Graphene nanopores toward DNA sequencing: a review of experimental aspects

Controllable Fabrication of Sub-10 nm Graphene Nanopores via Helium Ion Microscopy and DNA Detection

Solid-state nanopores have become a prominent tool in the field of single-molecule detection. Conventional solid-state nanopores are thick, which affects the spatial resolution of the detection results. Graphene is the thinnest 2D material and has the highest spatial detection resolution. In this study, a graphene membrane chip was fabricated by combining a MEMS process with a 2D material wet transfer process. Raman spectroscopy was used to assess the quality of graphene after the transfer. The mechanism behind the influence of the processing dose and residence time of the helium ion beam on the processed pore size was investigated. Subsequently, graphene nanopores with diameters less than 10 nm were fabricated via helium ion microscopy. DNA was detected using a 5.8 nm graphene nanopore chip, and the appearance of double-peak signals on the surface of 20 mer DNA was successfully detected. These results serve as a valuable reference for nanopore fabrication using 2D material for DNA analysis.

Functionalized nanopores based on hybridization chain reaction: Fabrication and microRNA sensing

Enzyme-free hybridization chain reaction (HCR) technology is often used as a signal amplification tool for the detection of different targets. In this study, an ultrasensitive and label-free method for detecting miRNA-21 was developed using the nanopore ionic current rectification (ICR) technology coupled with HCR technology. The probe oligonucleotide (DNA1) was combined with the gold-coated nanopore through the Au-S bond to form a DNA1-functionalized gold-coated nanopore (DNA1-Au-coated nanopore). Since miRNA-21 is partially complementary to DNA1, it can be selectively recognized by DNA1-functionalized gold-coated nanopores. The target (miRNA-21) can induce the opening of hairpin DNA and HCR reaction after the introduction of hairpin DNA H1 and H2. The concentration of miRNA-21 will affect the combination of H1 and H2 on the inner wall of the nanopore, and its surface charge will change with the internal modification, thereby changing the ion current rectification ratio. Under the condition that the concentration of H1, H2 and HCR reaction time are constant, the change of ICR ratio is linearly correlated with the logarithm of miRNA-21 concentration within a certain range, which shows that the sensing strategy we designed can achieve target miRNA-21 detection. This ultrasensitive miRNA holds great promise in the field of cancer diagnosis.

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.

DNA-Mediated Assembly of Carbon Nanomaterials

Carbon nanomaterials (CNMs) have attracted extensive attentions on account of their superior electrical, mechanical, optical, and biological properties. However, the dimensional limit and irregular arrangement have hampered their further application. It is necessary to find an easy, efficient and controllable way to assemble CNMs into well-ordered array. DNA nanotechnology, owning to the advantages of precise programmability, highly structural predictability and spatial addressability, has been widely applied in the assembly of CNMs. Summarizing the progress and achievements in this field will be of great value to related studies. Herein, based on the different dimensions of CNMs containing 0-dimensional (0D) carbon dots (CDs), fullerenes, 1-dimensional (1D) carbon nanotubes (CNTs) and 2-dimensional (2D) graphene, we introduced the conjugation strategies between DNA and CNMs, their different assembly methods and their applications. In addition, we also discuss the existing challenges and future opportunities in the field.

Two-dimensional material-based virus detection

Cost-effective, rapid, and accurate virus detection technologies play key roles in reducing viral transmission. Prompt and accurate virus detection enables timely treatment and effective quarantine of virus carrier, and therefore effectively reduces the possibility of large-scale spread. However, conventional virus detection techniques often suffer from slow response, high cost or sophisticated procedures. Recently, two-dimensional (2D) materials have been used as promising sensing platforms for the high-performance detection of a variety of chemical and biological substances. The unique properties of 2D materials, such as large specific area, active surface interaction with biomolecules and facile surface functionalization, provide advantages in developing novel virus detection technologies with fast response and high sensitivity. Furthermore, 2D materials possess versatile and tunable electronic, electrochemical and optical properties, making them ideal platforms to demonstrate conceptual sensing techniques and explore complex sensing mechanisms in next-generation biosensors. In this review, we first briefly summarize the virus detection techniques with an emphasis on the current efforts in fighting again COVID-19. Then, we introduce the preparation methods and properties of 2D materials utilized in biosensors, including graphene, transition metal dichalcogenides (TMDs) and other 2D materials. Furthermore, we discuss the working principles of various virus detection technologies based on emerging 2D materials, such as field-effect transistor-based virus detection, electrochemical virus detection, optical virus detection and other virus detection techniques. Then, we elaborate on the essential works in 2D material-based high-performance virus detection. Finally, our perspective on the challenges and future research direction in this field is discussed.

Graphene Nanoribbons: Prospects of Application in Biomedicine and Toxicity

Graphene nanoribbons are a type of graphene characterized by remarkable electrical and mechanical properties. This review considers the prospects for the application of graphene ribbons in biomedicine, taking into account safety aspects. According to the analysis of the recent studies, the topical areas of using graphene nanoribbons include mechanical, chemical, photo- and acoustic sensors, devices for the direct sequencing of biological macromolecules, including DNA, gene and drug delivery vehicles, and tissue engineering. There is evidence of good biocompatibility of graphene nanoribbons with human cell lines, but a number of researchers have revealed toxic effects, including cytotoxicity and genotoxicity. Moreover, the damaging effects of nanoribbons are often higher than those of chemical analogs, for instance, graphene oxide nanoplates. The possible mechanism of toxicity is the ability of graphene nanoribbons to damage the cell membrane mechanically, stimulate reactive oxidative stress (ROS) production, autophagy, and inhibition of proliferation, as well as apoptosis induction, DNA fragmentation, and the formation of chromosomal aberrations. At the same time, the biodegradability of graphene nanoribbons under the environmental factors has been proven. In general, this review allows us to conclude that graphene nanoribbons, as components of high-precision nanodevices and therapeutic agents, have significant potential for biomedical applications; however, additional studies of their safety are needed. Particular emphasis should be placed on the lack of information about the effect of graphene nanoribbons on the organism as a whole obtained from in vivo experiments, as well as about their ecological toxicity, accumulation, migration, and destruction within ecosystems.

Induced Pluripotent Stem Cell-Derived Endothelial Networks Accelerate Vascularization But Not Bone Regeneration

Vascularization is critical for engineering mineralized tissues. It has been previously shown that biomaterials containing preformed endothelial networks anastomose to host vasculature following implantation. However, the networks alone may not increase regeneration. In addition, a clinically applicable source of cells for vascularization is needed. In this study, vascular networks were generated from endothelial cells (ECs) derived from human induced pluripotent stem cells (iPSCs). Network formation by iPSC-ECs within fibrin gels was investigated in a mesenchymal stem cells (MSCs) coculture spheroid model. Statistical design of experiments technique was evaluated for its predicting capability during the optimization of experimental parameters. The prevascularized units were combined with hydroxyapatite nanoparticles to develop a vascularized composite hydrogel that was implanted in a rodent critical-sized cranial defect model. Immunohistological staining for human-specific CD31 at week 1 indicated the presence and maintenance of the implanted vessels. At 8 weeks, the prevascularized systems resulted in higher vessel density over MSC-only scaffolds. The implanted vessels appeared to establish flow with host vasculature. While there was a slight increase in bone volume in the prevascularized bone construct compared to MSC-only bone constructs, there was not a profound increase in bone regeneration. These results show that scaffolds with network structures can be generated from ECs derived from iPSC and that the networks survive and inosculate with the host postimplantation in a bone model. Impact statement Vascularization is critical for engineering bone. Prevascularized scaffolds have been shown to improve postimplantation vascularization. Herein, vascularized networks were generated from induced pluripotent cells derived from endothelial cells. These vascularized units were combined with a fibrin/hydroxyapatite scaffold to develop a prevascularized construct for bone regeneration. Implantation of these scaffolds in a small animal cranial defect model resulted in network inosculation and increased vascularization, but exhibited only a limited effect on bone formation. This study provides insight into the challenges of generating vascularized bone.

Nanopores in two-dimensional materials: accurate fabrication

Two-dimensional (2D) materials such as graphene and molybdenum disulfide have been demonstrated with a wide range of applications in electronic devices, chemical catalysis, single-molecule detection, and energy conversion. In the 2D materials, nanopores can be created, and the 2D nanoporous membranes possess many unique properties such as ultrathin thickness, high surface area, and excellent particle sieving capability, showing extraordinary promise in plenty of applications, such as sea water desalination, gas separation, and DNA sequencing. The performances of these membranes are mainly determined by the nanopore size, structure, and density, which, in turn, rely on the fabrication techniques of the nanopores. This review covers the important progress of nanopore fabrication in 2D materials and comprehensively compares these methods for the features of the introduced nanopores and their formation processes. Future perspectives are discussed on the opportunities and challenges in fabricating high-grade 2D nanopores.

Single nucleotide detection using bilayer MoS2 nanopores with high efficiency

Single nucleotide detection is important for early detection of diseases and for DNA sequencing. Monolayer (ML) MoS₂ nanopores have been used to identify and distinguish single nucleotides with good signal-to-noise ratio in the recent past. Here, we use a bilayer (BL) MoS₂ nanopore (∼1.3 nm thick) to detect distinct single nucleotides with high spatial resolution and longer dwell time. In this study, the performance of similar sized (<3 nm) ML and BL MoS₂ nanopores for detection of a single nucleotide has been compared. Both single nucleotide and single stranded DNA translocations through them are studied. For single nucleotide detection, we observe that BL MoS₂ nanopores demonstrate twice the dwell time as compared to ML MoS₂ nanopores with 95% confidence. Single nucleotide detection rate for BL MoS₂ nanopores (50–60 nucleotides per s) is five-fold higher as compared to ML MoS₂ nanopores (10–15 nucleotides per s) in 10 pM analyte concentration. For single stranded DNA, we observe 89% (for 60 DNA molecules detected) single nucleotide detection efficiency with BL MoS₂ nanopores as compared to 85% for ML MoS₂. The DNA sequencing efficiency through BL MoS₂ nanopores is also found to be 8–10% better than through ML MoS₂ nanopores, irrespective of DNA sequencing orientation. Thus, owing to improved analyte/nanopore charge interaction BL MoS₂ nanopores can be used for single nucleotide detection with high resolution due to longer dwell time, detection rate and efficiency. This study demonstrates the improved ability of BL MoS₂ nanopores in sequencing DNA with 8–10% higher efficiency, two-times temporally resolved single-nucleotide current signatures and five-times higher detection rate, compared to ML MoS₂ nanopores.

Bilayer MoS₂ nanopores are suitable for fast and high-efficiency single nucleotide detection and DNA sequencing due to fast analyte capture and improved dwell time.

Ultrasensitive and regenerable nanopore sensing based on target induced aptamer dissociation

For ionic current rectification (ICR) based sensing, nanopore functionalizations are mostly designed for directly binding target molecules to generate detectable signals from surface charge variation. However, this strategy is highly dependent on the charge difference between the captured molecules and surface functionalization layers, which will increase the nanopore design difficulty and subsequently limit the nanopore applicability. Another key challenge for ICR based sensing is the nanopore regenerability that is critical if online monitoring or repeated determination needs to be performed with one sensor. Though some types of nanopore regeneration have been realized on some specific targets or with harsh conditions, it is still highly favored to develop a regenerability using mild conditions for various targets. To address these two challenges, we developed a novel and universal sensing strategy for aptamer-functionalized nanopore that can be easily regenerated after each usage without any harsh conditions and independent of target molecule charge or size for ICR based nanopore sensing. Ochratoxin A (OTA) was used as a model analyte and its corresponding aptamer partially hybridized with the pre-immobilized complementary DNA (cDNA) onto the nanopore inner surface. We demonstrated that the recognition and conjugation of OTA with its aptamer resulted in rectified ionic current variations due to the dissociation between the OTA aptamer and its partially paired cDNA. The performance of this nanopore sensor including sensitivity, selectivity, regenerability, and applicability was characterized using rectified ionic current. This nanopore sensing strategy will provide a promising platform for extensive targets and online sensing applications.

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.