Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size

A highly sensitive nanopore platform for measuring RNase A activity

Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.

The combination of DNA nanostructures and materials for highly sensitive electrochemical detection

Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.

Recent advances of small molecule detection in nanopore sensing

Due to its advantages of label-free and highly sensitive, the resistive pulse sensing with a nanopore has recently become even more potent for the discrimination of analytes in single molecule level. Generally, a transient interruption of ion current originated from the captured molecule passing through a nanopore will provide the rich information on the structure, charge and translocation dynamics of the analytes. Therefore, nanopore sensors have been widely used in the fields of DNA sequencing, protein recognition, and the portable detection of varied macromolecules and particles. However, the conventional nanopore devices are still lack of sufficient selectivity and sensitivity to distinguish more metabolic molecules involving ATP, glucose, amino acids and small molecular drugs because it is hard to receive a large number of identifiable signals with the fabricated pores comparable in size to small molecules for nanopore sensing. For all this, a series of innovative strategies developed in the past decades have been summarized in this review, including host-guest recognition, engineering alteration of protein channel, the introduction of nucleic acid aptamers and various delivery carriers integrating signal amplification sections based on the biological and solid nanopore platforms, to achieve the high resolution for the small molecules sensing in micro-nano environment. These works have greatly enhanced the powerful sensing capabilities and extended the potential application of nanopore sensors.

Electrochemical Sensors and Biosensors for Identification of Viruses: A Critical Review

Due to their life cycle, viruses can disrupt the metabolism of their hosts, causing diseases. If we want to disrupt their life cycle, it is necessary to identify their presence. For this purpose, it is possible to use several molecular-biological and bioanalytical methods. The reference selection was performed based on electronic databases (2020-2023). This review focused on electrochemical methods with high sensitivity and selectivity (53% voltammetry/amperometry, 33% impedance, and 12% other methods) which showed their great potential for detecting various viruses. Moreover, the aforementioned electrochemical methods have considerable potential to be applicable for care-point use as they are portable due to their miniaturizability and fast speed analysis (minutes to hours), and are relatively easy to interpret. A total of 2011 articles were found, of which 86 original papers were subsequently evaluated (the majority of which are focused on human pathogens, whereas articles dealing with plant pathogens are in the minority). Thirty-two species of viruses were included in the evaluation. It was found that most of the examined research studies (77%) used nanotechnological modifications. Other ones performed immunological (52%) or genetic analyses (43%) for virus detection. 5% of the reports used peptides to increase the method's sensitivity. When evaluable, 65% of the research studies had LOD values in the order of ng or nM. The vast majority (79%) of the studies represent proof of concept and possibilities with low application potential and a high need of further research experimental work.

Probe-assisted detection of Fe3+ ions in a multi-functionalized nanopore

Iron is an essential element that plays critical roles in many biological/metabolic processes, ranging from oxygen transport, mitochondrial respiration, to host defense and cell signaling. Maintaining an appropriate iron level in the body is vital to the human health. Iron deficiency or overload can cause life-threatening conditions. Thus, developing a new, rapid, cost-effective, and easy to use method for iron detection is significant not only for environmental monitoring but also for disease prevention. In this study, we report an innovative Fe3+ detection strategy by using both a ligand probe and an engineered nanopore with two binding sites. In our design, one binding site of the nanopore has a strong interaction with the ligand probe, while the other is more selective toward interfering species. Based on the difference in the number of ligand DTPMPA events in the absence and presence of ferric ions, micromolar concentrations of Fe3+ could be detected within minutes. Our method is selective: micromolar concentrations of Mg2+, Ca2+, Cd2+, Zn2+, Ni2+, Co2+, Mn2+, and Cu2+ would not interfere with the detection of ferric ions. Furthermore, Cu2+, Ni2+, Co2+, Zn2+, and Mn2+ produced current blockage events with quite different signatures from each other, enabling their simultaneous detection. In addition, simulated water and serum samples were successfully analyzed. The nanopore sensing strategy developed in this work should find useful application in the development of stochastic sensors for other substances, especially in situations where multi-analyte concurrent detection is desired.

Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates

Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.

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.

A novel colorimetric biosensor for rapid detection of dengue virus upon acid-induced aggregation of colloidal gold

The dengue virus, once transmitted to people through a mosquito bite, causes an infectious disease called dengue fever. Dengue fever can develop into two fatal syndromes, namely dengue shock syndrome and dengue hemorrhagic fever. The existing strategies for detecting dengue infection mainly employ serological immunoassays and a real time PCR technique. Along with the positive features of efficiency, accuracy, and reproducibility, these procedures are limited by being time-consuming, costly, requiring special equipment for analysis, and unable to be carried out at the point-of-care level. Herein, we developed a colorimetric nanosensor for detecting dengue virus in clinical samples that is rapid, accurate, sensitive, and less expensive. The sensing platform relies on the specific binding between the DNA-conjugated AuNPs and genomic RNA of dengue, which results in the DNA-RNA heteroduplex structure formation that turns the gold colloid's ruby red color to blue due to the nano-aggregation in an acidic environment, which can be detected by the naked eye or measuring the absorbance. The DNA probe was designed to bind to a genomic RNA conserved region recognized in all four dengue serotypes. Dengue virus serotype 1 was utilized as a framework for virus detection; the designed nanosensor exhibited great specificity and selectivity, with the detection limit of ∼1 pg μL-1 (∼1.66 × 106 RNA copies per reaction) and time of analysis of about 1 h including the RNA extraction step. The proposed colorimetric nanosensor offers an alternative tool for specific and highly sensitive detection of dengue that eliminates the requirement for thermal cycling and primer sets in PCR-based assays.

Detection and Separation of DNA and Silver Nanoparticles Using a Solid-State Nanopore

Nanopore sensors, a new generation of single-molecule sensors, are increasingly used to detect and analyze various analytes and have great potential for rapid gene sequencing. However, there are still some problems in the preparation of small diameter nanopores, such as imprecise pore size and porous defects, while the detection accuracy of large-diameter nanopores is relatively low. Therefore, how to achieve more precise detection of large diameter nanopore sensors is an urgent problem to be studied. Here, SiN nanopore sensors were used to detect DNA molecules and silver nanoparticles (NPs) separately and in combination. The experimental results show that large-size solid-state nanopore sensors can identify and discriminate between DNA molecules, NPs, and NP-bound DNA molecules clearly according to resistive pulses. In addition, the detection mechanism of using NPs to assist in identifying target DNA molecules in this study is different from previous reports. We find that silver NPs can simultaneously bind to multiple probes and target DNA molecules and generate a larger blocking current than free DNA molecules when passing through the nanopore. In conclusion, our research indicates that large-sized nanopores can distinguish the translocation events, thereby identifying the presence of the target DNA molecules in the sample. This nanopore-sensing platform can produce rapid and accurate nucleic acid detection. Its application in medical diagnosis, gene therapy, virus identification, and many other fields is highly significant.

Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.

Solid-State Nanopore/Nanochannel Sensing of Single Entities

Solid-state nanopores/nanochannels, with their high stability, tunable geometry, and controllable surface chemistry, have recently become an important tool for constructing biosensors. Compared with traditional biosensors, biosensors constructed with solid-state nanopores/nanochannels exhibit significant advantages of high sensitivity, high specificity, and high spatiotemporal resolution in the detection single entities (such as single molecules, single particles, and single cells) due to their unique nanoconfined space-induced target enrichment effect. Generally, the solid-state nanopore/nanochannel modification method is the inner wall modification, and the detection principles are the resistive pulse method and the steady-state ion current method. During the detection process, solid-state nanopore/nanochannel is easily blocked by single entities, and interfering substances easily enter the solid-state nanopore/nanochannel to generate interference signals, resulting in inaccurate measurement results. In addition, the problem of low flux in the detection process of solid-state nanopore/nanochannel, these defects limit the application of solid-state nanopore/nanochannel. In this review, we introduce the preparation and functionalization of solid-state nanopore/nanochannel, the research progress in the field of single entities sensing, and the novel sensing strategies on solving the above problems in solid-state nanopore/nanochannel single-entity sensing. At the same time, the challenges and prospects of solid-state nanopore/nanochannel for single-entity electrochemical sensing are also discussed.

Nano-bio interaction: An overview on the biochemical binding of DNA to inorganic nanoparticles for the development of anticancer and antibacterial nano-platforms

It has long been known that inorganic nanoparticles (NPs) can interact with biological macromolecules and show a wider range of biomedical characteristics, including antibacterial, anticancer and antioxidant effects, which cannot be mimicked by their bulky counterparts. It is of great importance in their biomedical applications to study DNA damage in bacterial and cancer cells to develop biocompatible therapeutic nano-platforms derived from inorganic NPs. Therefore, to determine how DNA interacts with inorganic NPs serving as therapeutic agents, thermodynamic and structural studies are essential for an understanding of those mechanisms, thereby allowing for their modulation and manipulation of nano-bio interface. In this paper, we aimed to overview the biophysical techniques typically employ to study DNA-NP interactions as well as the mechanistic aspects of the interaction between different inorganic NPs and calf thymus DNA (CT-DNA), a well-known laboratory model, followed by a survey of different parameters affecting the interaction of NPs and DNA. The molecular interactions between inorganic NPs and DNA were then discussed in relation to their anticancer and antibacterial properties. As a final point, we discussed challenges and future perspectives to put forward the possible applications of the field. In conclusion, the interaction between NPs and DNA needs to be studied more deeply in order to develop potential NP-based anticancer and antibacterial platforms for future clinical applications.

Large-scale production of polyimide micropore-based flow cells for detecting nano-sized particles in fluids

In diagnostic and sequencing applications, solid-state nanopores hold significant promise as a single-molecule sensing platform. The fabrication of precisely sized pores has traditionally been challenging, laborious, expensive, and inefficient, which has limited its applications until recently. To overcome this problem, this paper proposes a novel, reliable, cost-effective, portable, mass-productive, robust, and ease-of-use micropore flow cell that works based on the resistive pulse sensor (RPS) technique in order to distinguish the different sizes of c nanoparticles. RPS is a robust and informative technique that can provide valuable details of the size, shape, charge, and individual particle concentrations in the media. By femtosecond laser drilling of a polyimide substrate as an alternate material, translocation of 100, 300, and 350 nm polystyrene nanoparticles in PBS buffer was distinguished by 0.1, 1, and 2 nA current blockade levels, respectively. This is the first time a micropore has been opened in a polyimide membrane using a femtosecond laser in a single step. The experimental and theoretical investigation, scanning electron microscopy and focused ion beam spectroscopy were performed to comprehensively explain the micropore's performance. We showed that our innovative micropore-based flow cell could distinguish nano-sized particles in fluids, and it can be used in large-scale production because of its simplicity and cost-effectiveness.

Chemistry solutions to facilitate nanopore detection and analysis

Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.