PEI/Zr⁴⁺-coated nanopore for selective and sensitive detection of ATP in combination with single-walled carbon nanotubes

Solid-State Nanopore/Nanochannel Sensors with Enhanced Selectivity through Pore-in Modification

Nanopore sensing technology, as an emerging analytical method, has the advantages of simple operation, fast output, and label-free and has been widely used in fields such as protein analysis, gene sequencing, and biomarker detection. Inspired by biological ion channels, scientists have prepared various artificial solid-state nanopores/nanochannels. Biological ion channels have extremely high ion transport selectivity, while solid-state nanopores/nanochannels have poor selectivity. The selectivity of solid-state nanopores and nanochannels can be enhanced by modifying channel charge, varying pore size, incorporating specific chemical functionality, and adjusting operating (or solution) conditions. This Perspective highlights pore-in modification strategies for enhancing the selectivity of solid-state nanopore/nanochannel sensors by summarizing the articles published in the last 10 years. The future development prospects and challenges of pore-in modification in solid-state nanopore and nanochannel sensors are discussed. This Perspective helps readers better understand nanopore sensing technology, especially the importance of detection selectivity. We believe that solid-state nanopore/nanochannel sensors will soon enter our homes after various challenges.

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.

Recent advance in solid state nanopores modification and characterization

Nanopore, due to its advantages of modifiable, controllability and sensitivity, has made a splash in recent years in the fields of biomolecular sequencing, small molecule detection, salt differential power generation, and biomimetic ion channels, etc. In these applications, the role of chemical or biological modification is indispensable. Compared with small molecules, the modification of polymers is more difficult and the methods are more diverse. Choosing appropriate modification method directly determines the success or not of the research, therefore, it is necessary to summarize the polymer modification methods toward nanopores. In addition, it is also important to provide clear and convincing evidence that the nanopore modification is successful, the corresponding characterization methods are also indispensable. Therefore, this review will summarize the methods of polymer modification of nanopores and efficient characterization methods. And we hope that this review will provide some reference value for like-minded researchers.

Nanosensing of Acetylcholine Molecules: Influence of the Association Mechanism

A bullet-shaped nanopore surface modified by two polyelectrolyte (PE) layers, an inner polyethyleneimine (PEI) layer and an outer p-sulfonatocalix[4]-arene (SCX4) layer, is applied to sense trace levels of acetylcholine (Ach) molecules. We show that the higher the order of the association reaction of Ach with SCX4, the smaller the difference between the ionic current when Ach is present and that when it is absent, and so is the difference in the space charge density. In addition, the larger the binding constant K of that reaction, the lower the detection limit but narrower the detection range. Choosing pH 7 is most appropriate because if the pH is low, the concentration polarization of H⁺ is significant, and as it gets high, both PE layers become uncharged. At pH 7 and K = 2 × 10⁷ L/mol, the detection limit of the nanopore ranges from 1 to 10 nM, which is orders of magnitude lower than that of the other approaches.

Sensing with Nanopores and Aptamers: A Way Forward

In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.

SERS Detection of Nucleobases in Single Silver Plasmonic Nanopores

Conventional ion current-based nanopore techniques that identify single molecules are hampered by limitations of providing only the ionic current information. Here, we introduce a silver nanotriangle-based nanopore (diameter < 50 nm) system for detecting molecule translocation using surface-enhanced Raman scattering. Rhodamine 6G is used as a model molecule to study the effect of an electric field (-1 V) on the mass transport. The four DNA bases also show significantly different SERS signals when they are transported into the plasmonic nanopore. The observations suggest that in the electric field, analyte molecules are driven into the nanopipette through the hot spot of the silver nanopore. The plasmonic nanopore shows great potential as a highly sensitive SERS platform for detecting molecule transport and paves the way for single molecule probing.

Fabrication of a Biomimetic Nanochannel Logic Platform and Its Applications in the Intelligent Detection of miRNA Related to Liver Cancer

Nanochannel-based analytical techniques have great potential applications for nucleic acid sequencing and high sensitivity detection of biological molecules. However, the sensitivity of conventional solid-state nanochannel sensors is hampered by a lack of effective signal amplification strategies, which has limited its utility in the field of analytical chemistry. Here we selected a solid-state nanochannnel modified with polyethylenimine and Zr⁴⁺ in combination with graphene oxide as the sensing platform. The high-performance sensor is based upon the change of the surface charge of the nanochannel, which is resulted from DNA cascade signal amplification in solution. The target miRNA (miR-122) can be indirectly quantitated with a detection limit of 97.2 aM with an excellent selectivity. Depending on the nucleic acid's hybridization and configuration transform, the designed nanochannel sensing systems can realize the intelligent detection of multiple liver cancer-related miRNA (miR-122 and miR Let-7a) integrating with cascaded INHIBIT-OR logic gate to provide theoretical guidance and technical support for clinical diagnosis and therapeutic evaluation of liver cancer.

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.

Ternary NiFeZr layered double hydroxides: a highly efficient catalyst for the oxygen evolution reaction

A novel Zr-doping strategy was highly effective to enhance the OER activity of NiFe LDHs via accelerating the charge transfer.

A fluorescence aptasensor based on two-dimensional sheet metal-organic frameworks for monitoring adenosine triphosphate

In the present study, a facile fluorescence aptasensor based on two-dimensional sheet metal-organic frameworks of N,N-bis(2-hydroxyethyl)dithiooxamidato copper(II) (H₂dtoaCu) was developed for the sensitive detection of adenosine triphosphate (ATP). The sensing mechanism was based on the noncovalent interaction between FAM-labeled (fluorescein amidite) ATP aptamers and H₂dtoaCu. In the absence of ATP, the FAM-labeled aptamer readily adsorbs onto H₂dtoaCu, mainly via π-π stacking and hydrogen bond interactions between the nucleotide bases and the H₂dtoaCu surface, leading to the reduction of fluorescence intensity of the FAM by photoinduced electron transfer (PET). In the presence of ATP, the FAM-labeled aptamer specifically forms ATP-binding aptamer complexes which exhibit only weak adsorption on the H₂dtoaCu surface. Thus, the fluorescence of the FAM-labeled ATP aptamer remained largely unchanged. The fluorescence aptasensor exhibited a good linear relationship between the fluorescence intensity and the logarithm concentration of ATP over a range of 25-400 nM, with a detection limit of 8.19 nM (3S/N). ATP analogs such as guanosine triphosphate, uridine triphosphate, and cytidine triphosphate have negligible effect on the aptasensor performance due to the high selectivity of the ATP aptamer to its target, showing promising potential in real sample analysis.

A visible and colorimetric aptasensor based on DNA-capped single-walled carbon nanotubes for detection of exosomes

Recently, many studies have shown the potential use of circulating exosomes as novel biomarkers for monitoring and predicting a number of complex diseases, including cancer. However, reliable and cost-effective detection of exosomes in routine clinical settings, still remain a difficult task, mainly due to the lack of adequately easy and fast assay platforms. Therefore, we demonstrate here the development of a visible and simple method for the detection of exosomes by integrating single-walled carbon nanotubes that being excellent water solubility (s-SWCNTs) and aptamer. Aptamers, specific to exosomes transmembrane protein CD63, are absorbed onto the surface of s-SWCNTs and improve the minic peroxidase activity of s-SWCNTs, which can efficiently catalyze H₂O₂-mediated oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) and lead to a change from colorless to blue in solution. However, after adding exosomes, the aptamers are bound with CD63, leaving from the surface of s-SWCNTs through conformational changes, which results the color of solution from deep to moderate, and this can be observed by the naked eye and monitored by UV-vis spectrometry. Under optimal conditions, the linear range of exosomes is estimated to be 1.84×10⁶ to 2.21×10⁷ particles/μL with a detection of limit (LOD) of 5.2×10⁵ particles/μL. Consequently, a visible and simple approach detecting exosomes is successfully constructed. Moreover, this proposed colorimetric aptasensor can be universally applicable for the detection of other targets by simple change the aptamer.

A conformation and charge co-modulated ultrasensitive biomimetic ion channel

For the first time, an ultrasensitive nanopore-based sensor that co-modulated simultaneously by conformation and charge has been developed for the detection of ATP.

Reconfigurable and resettable arithmetic logic units based on magnetic beads and DNA

Based on the characteristics of magnetic beads and DNA, a simple and universal platform was developed for the integration of multiple logic gates to achieve resettable half adder and half subtractor functions. The signal reporter was composed of a split G-quadruplex DNAzyme and AuNP-surface immobilized molecular beacon molecule. The novel feature of the designed system is that the inputs (split G-quadruplexes) can interact with hairpin-modified Au NPs linked to magnetic particles. Another novel feature is that the logic operations can be reset by heating the output system and by using the magnetic separation of the computing modules. Moreover, the developed half adder and half subtractor are realized on a simple DNA/magnetic bead platform in an enzyme-free system and share a constant threshold setpoint. Due to the diversity and design flexibility of DNA, these investigations may provide a new method for the development of resettable DNA-based arithmetic operations.

Surface charge modulated aptasensor in a single glass conical nanopore

In this work, we have proposed a label-free nanopore-based biosensing strategy for protein detection by performing the DNA-protein interaction inside a single glass conical nanopore. A lysozyme binding aptamer (LBA) was used to functionalize the walls of glass nanopore via siloxane chemistry and negatively charged recognition sites were thus generated. The covalent modification procedures and their recognition towards lysozyme of the single conical nanopore were characterized via ionic current passing through the nanopore membrane, which was measured by recording the current-voltage (I-V) curves in 1mM KCl electrolyte at pH=7.4. With the occurring of recognition event, the negatively charged wall was partially neutralized by the positively charged lysozyme molecules, leading to a sensitive change of the surface charge-dependent current-voltage (I-V) characteristics. Our results not only demonstrate excellent selectivity and sensitivity towards the target protein, but also suggest a route to extend this nanopore-based sensing strategy to the biosensing platform designs of a wide range of proteins based on a charge modulation.

Highly efficient colorimetric detection of ATP utilizing a split aptamer target binding strategy and superior catalytic activity of graphene oxide–platinum/gold nanoparticles

The specific binding of ATP and its aptamer linked the split aptamer-modified GO/PDDA/PtAuNPs and magnetic beads together. Using magnetic separation, TMB was catalyzed into a colored product by nanocomposites, which enabled rapid detection of ATP.