virus (DENV), an arbovirus transmitted by mosquitoes, causes infectious diseases such as dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Despite the dangers posed by DENV, there are no approved antiviral drugs for treatment of DENV infection. Considering the potential for a global dengue outbreak, rapid development of antiviral agents against DENV infections is crucial as a preemptive measure; thus, the selection of apparent drug targets, such as the viral enzymes involved in the viral life cycle, is recommended. Helicase, a potential drug target in DENV, is a crucial viral enzyme that unwinds double-stranded viral RNA, releasing single-stranded RNA genomes during viral replication. Therefore, an inhibitor of helicase activity could serve as a direct-acting antiviral agent. Here, we introduce an RNA helicase assay based on graphene oxide, which enables fluorescence-based analysis of RNA substrate-specific helicase enzyme activity. This assay demonstrated high reliability and ability for high-throughput screening, identifying a new helicase inhibitor candidate, micafungin (MCFG), from an FDA-approved drug library. As a direct-acting antiviral agent targeting RNA helicase, MCFG inhibits DENV proliferation in cells and an animal model. Notably, in vivo, MCFG treatment reduced viremia, inflammatory cytokine levels, and viral loads in several tissues and improved survival rates by up to 40% in a lethal mouse model. Therefore, we suggest MCFG as a potential direct-acting antiviral drug candidate.

An optic-fiber graphene field effect transistor biosensor for the detection of single-stranded DNA

Herein, a graphene field effect transistor (GFET) was constructed on an optic fiber end face to develop an integrated optical/electrical double read-out biosensor, which was used to detect target single-stranded DNA (tDNA). Two isolated Au electrodes were, respectively, prepared as the drain and source at the ends of an optic fiber and coated with a graphene film to construct a field effect transistor (FET). Probe aptamers modified with fluorophore 6'-carboxy-fluorescein (6'-FAM) were immobilized on the graphene for specific capture of tDNA. Graphene oxide (GO) was introduced to quench 6'-FAM and construct a fluorescence biosensor. Thus, a dual GFET and fluorescence biosensor was integrated on the end-face of an optic fiber. Following synchronous detection by fluorescence and FET methods, results showed satisfactory sensitivity for DNA detection. Compared with conventional biosensors using a single sensing technology, these dual sensing integrated biosensors significantly improved the reliability and accuracy of DNA detection. Furthermore, this proposed technique provides both a new biosensor for single-stranded DNA detection and a strategy for designing multi-sensing integrated biosensors.

Monodisperse functionalized GO for high-performance sensing and bioimaging of Cu2+ through synergistic enhancement effect

The metal ion fluorescence probes based on chemical reactions triggered by specific metal ions is characterized by high selectivity. However, they are also subject to inherent limitations, such as easy aggregation under water solution, poor optical stability, and long response time. In order to solve these problems, a simple and effective method was studied. The specific design is as follows. Fluorescence probe RACD is assembled onto a single layer graphene oxide (GO) via π-π interaction and hydrogen bonding to prepare RACD functionlized graphene oxide RACD/GO. The experimental results show that the resulting RACD/GO possesses very well monodispersion, hydrophilicity and photostability, particularly reduce the aggregation degree of RACD owing to π-π effect. Simultaneously, it was found that due to the strong synergy between GO and RACD, the response time, selectivity, anti-interference ability, detection sensitivity, detection limit and bioimaging ability of RACD/GO were significantly improved compared with RACD. The resulting RACD/GO not only possesses very well photostability, multiple repeated cycles, but also have been triumphantly put into the monitoring Cu²⁺ of environmental water, sewage, cells and zebrafish specimens in practice. The detection limit is as low as 1.76 nM, and the correlation coefficient is 0.9998.

A low-background fluorescent aptasensor for acetamiprid detection based on DNA three-way junction-formed G-quadruplexes and graphene oxide

A simple fluorescence detection platform has been established for acetamiprid assay based on DNA three-way junctions (TWJs), which can triple the fluorescence signal without any other amplification. It is designed with three single-stranded DNAs (ssDNA), each of which contains one-third or two-thirds of the G-quadruplex sequence at each end. Upon the addition of acetamiprid, the conformation of the aptamer-containing double-stranded DNA (dsDNA) changes from its original conformation and releases a strand of ssDNA. This ssDNA, with the other two ssDNAs, can assemble into DNA TWJs, and the three pairs of the branched ends of the DNA TWJs are adjacent to each other, allowing them to form three units of G-quadruplexes. Hence, the fluorescence of N-methyl mesoporphyrin IX (NMM) is lighted by the nascent G-quadruplexes. Graphene oxide (GO) is then added to minimize the detection background by absorbing the free NMM and non-target-induced ssDNA. The proposed strategy can assay acetamiprid in a wide linear range of 0-500 nM with a detection limit of 5.73 nM. More importantly, this assay platform demonstrates high potential for acetamiprid assay in food control and environmental monitoring.

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.

Nanobiosensors for the Detection of Novel Coronavirus 2019-nCoV and Other Pandemic/Epidemic Respiratory Viruses: A Review

The coronavirus disease 2019 (COVID-19) pandemic is considered a public health emergency of international concern. The 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused this pandemic has spread rapidly to over 200 countries, and has drastically affected public health and the economies of states at unprecedented levels. In this context, efforts around the world are focusing on solving this problem in several directions of research, by: (i) exploring the origin and evolution of the phylogeny of the SARS-CoV-2 viral genome; (ii) developing nanobiosensors that could be highly effective in detecting the new coronavirus; (iii) finding effective treatments for COVID-19; and (iv) working on vaccine development. In this paper, an overview of the progress made in the development of nanobiosensors for the detection of human coronaviruses (SARS-CoV, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV) is presented, along with specific techniques for modifying the surface of nanobiosensors. The newest detection methods of the influenza virus responsible for acute respiratory syndrome were compared with conventional methods, highlighting the newest trends in diagnostics, applications, and challenges of SARS-CoV-2 (COVID-19 causative virus) nanobiosensors.

Can graphene take part in the fight against COVID-19?

The pneumonia outbreak of coronavirus disease 2019 (COVID-19) represents a global issue. The bidimensional material graphene has captured much attention due to promising antimicrobial applications and has also demonstrated antiviral efficacy. In response to this global outbreak, we summarized the current state of knowledge of graphene and virus interaction as well as possible successful applications to fight COVID-19. Antibody-conjugated graphene sheets can rapidly detect targeted virus proteins and can be useful for large population screening, but also for the development of environmental sensors and filters, given the low cost of graphene materials. Functionalized graphene has demonstrated a good viral capture capacity that, combined with heat or light-mediated inactivation, could be used as a disinfectant. Graphene sensors arrays can be implemented on standard utility textiles and drug efficacy screening. Thanks to its high versatility, we foresee that graphene may have a leading role in the fight against COVID-19.

Can graphene take part in the fight against COVID-19?

The pneumonia outbreak of coronavirus disease 2019 (COVID-19) represents a global issue. The bidimensional material graphene has captured much attention due to promising antimicrobial applications and has also demonstrated antiviral efficacy. In response to this global outbreak, we summarized the current state of knowledge of graphene and virus interaction as well as possible successful applications to fight COVID-19. Antibody-conjugated graphene sheets can rapidly detect targeted virus proteins and can be useful for large population screening, but also for the development of environmental sensors and filters, given the low cost of graphene materials. Functionalized graphene has demonstrated a good viral capture capacity that, combined with heat or light-mediated inactivation, could be used as a disinfectant. Graphene sensors arrays can be implemented on standard utility textiles and drug efficacy screening. Thanks to its high versatility, we foresee that graphene may have a leading role in the fight against COVID-19.

Toward Nanotechnology-Enabled Approaches against the COVID-19 Pandemic

The COVID-19 outbreak has fueled a global demand for effective diagnosis and treatment as well as mitigation of the spread of infection, all through large-scale approaches such as specific alternative antiviral methods and classical disinfection protocols. Based on an abundance of engineered materials identifiable by their useful physicochemical properties through versatile chemical functionalization, nanotechnology offers a number of approaches to cope with this emergency. Here, through a multidisciplinary Perspective encompassing diverse fields such as virology, biology, medicine, engineering, chemistry, materials science, and computational science, we outline how nanotechnology-based strategies can support the fight against COVID-19, as well as infectious diseases in general, including future pandemics. Considering what we know so far about the life cycle of the virus, we envision key steps where nanotechnology could counter the disease. First, nanoparticles (NPs) can offer alternative methods to classical disinfection protocols used in healthcare settings, thanks to their intrinsic antipathogenic properties and/or their ability to inactivate viruses, bacteria, fungi, or yeasts either photothermally or via photocatalysis-induced reactive oxygen species (ROS) generation. Nanotechnology tools to inactivate SARS-CoV-2 in patients could also be explored. In this case, nanomaterials could be used to deliver drugs to the pulmonary system to inhibit interaction between angiotensin-converting enzyme 2 (ACE2) receptors and viral S protein. Moreover, the concept of "nanoimmunity by design" can help us to design materials for immune modulation, either stimulating or suppressing the immune response, which would find applications in the context of vaccine development for SARS-CoV-2 or in counteracting the cytokine storm, respectively. In addition to disease prevention and therapeutic potential, nanotechnology has important roles in diagnostics, with potential to support the development of simple, fast, and cost-effective nanotechnology-based assays to monitor the presence of SARS-CoV-2 and related biomarkers. In summary, nanotechnology is critical in counteracting COVID-19 and will be vital when preparing for future pandemics.

Toehold-regulated competitive assembly to accelerate the kinetics of graphene oxide-based biosensors

With effective adsorption and quenching efficiency, graphene oxide (GO) can be utilized for sensing biomolecules such as nucleic acids and proteins. In these assays, the fluorophore-labeled nucleic acid (reporter) is usually adsorbed by GO first, followed by adding the target molecules to bind the reporter, thus restoring the fluorescence signal. However, the kinetics of fluorescence recovery is usually very slow because the target is probably adsorbed by GO and compromises the binding of the target and the reporter. Herein, we proposed a toehold-regulated strand displacement strategy to accelerate the kinetics of GO-based biosensing. In this strategy, the toehold of the duplex mediated a competitive assembly with the aim of eliminating the adsorption of the target by GO, facilitating the binding of the target and the reporter. While the duplex with the toehold of the target-blocker DNA or reporter-blocker DNA was formed, the rigid structure of the duplex weakened the adsorption of the target by GO and enhanced the recognition of the target by the reporter. This strategy achieved up to 2.6-fold enhancement in fluorescence signal restoration for nucleic acid detection, while there was 3.2-fold enhancement in fluorescence signal restoration for thrombin detection. It has also been demonstrated that this strategy can be used for the determination of DNA and thrombin in diluted serum with excellent specificity.

A fluorescence/colorimetric dual-mode sensing strategy for miRNA based on graphene oxide

MicroRNAs (miRNAs) are small non-coding RNAs, which are involved in RNA silencing and post-transcriptional regulation of gene expression. Numerous studies have determined the expression of certain miRNAs in specific tissues and cell types, and their aberrant expression is associated with a variety of serious diseases such as cancers, immune-related diseases, and many infectious diseases. This suggests that miRNAs may be attractive and promising non-invasive biomarkers of diseases. In this study, we established a graphene oxide (GO)-based fluorescence/colorimetric dual sensing platform for miRNA by using a newly designed probe. The probe was designed to form a hairpin-like configuration with a fluorescent dye-labeled long tail, possessing a guanine (G)-rich DNAzyme domain in the loop region and target binding domain over the stem region and tail. By introducing this new hairpin-like probe in a conventional GO-based fluorescence platform, we observed both the miRNA-responsive color change by direct observation and sensitive fluorescence increase even below the nanomolar levels in a single solution without an additional separation step.

Graphene Oxide-Based Suppression of Nonspecificity in Loop-Mediated Isothermal Amplification Enabling the Sensitive Detection of Cyclooxygenase-2 mRNA in Colorectal Cancer

Cyclooxygenase-2 (COX2) mRNA represents a key biomarker for identifying subjects with colorectal cancer (CRC), while there is still no rapid and sensitive detection method for COX2 mRNA. Loop-mediated isothermal amplification (LAMP) is extensively developed for the amplification of nucleic acids; however, its application is frequently hindered by serious nonspecific amplification. Herein, this work reported a graphene oxide (GO)-based LAMP method to enable the one-step detection of COX2 mRNA in cancer cells and serum samples. We found that GO greatly enhanced the specificity of LAMP through decreasing nonspecific hybridization and the fluorescence background signal because of the simultaneous adsorption of single-stranded primers and DNA staining dyes on GO. The detection limit of developed GO-based LAMP was 2 orders of magnitude more sensitive compared to that of classical LAMP. Then a GO-based reverse transcription (RT)-LAMP strategy was further developed and applied to detect COX2 mRNA in CRC cancer cells and serum samples with high specificity. The GO-based LAMP platform with advantages of low cost, simplicity, high specificity, and sensitivity holds considerable potential for real-time fluorescence monitoring of nucleic acid amplification in a wide range of fields.

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations

The integration of nucleic acids with nanomaterials has attracted great attention from various research communities in search of new nanoscale tools for a range of applications, from electronics to biomedical uses. MXenes are a new class of multielement 2D materials baring exciting properties mostly directed to energy-related fields. These advanced materials are now beginning to enter the biomedical field given their biocompatibility, hydrophilicity and near-infrared absorption. Herein, we elucidate the interaction of MXene Ti3C2T x with fluorophore-tagged DNA by fluorescence measurements and molecular dynamics simulations. The system showed potential for biosensing with unequivocal detection at picomole levels and single-base discrimination. We found that this material possesses a kinetically unique entrapment/release behavior, with potential implications in time-controlled biomolecule delivery. Our findings present MXenes as platforms for binding nucleic acids, contributing to their potential for hybridization-based biosensing and related bio-applications.

Fluorescent DNA Biosensor for Single-Base Mismatch Detection Assisted by Cationic Comb-Type Copolymer

Simple and rapid detection of DNA single base mismatch or point mutation is of great significance for the diagnosis, treatment, and detection of single nucleotide polymorphism (SNP) in genetic diseases. Homogeneous mutation assays with fast hybridization kinetics and amplified discrimination signals facilitate the automatic detection. Herein we report a quick and cost-effective assay for SNP analysis with a fluorescent single-labeled DNA probe. This convenient strategy is based on the efficient quenching effect and the preferential binding of graphene oxide (GO) to ssDNA over dsDNA. Further, a cationic comb-type copolymer (CCC), poly(l-lysine)-graft-dextran (PLL-g-Dex), significantly accelerates DNA hybridization and strand-exchange reaction, amplifying the effective distinction of the kinetic barrier between a perfect matched DNA and a mismatched DNA. Moreover, in vitro experiments indicate that RAW 264.7 cells cultured on PLL-g-Dex exhibits excellent survival and proliferation ability, which makes this mismatch detection strategy highly sensitive and practical.

Differential neural cell adhesion and neurite outgrowth on carbon nanotube and graphene reinforced polymeric scaffolds

Carbon nanomaterials, such as graphene nanoplatelets (GNPs) and multiwalled carbon nanotubes (MWCNTs) are potential candidates in a large number of biomedical applications. The present study investigates the effect of the difference in morphology of these materials on neural cell regeneration on a biodegradable scaffold. Electrical conductivities of all the hybrid scaffolds are found to be in between that of MWCNT/chitosan scaffold (highest-conductivity) and GNP/chitosan scaffold (lowest-conductivity). While, hybrid scaffolds show improvement in elastic modulus and ultimate tensile strength over MWCNT/chitosan and GNP/chitosan scaffolds. The protein adsorption isotherms of bovine serum albumin (BSA) show greater equilibrium constant (Keq) on GNP/chitosan composites as compared to MWCNT/chitosan composites, proving more potential for cell adhesion in the former. Interactions of HT-22 hippocampal neurons with MWCNT/chitosan, GNP/chitosan and various MWCNT/GNP hybrid chitosan matrices prove cytocompatibility. The neurons acquire elongated geometry on the MWCNT/chitosan scaffold, while GNP reinforcement drives the neurons to spread cellular processes radially.

Development of a single-step immunoassay microdevice based on a graphene oxide-containing hydrogel possessing fluorescence quenching and size separation functions

An immunoassay, which is an indispensable analytical method both in biological research and in medical fields was successfully integrated into a "single-step" by developing a microdevice composed of a graphene oxide (GO)-containing hydrogel and a poly (dimethylsiloxane) (PDMS) microchannel array with a polyethylene glycol (PEG) coating containing a fluorescently-labelled antibody. Here we used 2-hydroxyethylmethacrylate (HEMA) as a monomer that is easily, and homogeneously, mixed with GO to synthesize the hydrogel. The fluorescence quenching and size separation functions were then optimized by controlling the ratios of HEMA and GO. Free fluorescently-labelled antibody was successfully separated from the immunoreaction mixture by the hydrogel network structure, and the fluorescence was subsequently quenched by GO. In comparison to the previously reported immunoassay system using GO, the present system achieved a very high fluorescence resonance energy transfer (FRET) efficiency (∼90%), due to the use of direct adsorption of the fluorescently-labelled antibody to the GO surface; in contrast, the former reported method relied on indirect adsorption of the fluorescently-labelled antibody via immunocomplex formation at the GO surface. Finally, the single-step immunoassay microdevice was made by combining the developed hydrogel and the PDMS microchannel with a coating containing the fluorescently-labelled antibody, and successfully applied for the single-step analysis of IgM levels in diluted human serum by simple introduction of the sample via capillary action.

Polyhydroxybutyrate-co-hydroxyvalerate copolymer modified graphite oxide based 3D scaffold for tissue engineering application

In this study, we have fabricated the PHBV functionalized graphite oxide using freeze drying technique, followed by 'in situ' pay loading of Fe₃O₄ nanoparticles onto the hydrophobic plate of the composite basal plane; thereby, mechanically and thermally stable, bio-imaging Fe₃O₄/GO-g-PHBV composites have been developed. The synthesis of Fe₃O₄/GO-g-PHBV composite was confirmed by field emission SEM and TEM analyses, X-ray diffraction and Fourier transform infrared spectroscopy. The wrapping of PHBV copolymer into the graphene layers was investigated by atomic force microscopy and Raman spectral analyses which provided the shifting of the 2D band with low signal intensity in the range of 2600-3000 cm^-1. The bactericidal activities of the Fe₃O₄/GO-g-PHBV composite films were found to exhibit more efficiency against Gram-negative bacteria strains compared to Gram-positive strains. In vibrating sample magnetometer (VSM) analysis, the zero value of coercivity revealed the super-paramagnetic nature of the Fe₃O₄/GO-g-PHBV composites. The Phantom agar magnetic resonance imaging analysis revealed the efficiency of Fe₃O₄ nanoparticles as a negative contrast (T₂ contrast) along with higher relaxivity value. The significant fibroblast cell (NIH 3T3) adhesion and proliferation (85%) on the Fe₃O₄/GO-g-PHBV composite surface indicated the physiological and biocompatible stability of that composite along with the presence of large π conjugated aromatic domain.

Fast and single-step immunoassay based on fluorescence quenching within a square glass capillary immobilizing graphene oxide-antibody conjugate and fluorescently labelled antibody

A single-step, easy-to-use, and fast capillary-type immunoassay device composed of a polyethylene glycol (PEG) coating containing two kinds of antibody-reagents, including an antibody-graphene oxide conjugate and fluorescently labelled antibody, was developed in this study. The working principle involved the spontaneous dissolution of the PEG coating, diffusion of reagents, and subsequent immunoreaction, triggered by the capillary action-mediated introduction of a sample solution. In a sample solution containing the target antigen, two types of antibody reagents form a sandwich-type antigen-antibody complex and fluorescence quenching takes place via fluorescence resonance energy transfer between the labelled fluorescent molecules and graphene oxide. Antigen concentration can be measured based on the decrease in fluorescence intensity. An antigen concentration-dependent response was obtained for the model target protein sample (human IgG, 0.2-10 μg mL(-1)). The present method can shorten the reaction time to within 1 min (approximately 40 s), while conventional methods using the same reagents require reaction times of approximately 20 min because of the large reaction scale. The proposed method is one of the fastest immunoassays ever reported. Finally, the present device was used to measure human IgG in diluted serum samples to demonstrate that this method can be used for fast medical diagnosis.

Graphene and Graphene-Based Nanomaterials for DNA Detection: A Review

DNA detection with high sensitivity and specificity has tremendous potential as molecular diagnostic agents. Graphene and graphene-based nanomaterials, such as graphene nanopore, graphene nanoribbon, graphene oxide, and reduced graphene oxide, graphene-nanoparticle composites, were demonstrated to have unique properties, which have attracted increasing interest towards the application of DNA detection with improved performance. This article comprehensively reviews the most recent trends in DNA detection based on graphene and graphene-related nanomaterials. Based on the current understanding, this review attempts to identify the future directions in which the field is likely to thrive, and stimulate more significant research in this subject.

Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA

Much remains to be understood about the kinetics and thermodynamics of DNA helicase binding and activity. Here, we utilize probe-modified DNA monolayers on multiplexed gold electrodes as a sensitive recognition element and morphologically responsive transducer of helicase-DNA interactions. The electrochemical signals from these devices are highly sensitive to structural distortion of the DNA produced by the helicases. We used this DNA electrochemistry to distinguish the details of the DNA interactions of three distinct XPB helicases, which belong to the superfamily-2 of helicases. Clear changes in DNA melting temperature and duplex stability were observed upon helicase binding, shifts that could not be observed with conventional UV-visible absorption measurements. Binding dissociation constants were estimated in the range from 10 to 50 nM and correlated with observations of activity. ATP-stimulated DNA unwinding activity was also followed, revealing exponential time scales and distinct time constants associated with conventional and molecular wrench modes of operation further confirmed by crystal structures. These devices thus provide a sensitive measure of the structural thermodynamics and kinetics of helicase-DNA interactions.

Study of Fluorescence Quenching Ability of Graphene Oxide with a Layer of Rigid and Tunable Silica Spacer

The fluorescence quenching property of graphene oxide (GO) has been newly demonstrated and applied for fluorescence imaging and biosensing. In this work, a new nanostructure was designed for effectively studying the quenching ability of GO. The key element in this design is the fabrication of a layer of rigid and thickness adjustable silica spacer for manipulating the distance between the GO and fluorophores. First, a silica core modified with organic dye molecules was prepared, followed by the formation of a silica shell with a tunable thickness. Afterward, the GO was wrapped around silica nanoparticles based on the electrostatic interaction between the negatively charged GO and positively charged silica. The quenching efficiency of GO to different dye molecules was studied at various spacer thicknesses and varying concentrations of GO. Fluorescence lifetime of fluorophores was measured to determine the quenching mechanism. We found that the quenching efficiency of GO was still around 30% when the distance between dyes and GO was increased to more than 30 nm, which indicated the long-distance quenching ability of GO and confirmed the previous theoretical calculation. The quenching mechanisms were proposed schematically based on our experimental results. We expected that the proposed nanostructure could act as a feasible model for studying GO quenching property and shed light on designing GO-based fluorescence sensing systems.

A turn-on fluorescent sensor for Hg2+ detection based on graphene oxide and DNA aptamers

Hg²⁺-Induced conformational change of DNA aptamers can cause the release of AO from GO surface, which leads to fluorescence recovery.

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.

The interfacing structural effect of Ag/graphene oxide nanohybrid films on surface enhanced Raman scattering

The interfacing structural effect of Ag/graphene oxide (GO) nanohybrid films on SERS was investigated by using Ag nanostructures immobilized on polyallylamine hydrochloride (PAA) functionalized-GO and reduced GO (RGO) films. We found that the electron transfer from Ag nanostructures to GO derivatives dominantly occurred at the interfaces between Ag nanostructures and the sp² carbon domains of GO and RGO films. By utilizing 4-aminothiophenol (4-ATP) as a Raman probe, it was revealed that this electron transfer process augmented the enhancement factor (EF) of 4-ATP up to ∼1.8 fold on Ag/PAA-RGO nanohybrid films compared to Ag/PAA-GO nanohybrid films with the increasing interfacing area between Ag nanostructures and the sp² carbon domains of GO derivatives through wet-chemical processes.

Biofunctionalized 3-D Carbon Nano-Network Platform for Enhanced Fibroblast Cell Adhesion

Carbon nanomaterials have been investigated for various biomedical applications. In most cases, however, these nanomaterials must be functionalized biologically or chemically due to their biological inertness or possible cytotoxicity. Here, we report the development of a new carbon nanomaterial with a bioactive phase that significantly promotes cell adhesion. We synthesize the bioactive phase by introducing self-assembled nanotopography and altered nano-chemistry to graphite substrates using ultrafast laser. To the best of our knowledge, this is the first time that such a cytophilic bio-carbon is developed in a single step without requiring subsequent biological/chemical treatments. By controlling the nano-network concentration and chemistry, we develop platforms with different degrees of cell cytophilicity. We study quantitatively and qualitatively the cell response to nano-network platforms with NIH-3T3 fibroblasts. The findings from the in vitro study indicate that the platforms possess excellent biocompatibility and promote cell adhesion considerably. The study of the cell morphology shows a healthy attachment of cells with a well-spread shape, overextended actin filaments, and morphological symmetry, which is indicative of a high cellular interaction with the nano-network. The developed nanomaterial possesses great biocompatibility and considerably stimulates cell adhesion and subsequent cell proliferation, thus offering a promising path toward engineering various biomedical devices.

Single-probe multistate detection of DNA via aggregation-induced emission on a graphene oxide platform

Graphene and graphene oxides (GO), or their reduced forms, have been introduced in a variety of biosensing platforms and have exhibited enhanced performance levels in these forms. We herein report a DNA sensing platform consisting of aggregation-induced emission (AIE) molecules and complementary DNA (comDNA) adsorbed on GO. We experimentally turned the AIE molecule on and off by adjusting its distance, which correlates with DNA structures as shown in our computational results, from the GO sheet, which quenches depending on its distance from the graphene plane. The changes in florescence are reproducible, which demonstrates the probe's ability to identify the binding state of the DNA. Our molecular dynamics simulation results reveal strong π-π interactions between single-strand DNA (ssDNA) and GO, which enable the ssDNA molecule to move closer to the graphene oxide. This reduces the center of mass and binding free energies in the simulation. When hybridized with comDNA, the increased distance, evidenced by the reduced interaction, eliminates the quenching effect and turns on the AIE molecule. Our protocol use of the AIE molecule as a probe thus avoids the complicated steps involved in covalent functionalization and allows the rapid and label-free detection of DNA molecules.

STATEMENT OF SIGNIFICANCE

A simple, rapid method of fluorescent measurement of DNA hybridization in the presence of graphene (oxide) is presented. Conventional fluorescent dyes offer high performance in biosensors. However, labeling procedures are synthetically demanding in time and resources making it less cost-effective. Molecules with aggregation-induced-emission (AIE) property have advantages over traditional fluorescent molecules because of their intrinsic preference for detection as a turn-on probe and their single-molecule detection ability. Previous work has shown AIE dyes act as excellent "label-free" bioprobes with high sensitivity but with limited selectivity. Graphene oxide (GO) with its unique optical properties and affinity to different kinds of biomolecules can be used as an auxiliary to enhance selectivity of AIE dyes. In this work, we report a label-free strategy to detect DNA of particular sequence by water-soluble AIE probes with the aid of GO, supported by the computational explanations for this phenomenon.

A new two-mode fluorescence signal amplification strategy for protease activity assay based on graphene oxide

A new graphene oxide-based two-mode fluorescence signal amplification strategy for the detection of protease activity has been established.

A graphene oxide-based tool-kit capable of characterizing and classifying exonuclease activities

Exonuclease kinetics and classification assay by graphene oxide-based fluorometric quenching.

Comparison of Graphene Oxide and Reduced Graphene Oxide for DNA Adsorption and Sensing

Fluorescently labeled DNA adsorbed on graphene oxide (GO) is a well-established sensing platform for detecting a diverse range of analytes. GO is a loosely defined material and its oxygen content may vary depending on the condition of preparation. Sometimes, a further reduction step is intentionally performed to decrease the oxygen content, and the resulting material is called reduced GO (rGO). In this study, DNA adsorption and desorption from GO and rGO is systematically compared. Under the same salt concentration, DNA adsorbs slightly faster with a 2.6-fold higher capacity on rGO. At the same time, DNA adsorbed on rGO is more resistant to desorption induced by temperature, pH, urea, and organic solvents. Various lengths and sequences of DNA probes have been tested. When its complementary DNA is added as a model target analyte, the rGO sample has a higher signal-to-background and signal-to-noise ratio, whereas the GO sample has a slightly higher absolute signal increase and faster signaling kinetics. DNAs adsorbed on GO or rGO are still susceptible to nonspecific displacement by other DNA and proteins. Overall, although rGO adsorbs DNA more tightly, it allows efficient DNA sensing with an extremely low background fluorescence signal.

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.

Biosensors based on graphene oxide and its biomedical application

Graphene oxide (GO) is one of the most attributed materials for opening new possibilities in the development of next generation biosensors. Due to the coexistence of hydrophobic domain from pristine graphite structure and hydrophilic oxygen containing functional groups, GO exhibits good water dispersibility, biocompatibility, and high affinity for specific biomolecules as well as properties of graphene itself partly depending on preparation methods. These properties of GO provided a lot of opportunities for the development of novel biological sensing platforms, including biosensors based on fluorescence resonance energy transfer (FRET), laser desorption/ionization mass spectrometry (LDI-MS), surface-enhanced Raman spectroscopy (SERS), and electrochemical detection. In this review, we classify GO-based biological sensors developed so far by their signal generation strategy and provide the comprehensive overview of them. In addition, we offer insights into how the GO attributed in each sensor system and how they improved the sensing performance.

A self-assembling RNA aptamer-based graphene oxide sensor for the turn-on detection of theophylline in serum

To date, few effective fluorescent biosensors based on RNA aptamers have been developed because the intrinsic instability of RNA in the presence of nucleases precludes the application of RNA aptamers for the analysis of biological fluids. In this study, we developed a simple, sensitive, selective turn-on fluorescent aptasensor for theophylline detection in serum, utilizing ligand-induced self-assembling RNA aptamers and two different interaction stages of the aptamer fragments with graphene oxide (GO). A single strand of the theophylline RNA aptamer (33-mer) was split at the end loop region into two shorter fragments, one of which was labeled with a fluorophore (FAM). In the absence of theophylline, the adsorption of the two individual fragments on GO brought the fluorophore in close proximity to the GO surface, resulting in highly efficient quenching of fluorescence. The system showed very low background fluorescence. Conversely, the fragments self-assembled into an RNA aptamer/theophylline complex and were dissociated from GO. The quenched fluorescence was significantly recovered, and theophylline could be detected at a wide range of concentrations from 1 to 100μM, with a detection limit of 0.155μM and good selectivity in serum. Moreover, because of the shorter RNA fragments and the effective protection ability of GO from nuclease cleavage, the RNA sequences remained stable during the experiments. This design may serve as an example for the application of RNA aptasensors in the clinical setting.

On-chip FRET Graphene Oxide Aptasensor: Quantitative Evaluation of Enhanced Sensitivity by Aptamer with a Double-stranded DNA Spacer

We propose a molecular design for a biomolecular probe to realize an on-chip graphene oxide (GO) aptasensor with enhanced sensitivity. Here, GO works as an excellent acceptor for fluorescence resonance energy transfer. We inserted a rigid double-stranded DNA as a spacer between the GO surface and the aptamer sequence to extend the distance between a fluorescence dye and the GO surface during molecular recognition. We examined the dependence of the sensitivity on the length of the spacer quantitatively by using a 2×2 linear-array aptasensor. We used the modified aptamer with 10 and 30 base pair (bp) double-stranded DNA spacers. The signal with a 30bp-spacer was about twice as strong that with a 10bp-spacer as regards both thrombin and prostate specific antigen detections. The improvement in the sensitivity was supported by a model calculation that estimated the effect of spacer length on fluorescence recovery efficiency.

Exonuclease III-assisted graphene oxide amplified fluorescence anisotropy strategy for ricin detection

Graphene oxide (GO) is an excellent fluorescence anisotropy (FA) amplifier. However, in the conventional GO amplified FA strategy, one target can only induce the FA change of one fluorophore on probe, which limits the detection sensitivity. Herein, we developed an exonuclease III (Exo III) aided GO amplified FA strategy by using aptamer as an recognition element and ricin B-chain as a proof-of-concept target. The aptamer was hybridized with a blocker sequence and linked onto the surface of magnetic beads (MBs). Upon the addition of ricin B-chain, blocker was released from the surface of MBs and hybridized with the dye-modified probe DNA on the surface of GO through the toehold-mediated strand exchange reaction. The formed blocker-probe DNA duplex triggered the Exo III-assisted cyclic signal amplification by repeating the hybridization and digestion of probe DNA, liberating the fluorophore with several nucleotides (low FA value). Thus, ricin B-chain could be sensitively detected by the significantly decreased FA. The linear range was from 1.0μg/mL to 13.3μg/mL and the limit of detection (LOD) was 400ng/mL. This method improved the sensitivity of FA assay and it could be generalized to any kind of target detection based on the use of an appropriate aptamer.

A biosensor for the detection of single base mismatches in microRNA

Graphene oxide quenches fluorescence corresponding to only a mismatched target due to selective denaturing of the thermo-unstable duplex composed of probe peptide nucleic acid and single base mismatched target RNA and thus, the fluorescence signal only from perfectly matched target RNA is measured.