Rapid, Sensitive, and Label-Free Impedimetric Detection of a Single-Nucleotide Polymorphism Correlated to Kidney Disease

Molybdenum disulfide (MoS2) nanoflakes as inherently electroactive labels for DNA hybridization detection

The detection of specific DNA sequences plays a critical role in the areas of medical diagnostics, environmental monitoring, drug discovery and food safety. This has therefore become a strong driving force behind the ever-increasing demand for simple, cost-effective, highly sensitive and selective DNA biosensors. In this study, we report for the first time, a novel approach for the utilization of molybdenum disulfide nanoflakes, a member of the transition metal dichalcogenides family, in the detection of DNA hybridization. Herein, molybdenum disulfide nanoflakes serve as inherently electroactive labels, with the inherent oxidation peak exploited as the analytical signal. The principle of detection is based on the differential affinity of molybdenum disulfide nanoflakes towards single-stranded DNA and double-stranded DNA. The employment of transition metal dichalcogenide nanomaterials for sensing and biosensing purposes represents an upcoming research area which holds great promise. Hence, our findings are anticipated to have significant contributions towards the fabrication of future DNA biosensors.

An insight into the hybridization mechanism of hairpin DNA physically immobilized on chemically modified graphenes

There is an emerging interest in developing electrochemical DNA biosensors which rely on label-free protocols for the detection of DNA hybridization and polymorphism. Lately, many of them have been using DNA probes which were physically adsorbed onto different graphene platforms. In these works, the biorecognition event is monitored by electrochemical impedance spectroscopy and the detection mechanism proposed needs verification by orthogonal methods. Here, we aim to provide an insight into the mechanism behind the impedimetric signal change upon the hybridization event on graphene platforms. For this aim, we used an orthogonal electrochemical method, differential pulse voltammetry, to examine the oxidation of guanine on target DNA molecules hybridized with an inosine-substituted hairpin DNA probe. We show that the successful biorecognition event leads to desorption of dsDNA from graphenic surfaces on a wide range of graphenic surfaces, such as graphene oxide, electrochemically reduced graphene oxide and thermally reduced graphene oxide. These results confirm the previous hypothesis based on electrochemical impedance spectroscopy data. In addition, these findings also have a profound impact on the understanding of both the interactions between DNA and graphene platforms and the DNA recognition event on graphene platforms for the construction of biosensors.

Label-free luminescent oligonucleotide-based probes

Breakthrough advances in chemistry and biology over the last two decades have vastly expanded the repertoire of nucleic acid structure and function with potential application in multiple areas of science and technology, including sensing and analytical applications. DNA oligonucleotides represent popular tools for the development of sensing platforms due to their low cost, rich structural polymorphism, and their ability to bind to cognate ligands with sensitivity and specificity rivaling those for protein enzymes and antibodies. In this review, we give an overview of the "label-free" approach that has been a particular focus of our group and others for the construction of luminescent DNA-based sensing platforms. The label-free strategy aims to overcome some of the drawbacks associated with the use of covalently-labeled oligonucleotides prevalent in electrochemical and optical platforms. Label-free DNA-based probes harness the selective interaction between luminescent dyes and functional oligonucleotides that exhibit a "structure-switching" response upon binding to analytes. Based on the numerous examples of label-free luminescent DNA-based probes reported recently, we envisage that this field would continue to thrive and mature in the years to come.

Inherently electroactive graphene oxide nanoplatelets as labels for specific protein-target recognition

Graphene related materials have been widely employed as highly efficient transducers for biorecognition. Here we show a conceptually new approach of using graphene oxide nanoplatelets (50 × 50 nm) as voltammetric inherently active labels for specific protein-target molecule recognition. This proof-of-principle is demonstrated by biotin-avidin recognition, which displays that graphene oxide nanoplatelet labels show excellent selectivity. Therefore, it is expected that inherently electroactive graphene oxide nanoplatelet labels will play a similar role as electroactive gold nanoparticle labels which were developed more than a decade ago.

Thrombin aptasensing with inherently electroactive graphene oxide nanoplatelets as labels

Graphene and its associated materials are commonly used as the transducing platform in biosensing. We propose a different approach for the application of graphene in biosensing. Here, we utilized graphene oxide nanoplatelets as the inherently electroactive labels for the aptasensing of thrombin. The basis of detection lies in the ability of graphene oxide to be electrochemically reduced, thereby providing a well-defined reduction wave; one graphene oxide nanoplatelet of dimension 50 × 50 nm can provide a reduction signal by accepting ~22,000 electrons. We demonstrate that by using graphene oxide nanoplatelets as an inherently electroactive label, we can detect thrombin in the concentration range of 3 pM-0.3 μM, with good selectivity of the aptamer towards interferences by bovine serum albumin, immunoglobulin G and avidin. Therefore, the inherently electroactive graphene oxide nanoplatelets are a material which can serve as an electroactive label, in a manner similar to metallic nanoparticles.

Biorecognition on graphene: physical, covalent, and affinity immobilization methods exhibiting dramatic differences

The preparation of biorecognition layers on the surface of a sensing platform is a very crucial step for the development of sensitive and selective biosensors. Different protocols have been used thus far for the immobilization of biomolecules onto various electrode surfaces. In this work, we investigate how the protocol followed for the immobilization of a DNA aptamer affects the performance of the fabricated thrombin aptasensor. Specifically, the differences in selectivity and optimum amount of immobilized aptamer of the fabricated aptasensors adopting either physical, covalent, or affinity immobilization were compared. It was discovered that while all three methods of immobilization uniformly show a similar optimum amount of immobilized aptamer, physical, and covalent immobilization methods exhibit higher selectivity than affinity immobilization. Hence, it is believed that our findings are very important in order to optimize and improve the performance of graphene-based aptasensors.

Impedimetric thrombin aptasensor based on chemically modified graphenes

Highly sensitive biosensors are of high importance to the biomedical field. Graphene represents a promising transducing platform for construction of biosensors. Here for the first time we compare the biosensing performance of a wide set of graphenes prepared by different methods. In this work, we present a simple and label-free electrochemical impedimetric aptasensor for thrombin based on chemically modified graphene (CMG) platforms such as graphite oxide (GPO), graphene oxide (GO), thermally reduced graphene oxide (TR-GO) and electrochemically reduced graphene oxide (ER-GO). Disposable screen-printed electrodes were first modified with chemically modified graphene (CMG) materials and used to immobilize a DNA aptamer which is specific to thrombin. The basis of detection relies on the changes in impedance spectra of redox probe after the binding of thrombin to the aptamer. It was discovered that graphene oxide (GO) is the most suitable material to be used as compared to the other three CMG materials. Furthermore, the optimum concentration of aptamer to be immobilized onto the modified electrode surface was determined to be 10 μM and the linear detection range of thrombin was 10-50 nM. Lastly, the aptasensor was found to demonstrate selectivity for thrombin. Such simply fabricated graphene oxide aptasensor shows high promise for clinical diagnosis of biomarkers and point-of-care analysis.

Nucleic acid functionalized graphene for biosensing

There is immense demand for complex nanoarchitectures based on graphene nanostructures in the fields of biosensing or nanoelectronics. DNA molecules represent the most versatile and programmable recognition element and can provide a unique massive parallel assembly strategy with graphene nanomaterials. Here we demonstrate a facile strategy for covalent linking of single stranded DNA (ssDNA) to graphene using carbodiimide chemistry and apply it to genosensing. Since graphenes can be prepared by different methods and can contain various oxygen containing groups, we thoroughly investigated the utility of four different chemically modified graphenes for functionalization by ssDNA. The materials were characterized in detail and the different DNA functionalized graphene platforms were then employed for the detection of DNA hybridization and DNA polymorphism by using impedimetric methods. We believe that our findings are very important for the development of novel devices that can be used as alternatives to classical techniques for sensitive and fast DNA analysis. In addition, covalent functionalization of graphene with ssDNA is expected to have broad implications, from biosensing to nanoelectronics and directed, DNA programmable, self-assembly.

Detection of DNA hybridization on chemically modified graphene platforms

The increasing demand for simple, low-cost, rapid, sensitive and label-free methods for the detection of DNA sequences and the presence of single nucleotide polymorphisms (SNPs) has become an important issue in biomedical research. In this work, we studied the performances of several chemically modified graphene nanomaterials as sensing platforms by using the electrochemical impedance spectroscopy technique for the detection. We employed a hairpin DNA as a highly selective probe for the detection of SNP correlated to Alzheimer's disease. We believe that our findings may present a foundation for further research and development in graphene-based impedimetric biosensing.

Contribution of potassium ion and split modes of G-quadruplex to the sensitivity and selectivity of label-free sensor toward DNA detection using fluorescence

In recent years, bioanalytical technology based on G-quadruplex has been paid significant attention due to its versatility and stimulus-responsive reconfiguration. Notwithstanding, several key issues for template-directed reassembly of G-quadruplex have not been resolved: what is the key factor for determining the sensitivity and selectivity of split G-quadruplex probes toward target DNA. Therefore, in this study, we designed three pairs of split G-quadruplex probes and investigated the sensitivity and selectivity of these systems in terms of potassium ion concentration and split modes of G-quadruplex. Due to its simplicity and sensitivity, N-methyl-mesoporphyrin (NMM) as fluorescence probes was used to monitor the target-directed reassembling process of G-quadruplex. A G-quadruplex sequence derived from the c-Myc promoter was split into "symmetric" probes, where each fragment contained two runs of guanine residues (2+2), or into "asymmetric" fragments each containing (3+1 or 1+3) runs of guanine residues. In all three cases, the sensitivity of target detection was highly dependent on the thermodynamic stability of the hybrid structure, which can be modulated by potassium ion concentrations. Using a combination of CD, fluorescence, and UV spectroscopy, we found that increasing potassium concentrations can increase the sensitivity of target detection, but can decrease the selectivity of discriminating cognate versus mismatched "target" DNA. The previous argument that asymmetrically split probes were always better than symmetrically split probes in terms of selectivity was not plausible anymore. These results demonstrate how the sensitivities and selectivity of split probes to mutations can be optimized by tuning the thermodynamic stability of the three-way junction complex.

Graphene platform for hairpin-DNA-based impedimetric genosensing

There is enormous need for sensitive and selective detection of single nucleotide polymorphism of a DNA strand as this issue is related to many major diseases and disorders, such as Parkinson's and Alzheimer's disease. To achieve sensitivity and selectivity of the detection, a highly sensitive transducer of the signal with high surface area is required. In this work we employ a graphene platform to combine the sensitivity of electrochemical impedance spectroscopy with the high selectivity of hairpin-shaped DNA probes for the rapid detection of single nucleotide polymorphism correlated to the development of Alzheimer's disease. We investigate the influence of various graphene platforms consisting of different numbers of same-sized graphene layers. We believe that our findings are an important step toward highly sensitive and selective sensing architectures.