Highly tunable aptasensing microarrays with graphene oxide multilayers

Enhanced Probe Bonding and Fluorescence Properties through Annealed Graphene Oxide Nanosheets

Graphene oxide (GO) has been widely used in biological sensing studies because of its excellent physical and chemical properties. In particular, the rich functional groups on the surface of GO can effectively enhance the bonding of biomolecules and serve as an efficient sensing substrate. However, when biomolecules are labeled with fluorescence, the GO interface affects the biomolecules by reducing the fluorescence properties and limiting their applications in biosensing. Here, we establish an annealed GO (aGO) substrate through the annealing process, which can effectively increase the bonding amount of a DNA probe because of the accumulation of oxygen atoms on the surface without significantly damaging the nanosheet structure. Furthermore, we prove that the aGO substrate can effectively maintain its fluorescence performance and stability by exposing more graphic domains. Overall, this study successfully verifies that GO's interface annealing modification can be used as an alternative innovative interface application in biosensing.

Layer-by-Layer Assembly: Recent Progress from Layered Assemblies to Layered Nanoarchitectonics

As an emerging concept for the development of new materials with nanoscale features, nanoarchitectonics has received significant recent attention. Among the various approaches that have been developed in this area, the fixed-direction construction of functional materials, such as layered fabrication, offers a helpful starting point to demonstrate the huge potential of nanoarchitectonics. In particular, the combination of nanoarchitectonics with layer-by-layer (LbL) assembly and a large degree of freedom in component availability and technical applicability would offer significant benefits to the fabrication of functional materials. In this Minireview, recent progress in LbL assembly is briefly summarized. After introducing the basics of LbL assembly, recent advances in LbL research are discussed, categorized according to physical, chemical, and biological innovations, along with the fabrication of hierarchical structures. Examples of LbL assemblies with graphene oxide are also described to demonstrate the broad applicability of LbL assembly, even with a fixed material.

Specific detection of avian influenza H5N2 whole virus particles on lateral flow strips using a pair of sandwich-type aptamers

We report a selection of a cognate pair of aptamers for whole avian influenza virus particles of H5N2 by using graphene-oxide based systemic evolution of ligands by exponential enrichment (GO-SELEX), and the application of a pair of sandwich-type binding aptamers on the lateral flow strips. The aptamers were characterized by GO-FRET assay, and Kd values of the selected aptamers were estimated to be from 6.913 × 10⁵ to 1.27 × 10⁶ EID₅₀/ml (EID₅₀/ml: 50% egg infective dose). Based on the evidence from confocal laser scanning microscope (CLSM), surface plasmon resonance (SPR), and circular dichroism (CD) spectrum analysis, the aptamers, J₃APT and JH₄APT, were found to be working as a cognate pair that binds to the target virus at the different sites simultaneously. This cognate pair of aptamers then was successfully applied on the lateral flow strips, clearly showing sandwich-type binding images with the presence of the certain numbers of H5N2 virus particles. On the newly developed lateral flow strips, the target virus was detectable down to 6 × 10⁵ EID₅₀/ml in the buffer and 1.2 × 10⁶ EID₅₀/ml in the duck's feces, respectively, by the naked eye. By using the ImageJ software, the LOD was found to be 1.27 × 10⁵ EID₅₀/ml in the buffer and 2.09 × 10⁵ EID₅₀/ml in the duck's feces, respectively. Interestingly, on the lateral flow strips, enhanced specificity towards the target virus (H5N2) appeared over other subtypes of H5Nx. To the best of our knowledge, this is the first report about the application of the cognate pair of aptamers for the detection of influenza virus on the lateral flow strips. This study shows the promising perspective of a cognate pair of aptamers for the on-site detection system which could be useful for rapid detection of avian influenza viruses for preventing the pandemic influenza viruses from spreading.

Luminescence-Based Optical Sensors Fabricated by Means of the Layer-by-Layer Nano-Assembly Technique

Luminescence-based sensing applications range from agriculture to biology, including medicine and environmental care, which indicates the importance of this technique as a detection tool. Luminescent optical sensors are required to be highly stable, sensitive, and selective, three crucial features that can be achieved by fabricating them by means of the layer-by-layer nano-assembly technique. This method permits us to tailor the sensors' properties at the nanometer scale, avoiding luminophore aggregation and, hence, self-quenching, promoting the diffusion of the target analytes, and building a barrier against the undesired molecules. These characteristics give rise to the fabrication of custom-made sensors for each particular application.

Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays

In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with K_ds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.

A Graphene Oxide-Based Sensing Platform for the Determination of Methicillin-Resistant Staphylococcus aureus Based on Strand-Displacement Polymerization Recycling and Synchronous Fluorescent Signal Amplification

To develop new technology for detecting methicillin-resistant Staphylococcus aureus (MRSA), a novel fluorescent biosensor based on Klenow fragment (KF)-assisted target recycling amplification and synchronous fluorescence analysis was created. Carboxy-fluorescein (FAM)-labeled single-stranded DNA (ssDNA) containing a capture probe and a signal probe was adsorbed onto the surface of graphene oxide (GO) via π-stacking interactions, resulting in the fluorescence quenching of the dye. When target and primer were introduced, the fluorescence was restored due to P0 being completely released from the surface of the GO. Meanwhile, by using the KF and exploiting the synergistic effect of FAM and the double-stranded DNA (dsDNA)-SYBR Green I duplex structure, the fluorescence in this detection system was considerably amplified and the sensitivity was improved. The proposed strategy for mecA gene analysis showed a good linear range from 1 to 40 nmol/L, with a lower limit of detection of 0.5 nmol/L. In addition, a bacterial sample harboring the mecA gene was also detected, and its lower detection limit was up to 300 colony-forming units (CFU)/mL. Accordingly, this biosensor exhibits high sensitivity and selectivity and has great potential for early clinical diagnosis and treatment.

Photoluminescence Architectures for Disease Diagnosis: From Graphene to Thin-Layer Transition Metal Dichalcogenides and Oxides

Ever since the discovery of graphene, increasing efforts have been devoted to the use of this stellar material as well as the development of other graphene-like materials such as thin-layer transition metal dichalcogenides and oxides (TMD/Os) for a variety of applications. Because of their large surface area and unique optical properties, these two-dimensional materials with a size ranging from the micro- to the nanoscale have been employed as the substrate to construct photoluminescence architectures for disease diagnosis as well as theranostics. These architectures are built through the simple self-assembly of labeled biomolecular probes with the substrate material, leading to signal quenching. Upon the specific interaction of the architecture with a target biomarker, the signal can be spontaneously restored in a reversible manner. Meanwhile, by co-loading therapeutic agents and employing the inherent photo-thermal properties of the material substrates, a combined disease imaging and therapy (theranostics) can be achieved. This review highlights the latest advances in the construction and application of graphene and TMD/O based thin-layer material composites for single-target and multiplexed detection of a variety of biomarkers and theranostics. These versatile material architectures, owing to their ease in preparation, low cost and flexibility in functionalization, provide promising tools for both basic biochemical research and clinical applications.

Immunosensing procedures for carcinoembryonic antigen using graphene and nanocomposites

Two-dimensional (2D) graphene, sp²-hybridized carbon, and its two major derivatives, graphene oxide (GO) and reduced graphene oxide (rGO) have played an important role in immunoassays (IAs) and immunosensing (IMS) platforms for the detection of carcinoembryonic antigen (CEA), an implicated tumor biomarker found in several types of cancer. The graphene family with high surface area is functionalized to form stable nanocomposites with gold nanoparticles (AuNPs) and electron mediators. The capture anti-CEA antibody (Ab) with high density can be anchored on AuNPs of such composites to provide remarkable detection sensitivity, significantly below the level found in normal subjects and cancer patients. Electrochemical and fluorescence/chemiluminescence-quenching properties of graphene-based nanocomposites are exploited in various detection schemes. Future endeavors are envisioned for the development of an array platform with high-throughput for CEA together with other tumor biomarkers and C-reactive protein, a universal biomarker for infection and inflammation. The ongoing efforts dedicated to the replacement of a lab-based detector by a cellphone with smart applications will further enable cost-effective and frequent monitoring of CEA in order to establish its clinical relevance and provide tools for real-time monitoring of patients during chemotherapy.

Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices

In this study we have reported our efforts to address some of the challenges in the detection of miRNAs using water-soluble graphene oxide and DNA nanoassemblies. Purposefully inserting mismatches at specific positions in our DNA (probe) strands shows increasing specificity against our target miRNA, miR-10b, over miR-10a which varies by only a single nucleotide. This increased specificity came at a loss of signal intensity within the system, but we demonstrated that this could be addressed with the use of DNase I, an endonuclease capable of cleaving the DNA strands of the RNA/DNA heteroduplex and recycling the RNA target to hybridize to another probe strand. As we previously demonstrated, this enzymatic signal also comes with an inherent activity of the enzyme on the surface-adsorbed probe strands. To remove this activity of DNase I and the steady nonspecific increase in the fluorescence signal without compromising the recovered signal, we attached a thermoresponsive PEGMA polymer (poly(ethylene glycol) methyl ether methacrylate) to nGO. This smart polymer is able to shield the probes adsorbed on the nGO surface from the DNase I activity and is capable of tuning the detection capacity of the nGO nanoassembly with a thermoswitch at 39 °C. By utilizing probes with multiple mismatches, DNase I cleavage of the DNA probe strands, and the attachment of PEGMA polymers to graphene oxide to block undesired DNase I activity, we were able to detect miR-10b from liquid biopsy mimics and breast cancer cell lines. Overall we have reported our efforts to improve the specificity, increase the sensitivity, and eliminate the undesired enzymatic activity of DNase I on surface-adsorbed probes for miR-10b detection using water-soluble graphene nanodevices. Even though we have demonstrated only the discrimination of miR-10b from miR-10a, our approach can be extended to other short RNA molecules which differ by a single nucleotide.

Current approaches in SELEX: An update to aptamer selection technology

Systematic evolution of ligands by exponential enrichment (SELEX) is a well-established and efficient technology for the generation of oligonucleotides with a high target affinity. These SELEX-derived single stranded DNA and RNA molecules, called aptamers, were selected against various targets, such as proteins, cells, microorganisms, chemical compounds etc. They have a great potential in the use as novel antibodies, in cancer theragnostics and in biomedical research. Vast interest in aptamers stimulated continuous development of SELEX, which underwent numerous modifications since its first application in 1990. Novel modifications made the selection process more efficient, cost-effective and significantly less time-consuming. This article brings a comprehensive and up-to-date review of recent advances in SELEX methods and pinpoints advantages, main obstacles and limitations. The post-SELEX strategies and examples of application are also briefly outlined in this review.

Recent advances in aptasensors based on graphene and graphene-like nanomaterials

Graphene and graphene-like two-dimensional nanomaterials have aroused tremendous research interest in recent years due to their unique electronic, optical, and mechanical properties associated with their planar structure. Aptamers have exhibited many advantages as molecular recognition elements for sensing devices compared to traditional antibodies. The marriage of two-dimensional nanomaterials and aptamers has emerged many ingenious aptasensing strategies for applications in the fields of clinical diagnosis and food safety. This review highlights current advances in the development and application of two-dimensional nanomaterials-based aptasensors with the focus on two main signal-transducing mechanisms, i.e. electrochemical and optical. A special attention is paid to graphene, a one-atom thick layer of graphite with exceptional properties, representing a fastgrowing field of research. In view of the unique properties of two-dimensional nanostructures and their inherent advantages of synthetic aptamers, we expect that high-performance two-dimensional nanomaterials-based aptasensing devices will find extensive applications in environmental monitoring, biomedical diagnostics, and food safety.

Simultaneous detection of circulating oncomiRs from body fluids for prostate cancer staging using nanographene oxide

Circulating oncomiRs are highly stable diagnostic, prognostic, and therapeutic tumor biomarkers, which can reflect the status of the disease and response to cancer therapy. miR-141 is an oncomiR, which is overexpressed in advanced prostate cancer patients, whereas its expression is at the normal levels in the early stages of the disease. On the other hand, miR-21 is significantly elevated in the early stage, but not in the advanced prostate cancer. Here, we have demonstrated simultaneous detection of exogenous miR-21 and miR-141 from human body fluids including blood, urine and saliva using nanographene oxide. Our system enables us to specifically and reliably detect each oncomiR at different fluorescence emission channels from a large population of RNAs extracted from body fluids. We were also able to determine the content and the ratio of the miR-21 and miR-141 in 10 different miRNA cocktails composed of various, but unknown, concentrations of both oncomiRs. A strong agreement (around 90%) between the experimental results and the actual miRNA compositions was observed. Moreover, we have demonstrated that overexpressed miR-21 or miR-141 increases the fluorescence only at their signature wavelengths of 520 and 670 nm, respectively. The approach in this study combines two emerging fields of nanographene in biomedicine and the role of circulating miRNAs in cancer. Our strategy has the potential to address the current challenges in diagnosis, prognosis and staging of prostate cancer with a non- or minimally invasive approach.