Stochastic nanopore sensors for the detection of terrorist agents: current status and challenges

Alphatoxin Nanopore Detection of Aflatoxin, Ochratoxin and Fumonisin in Aqueous Solution

Mycotoxins are toxic and carcinogenic metabolites produced by groups of filamentous fungi that colonize food crops. Aflatoxin B1 (AFB1), ochratoxin A (OTA) and fumonisin B1 (FB1) are among the most relevant agricultural mycotoxins, as they can induce various toxic processes in humans and animals. To detect AFB1, OTA and FB1 in the most varied matrices, chromatographic and immunological methods are primarily used; however, these techniques are time-consuming and expensive. In this study, we demonstrate that unitary alphatoxin nanopore can be used to detect and differentiate these mycotoxins in aqueous solution. The presence of AFB1, OTA or FB1 inside the nanopore induces reversible blockage of the ionic current flowing through the nanopore, with distinct characteristics of blockage that are unique to each of the three toxins. The process of discrimination is based on the residual current ratio calculation and analysis of the residence time of each mycotoxin inside the unitary nanopore. Using a single alphatoxin nanopore, the mycotoxins could be detected at the nanomolar level, indicating that alphatoxin nanopore is a promising molecular tool for discriminatory analysis of mycotoxins in aqueous solution.

Aprotic Solvent Accumulation Amplifies Ion Current Rectification in Conical Nanopores

Ion current rectification is highly reported in aqueous electrochemical systems and sensors but lacks exploration in organic systems due to the additional complexity introduced by non-aqueous solvents. Herein, a detailed study on ion current rectification with highly polar and mildly polar aprotic organic solvents as a function of tetraethylammonium tetrafluoroborate supporting electrolyte concentration is presented. To explain our experimental results, we introduce a previously unreported phenomenon: the formation of a double-junction diode within the nanopore that arises due to a complex interplay between ion and solvent enrichment effects. Finite element simulations are used to explore this phenomenon and the subsequent effect on the rectifying behavior of conical quartz nanopores.

A single-molecule insight into the ionic strength dependent, cationic peptide nucleic acids - oligonucleotides interactions

To alleviate solubility-related shortcomings associated with the use of neutral peptide nucleic acids (PNA), a powerful strategy is incorporate various charged sidechains onto the PNA structure. Here we employ a single-molecule technique and prove that the ionic current blockade signature of free poly(Arg)-PNAs and their corresponding duplexes with target ssDNAs interacting with a single a-hemolysin (a-HL) nanopore is highly ionic strength dependent, with high salt-containing electrolytes facilitating both capture and isolation of such complexes. Our data illustrate the effect of low ionic strength in reducing the effective volume of free poly(Arg)-PNAs and augmentation of their electrophoretic mobility while traversing the nanopore.  We found that unlike in high salt electrolytes, the specific hybridization of cationic moiety-containing PNAs with complementary negatively charged ssDNAs in a salt concentration as low as 0.5 M is dramatically impeded. We suggest a scenario in which reduced charge screening by counterions in low salt electrolytes enables non-specific, electrostatic interactions with the anionic backbone of polynucleotides, thus reducing the ability of PNA-DNA complementary association via hydrogen bonding patterns. We applied an experimental strategy with spatially-separated poly(Arg)-PNAs and ssDNAs, and present evidence at the single-molecule level suggestive of the real-time, long-range interactions-driven formation of poly(Arg)-PNA-DNA complexes, as individual strands entering the nanopore from opposite directions collide inside a nanocavity.

Stochastic Microsensors Based on Carbon Nanotubes for Molecular Recognition of the Isocitrate Dehydrogenases 1 and 2

Two three-dimensional (3D) stochastic microsensors based on immobilization of protoporphyrin IX (PIX) in single-walled carbon nanotubes (SWCNT) and multi-walled carbon nanotubes (MWCNT) decorated with copper (Cu) and gold (Au) nanoparticles were designed and used for the molecular recognition of isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) in biological samples (brain tumor tissues, whole blood). The linear concentration ranges obtained for the molecular recognition and quantification of IDH1 and IDH2 were: IDH1 (1 × 10⁻⁵–1 × 10² ng mL⁻¹) and IDH2 (5 × 10⁻⁸ − 5 × 10² ng mL⁻¹). The limits of quantification obtained using the proposed microsensors were: 10 fg mL^–1 for IDH1 and 5 × 10⁻³ fg mL⁻¹ for IDH2. The highest sensitivities were obtained for the microsensor based on MWCNT. High recoveries versus enzyme-linked immunosorbent assay (ELISA) standard method were recorded for the assays of IDH1 and IDH2, all values being higher than 99.00%, with relative standard deviations (RSD) lower than 0.10%.

Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids

Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.

Sequence-specific detection of single-stranded DNA with a gold nanoparticle-protein nanopore approach

Fast, cheap and easy to use nucleic acids detection methods are crucial to mitigate adverse impacts caused by various pathogens, and are essential in forensic investigations, food safety monitoring or evolution of infectious diseases. We report here a method based on the α-hemolysin (α-HL) nanopore, working in conjunction to unmodified citrate anion-coated gold nanoparticles (AuNPs), to detect nanomolar concentrations of short single-stranded DNA sequences (ssDNA). The core idea was to use charge neutral peptide nucleic acids (PNA) as hybridization probe for complementary target ssDNAs, and monitor at the single-particle level the PNA-induced aggregation propensity AuNPs during PNA–DNA duplexes formation, by recording ionic current blockades signature of AuNP–α-HL interactions. This approach offers advantages including: (1) a simple to operate platform, producing clear-cut readout signals based on distinct size differences of PNA-induced AuNPs aggregates, in relation to the presence in solution of complementary ssDNAs to the PNA fragments (2) sensitive and selective detection of target ssDNAs (3) specific ssDNA detection in the presence of interference DNA, without sample labeling or signal amplification. The powerful synergy of protein nanopore-based nanoparticle detection and specific PNA–DNA hybridization introduces a new strategy for nucleic acids biosensing with short detection time and label-free operation.

Nanoscale Probing of Informational Polymers with Nanopores. Applications to Amyloidogenic Fragments, Peptides, and DNA-PNA Hybrids

The decades long advances in nanotechnology, biomolecular sciences, and protein engineering ushered the introduction of groundbreaking technologies devoted to understanding how matter behaves at single particle level. Arguably, one of the simplest in concept is the nanopore-based paradigm, with deep roots in what is originally known as the Coulter counter, resistive-pulse technique. Historically, a nanopore system comprising the oligomeric protein generated by Staphylococcus aureus toxin α-hemolysin (α-HL) was first applied to detecting polynucleotides, as revealed in 1996 by John J. Kasianowicz, Eric Brandin, Daniel Branton, and David W. Deamer, in the Proceedings of the National Academy of Sciences. Nowadays, a wide variety of other solid-state or protein-based nanopores have emerged as efficient tools for stochastic sensing of analytes as small as single metal ions, handling single molecules, or real-time, label-free probing of chemical reactions at single-molecule level. In this Account, we demonstrate the usefulness of the α-HL nanopore on probing metal-induced folding of peptides, and to investigating the reversible binding of various metals to physiologically relevant amyloid fragments. The widely recognized Achilles heel of the approach, is the relatively short dwell time of the analytes inside the nanopore. This hinders the collection of sufficient data required to infer statistically meaningful conclusions about the physical or chemical state of the studied analyte. To mitigate this, various approaches were successfully applied in particular experiments, including but not restricted to altering physical parameters of the aqueous solution, downsizing the nanopore geometry, the controlled tuning of the balance between the electrostatic and electro-osmotic forces, coating nanopores with a fluid lipid bilayer, employing a pressure-voltage biased pore. From our perspective, in this Account, we will present two strategies aimed at controlling the analyte passage across the α-HL. First, we will reveal how the electroosmotic flow can be harnessed to control residence time, direction, and the sequence of spatiotemporal dynamics of a single peptide along the nanopore. This also allows one to identify the mesoscopic trajectory of a peptide exiting the nanopore through either the vestibule or β-barrel moiety. Second, we lay out the principles of an approach dubbed "nanopore tweezing", enabling simultaneous capture rate increase and escape rate decrease of a peptide from the α-HL, with the applied voltage. At its core, this method requires the creation of an electrical dipole on the peptide under study, via engineering positive and negative amino acid residues at the two ends of the peptide. Concise applications of this approach are being demonstrated, as in proof-of-concept experiments we probed the primary structure exploration of polypeptides, via discrimination between selected neutral amino acid residues. Another useful venue provided by the nanopores is represented by single-molecule force experiments on captured analytes inside the nanopore, which proved useful in exploring force-induced rupture of nucleic acids duplexes, hairpins, or various nucleic acids-ligand conjugates. We will show that when applied to oppositely charged, polypeptide-functionalized PNA-DNA duplexes, the nanopore tweezing introduces a new generation of force-spectroscopy nanopore-based platforms, facilitating unzipping of a captured duplex and enabling the duplex hybridization energy estimation.

Quantitative Framework for Stochastic Nanopore Sensors Using Multiple Channels

Membrane protein channels employed as stochastic sensors offer large signal-to-noise ratios and high specificity in single molecule binding measurements. Stochastic events in a single ion channel system can be measured using current-time traces, which are straightforward to analyze. Signals arising from measurement using multiple ion channels are more complicated to interpret. We show that multiple independent ion channels offer improved detection sensitivity compared to single channel measurements and that increased signal complexity can be accounted for using binding event frequency. More specifically, the leading edge of binding events follows a Poisson point process, which means signals from multiple channels can be superimposed and the association times (between each binding event leading edge), allow for sensitive and quantitative measurements. We expand our calibration to high ligand concentrations and high numbers of ion channels to demonstrate that there is an upper limit of quantification, defined by the time resolution of the measurement. The upper limit is a combination of the instrumental time resolution and the dissociation time of a ligand and protein which limits the number of detectable events. This upper limit also allows us to predict, in general, the measurement requirements needed to observe any process as a Poisson point process. The nanopore-based sensing analysis has wide implications for stochastic sensing platforms that operate using multiple simultaneous superimposable signals.

Influence of the milling parameters on the nucleophilic substitution reaction of activated β-cyclodextrins

The present work focuses on the mechanochemical preparation of industrially important β-cyclodextrin (CD) derivatives. Activated CDs have been reacted with nitrogen and sulfur nucleophiles using a planetary mill equipped with stainless steel, zirconia and glass milling tools of different sizes. It is shown that the milling frequency and the number as well as the size of the milling balls have an effect on the nucleophilic reaction.

Sequence-Specific Detection of MicroRNAs Related to Clear Cell Renal Cell Carcinoma at fM Concentration by an Electroosmotically Driven Nanopore-Based Device

MicroRNAs (miRs) are small noncoding RNAs that play a critical role in gene regulation. Recently, traces of cancer-related miRs have been identified in body fluids, which make them remarkable noninvasive biomarkers. In this study, a new nanopore-based detection scheme utilizing a borosilicate micropipette and an assay of complementary γ-peptide nucleic acid (γ-PNA) probes conjugated to polystyrene beads have been reported for the detection of miR-204 and miR-210 related to the clear cell Renal Cell Carcinoma (ccRCC). Electroosmotic flow (EOF) is induced as the driving force to transport PNA-beads harboring target miRs to the tip of the pore (sensing zone), which results in pore blockades with unique and easily distinguishable serrated shape electrical signals. The concentration detection limit is investigated to be 1 and 10 fM for miR-204 and miR-210, respectively. The EOF transport mechanism enables highly sensitive detection of molecules with low surface charge density with 97.6% detection accuracy compared to the conventional electrophoretically driven methods. Furthermore, resistive-pulse experiments are conducted to study the correlation of the particles' surface charge density with their translocation time and verify the detection principle.

A Protein Nanopore-Based Approach for Bacteria Sensing

We present herein a first proof of concept demonstrating the potential of a protein nanopore-based technique for real-time detection of selected Gram-negative bacteria (Pseudomonas aeruginosa or Escherichia coli) at a concentration of 1.2 × 108 cfu/mL. The anionic charge on the bacterial outer membrane promotes the electrophoretically driven migration of bacteria towards a single α-hemolysin nanopore isolated in a lipid bilayer, clamped at a negative electric potential, and followed by capture at the nanopore's mouth, which we found to be described according to the classical Kramers' theory. By using a specific antimicrobial peptide as a putative molecular biorecognition element for the bacteria used herein, we suggest that the detection system can combine the natural sensitivity of the nanopore-based sensing techniques with selective biological recognition, in aqueous samples, and highlight the feasibility of the nanopore-based platform to provide portable, sensitive analysis and monitoring of bacterial pathogens.

Label-free nanopore single-molecule measurement of trypsin activity

Trypsin is the most important digestive enzyme produced in the pancreas, and is a useful biomarker for pancreatitis. In this work, a rapid and sensitive method for the quantitative determination of trypsin activity is developed by using a biological alpha-hemolysin protein nanopore. Due to its much larger molecular diameter than the narrow pore constriction, trypsin itself cannot transport through the alpha-hemolysin channel. Hence, an indirect trypsin detection method is developed by monitoring its proteolytic cleavage of a lysine-containing peptide substrate. Based on the current modulations produced by the translocation of the substrate degradation products in the nanopore, the activity levels of trypsin could be determined. The method is rapid and highly sensitive, with picomolar concentrations of trypsin detected in minutes. In addition, the effects of cation and temperature on the sensor sensitivity, trypsin inhibition, and serum sample analysis are also investigated.

Bioinspired Protein Channel-Based Scanning Ion Conductance Microscopy (Bio-SICM) for Simultaneous Conductance and Specific Molecular Imaging

The utility of stochastic single-molecule detection using protein nanopores has found widespread application in bioanalytical sensing as a result of the inherent signal amplification of the resistive pulse method. Integration of protein nanopores with high-resolution scanning ion conductance microscopy (SICM) extends the utility of SICM by enabling selective chemical imaging of specific target molecules, while simultaneously providing topographical information about the net ion flux through a pore under a concentration gradient. In this study, we describe the development of a bioinspired scanning ion conductance microscopy (bio-SICM) approach that couples the imaging ability of SICM with the sensitivity and chemical selectivity of protein channels to perform simultaneous pore imaging and specific molecule mapping. To establish the framework of the bio-SICM platform, we utilize the well-studied protein channel α-hemolysin (αHL) to map the presence of β-cyclodextrin (βCD) at a substrate pore opening. We demonstrate concurrent pore and specific molecule imaging by raster scanning an αHL-based probe over a glass membrane containing a single 25-μm-diameter glass pore while recording the lateral positions of the probe and channel activity via ionic current. We use the average channel current to create a conductance image and the raw current-time traces to determine spatial localization of βCD. With further optimization, we believe that the bio-SICM platform will provide a powerful analytical methodology that is generalizable, and thus offers significant utility in a myriad of bioanalytical applications.

Gated Silica Mesoporous Materials in Sensing Applications

Silica mesoporous supports (SMSs) have a large specific surface area and volume and are particularly exciting vehicles for delivery applications. Such container-like structures can be loaded with numerous different chemical substances, such as drugs and reporters. Gated systems also contain addressable functions at openings of voids, and cargo delivery can be controlled on-command using chemical, biochemical or physical stimuli. Many of these gated SMSs have been applied for drug delivery. However, fewer examples of their use in sensing protocols have been reported. The approach of applying SMSs in sensing uses another concept-that of loading pores with a reporter and designing a capping mechanism that is selectively opened in the presence of a target analyte, which results in the delivery of the reporter. According to this concept, we provide herein a complete compilation of published examples of probes based on the use of capped SMSs for sensing. Examples for the detection of anions, cations, small molecules and biomolecules are provided. The diverse range of gated silica mesoporous materials presented here highlights their usefulness in recognition protocols.

Micro- and nano-structure based oligonucleotide sensors

This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.

Label-free biomarker assay in a microresistive pulse sensor via immunoaggregation

We present a label-free biomarker detection method based on immunoaggregation and resistive pulse sensing technology. In this approach, target biomarkers and antibody (Ab)-functionalized microparticles are mixed to form biomarker-microparticle aggregates. A resistive pulse sensor is then used to measure the sizes and count the number of aggregates. The measured volume fraction of the aggregates represents the concentration of the targeted biomarker. In our tests, human ferritin, used as a biomarker, triggered the aggregation of antiferritin Ab-functionalized microparticles in phosphate-buffered saline (PBS). The volume fraction of aggregates increased with the increased ferritin concentration. We also demonstrated the detection of human ferritin in 10% fetal bovine serum (FBS) to mimic a real detection environment in complex media. The detection range from 0.1 to 208 ng/mL was achieved. In addition, we demonstrated that the detection range can be shifted to lower and higher concentrations by decreasing and increasing microparticle concentrations. This biomarker detection method is label-free, rapid, and able to quantitatively measure the concentration of any macromolecular biomarker as long as an antibody can be found, with simple measurement setup and sample preparations.

Pattern recognition of estradiol, testosterone and dihydrotestosterone in children's saliva samples using stochastic microsensors

Stochastic microsensors based on diamond paste and three types of electroactive materials (maltodextrin (MD), α-cyclodextrin (α-CD) and 5,10,15,20-tetraphenyl-21H,23H porphyrin (P)) were developed for the assay of estradiol (E2), testosterone (T2) and dihydrotestosterone (DHT) in children's saliva. The main advantage of utilization of such tools is the possibility to identify and quantify all three hormones within minutes in small volumes of childen's saliva. The limits of quantification obtained for DHT, T2, and E2 (1 fmol/L for DHT, 1 pmol/L for T2, and 66 fmol/L for E2) determined using the proposed tools allows the utilization of these new methods with high reliability for the screening of saliva samples from children. This new method proposed for the assay of the three hormones overcomes the limitations (regarding limits of determination) of ELISA method which is the standard method used in clinical laboratories for the assay of DHT, T2, and E2 in saliva samples. The main feature of its utilization for children's saliva is to identify earlier problems related to early puberty and obesity.

Solid-state nanopores and nanopore arrays optimized for optical detection

While conventional solid-state nanopore measurements utilize ionic current, there is a growing interest in alternative sensing paradigms, including optical detection. However, a limiting factor in the application of optical schemes in particular is the inherent background fluorescence created by the solid-state membrane itself, which can interfere with the desired signal and place restrictions on the fluorophores that can be employed. An ideal device would incorporate a localized reduction in membrane fluorescence using a method that can be integrated easily with the nanopore fabrication process. Here, we demonstrate that in addition to forming nanopores and nanopore arrays, a focused helium ion beam can be used to reduce the fluorescence of a conventional silicon nitride membrane controllably. The reduction in background produces low-fluorescence devices that can be used for optical detection of double-strand DNA, as well as for conventional resistive pulse sensing. This approach is used to identify the translocation of short single-strand DNA through individual nanopores within an array, creating potential for a massively-parallel detection scheme.

Nanopore biosensor for label-free and real-time detection of anthrax lethal factor

We report a label-free real-time nanopore sensing method for the detection of anthrax lethal factor, a component of the anthrax toxin, by using a complementary single-stranded DNA as a molecular probe. The method is rapid and sensitive: sub-nanomolar concentrations of the target anthrax lethal factor DNA could be detected in ∼1 min. Further, our method is selective, which can differentiate the target DNA from other single-stranded DNA molecules at the single-base resolution. This sequence-specific detection approach should find useful application in the development of nanopore sensors for the detection of other pathogens.

Monitoring charge flux to quantify unusual ligand-induced ion channel activity for use in biological nanopore-based sensors

The utility of biological nanopores for the development of sensors has become a growing area of interest in analytical chemistry. Their emerging use in chemical analysis is a result of several ideal characteristics. First, they provide reproducible control over nanoscale pore sizes with an atomic level of precision. Second, they are amenable to resistive-pulse type measurement systems when embedded into an artificial lipid bilayer. A single binding event causes a change in the flow of millions of ions across the membrane per second that is readily measured as a change in current with excellent signal-to-noise ratio. To date, ion channel-based biosensors have been limited to well-behaved proteins. Most demonstrations of using ion channels as sensors have been limited to proteins that remain in the open, conducting state, unless occupied by an analyte of interest. Furthermore, these proteins are nonspecific, requiring chemical, biochemical, or genetic manipulations to impart chemical specificity. Here, we report on the use of the pore-forming abilities of heat shock cognate 70 (Hsc70) to quantify a specific analyte. Hsc70 reconstitutes into phospholipid membranes and opens to form multiple conductance states specifically in the presence of ATP. We introduce the measurement of “charge flux” to characterize the ATP-regulated multiconductance nature of Hsc70, which enables sensitive quantification of ATP (100 μM–4 mM). We believe that monitoring protein-induced charge flux across a bilayer membrane represents a universal method for quantitatively monitoring ion-channel activity. This measurement has the potential to broaden the library of usable proteins in the development of nanopore-based biosensors.

Pore-forming compounds as signal transduction elements for highly sensitive biosensing

Pore-forming compounds are attracting much attention due to the signal transduction ability for the development of highly sensitive biosensing. In this review, we describe an overview of the recent advances made by our group in the design of molecular sensing interfaces of spherical and planar lipid bilayers and natural bilayers. The potential uses of pore-forming compounds, such as gramicidin and MCM-41, in lipid bilayers and natural glutamate receptor channels in biomembrane are presented.

Microfluidic systems with ion-selective membranes

When integrated into microfluidic chips, ion-selective nanoporous polymer and solid-state membranes can be used for on-chip pumping, pH actuation, analyte concentration, molecular separation, reactive mixing, and molecular sensing. They offer numerous functionalities and are hence superior to paper-based devices for point-of-care biochips, with only slightly more investment in fabrication and material costs required. In this review, we first discuss the fundamentals of several nonequilibrium ion current phenomena associated with ion-selective membranes, many of them revealed by studies with fabricated single nanochannels/nanopores. We then focus on how the plethora of phenomena has been applied for transport, separation, concentration, and detection of biomolecules on biochips.

Analysis of a single α-synuclein fibrillation by the interaction with a protein nanopore

The formation of an α-synuclein fibril is critical in the pathogenesis of Parkinson's disease. The native unfolded α-synuclein monomer will translocate through an α-hemolysin nanopore by applied potential at physiological conditions in vitro. Applying a potential transformed α-synuclein into a partially folded intermediate, which was monitored by capture inside the vestibule of an α-hemolysin nanopore with a capture current of 20 ± 1.0 pA. The procedure involves the critical early stage of α-synuclein structural transformation. Further elongation of the intermediate produces a block current to 5 ± 0.5 pA. It is revealed that the early stage fibril of α-synuclein inside the nanopore is affected by intrapeptide electrostatic interaction. In addition, trehalose cleared the fibrillation by changing the surface hydrophobic interaction of A53T α-synuclein, which did not show any inhibition effect from WT α-synuclein. The results proved that the interpeptide hydrophobic interactions in the elongation of A53T α-synuclein protofilaments can be greatly weakened by trehalose. This suggests that trehalose inhibits the interpeptide interaction involved in protein secondary structure. The hydrophobic and electrostatic interactions are associated with an increase in α-synuclein fibrillation propensity. This work provides unique insights into the earliest steps of the α-synuclein aggregation pathway and provides the potential basis for the development of drugs that can prevent α-synuclein aggregation at the initial stage.

Detection of miRNAs with a nanopore single-molecule counter

miRNAs are short noncoding RNA molecules that are important in regulating gene expression. Due to the correlation of their expression levels and various diseases, miRNAs are being investigated as potential biomarkers for molecular diagnostics. The fast-growing miRNA exploration demands rapid, accurate, low-cost miRNA detection technologies. This article will focus on two platforms of nanopore single-molecule approach that can quantitatively measure miRNA levels in samples from tissue and cancer patient plasma. Both nanopore methods are sensitive and specific, and do not need labeling, enzymatic reaction or amplification. In the next 5 years, the nanopore-based miRNA techniques will be improved and validated for noninvasive and early diagnosis of diseases.

Single-molecule investigation of G-quadruplex using a nanopore sensor

This review article introduces the nanopore single-molecule method for the study of G-quadruplex nucleic acid structures. Single G-quadruplexes can be trapped into a 2 nm protein pore embedded in the lipid bilayer membrane. The trapped G-quadruplex specifically blocks the current through the nanopore, creating a signature event for quantitative analysis of G-quadruplex properties, from cation-determined folding and unfolding kinetics to the interactions with the protein ligand. The nanopore single-molecule method is simple, accurate, and requires no labels. It can be used to evaluate G-quadruplex mechanisms and it may have applications in G-quadruplex-based biosensors, nanomachines, and nanostructure assembly.

Stochastic sensing of proteins with receptor-modified solid-state nanopores

Solid-state nanopores are capable of the label-free analysis of single molecules. It is possible to add biochemical selectivity by anchoring a molecular receptor inside the nanopore, but it is difficult to maintain single-molecule sensitivity in these modified nanopores. Here, we show that metallized silicon nitride nanopores chemically modified with nitrilotriacetic acid receptors can be used for the stochastic sensing of proteins. The reversible binding and unbinding of the proteins to the receptors is observed in real time, and the interaction parameters are statistically analysed from single-molecule binding events. To demonstrate the versatile nature of this approach, we detect His-tagged proteins and discriminate between the subclasses of rodent IgG antibodies.

Natural and artificial ion channels for biosensing platforms

The single-molecule selectivity and specificity of the binding process together with the expected intrinsic gain factor obtained when utilizing flow through a channel have attracted the attention of analytical chemists for two decades. Sensitive and selective ion channel biosensors for high-throughput screening are having an increasing impact on modern medical care, drug screening, environmental monitoring, food safety, and biowarefare control. Even virus antigens can be detected by ion channel biosensors. The study of ion channels and other transmembrane proteins is expected to lead to the development of new medications and therapies for a wide range of illnesses. From the first attempts to use membrane proteins as the receptive part of a sensor, ion channels have been engineered as chemical sensors. Several other types of peptidic or nonpeptidic channels have been investigated. Various gating mechanisms have been implemented in their pores. Three technical problems had to be solved to achieve practical biosensors based on ion channels: the fabrication of stable lipid bilayer membranes, the incorporation of a receptor into such a structure, and the marriage of the modified membrane to a transducer. The current status of these three areas of research, together with typical applications of ion-channel biosensors, are discussed in this review.

Translocation of single-stranded DNA through the α-hemolysin protein nanopore in acidic solutions

The effect of acidic pH on the translocation of single-stranded DNA through the α-hemolysin pore is investigated. Two significantly different types of events, i.e. deep blockades and shallow blockades, are observed at low pH. The residence times of the shallow blockades are not significantly different from those of the DNA translocation events obtained at or near physiological pH, whereas the deep blockades have much larger residence times and blockage amplitudes. With a decrease in the pH of the electrolyte solution, the percentage of the deep blockades in the total events increases. Furthermore, the mean residence time of these long-lived events is dependent on the length of DNA, and also varies with the nucleotide base, suggesting that they are appropriate for use in DNA analysis. In addition to being used as an effective approach to affect DNA translocation in the nanopore, manipulation of the pH of the electrolyte solution provides a potential means to greatly enhance the sensitivity of nanopore stochastic sensing.

Advances in Resistive Pulse Sensors: Devices bridging the void between molecular and microscopic detection

Since the first reported use of a biological ion channel to detect differences in single stranded genomic base pairs in 1996, a renaissance in nanoscale resistive pulse sensors has ensued. This resurgence of a technique originally outlined and commercialized over fifty years ago has largely been driven by advances in nanoscaled fabrication, and ultimately, the prospect of a rapid and inexpensive means for genomic sequencing as well as other macromolecular characterization. In this pursuit, the potential application of these devices to characterize additional properties such as the size, shape, charge, and concentration of nanoscaled materials (10 - 900 nm) has been largely overlooked. Advances in nanotechnology and biotechnology are driving the need for simple yet sensitive individual object readout devices such as resistive pulse sensors. This review will examine the recent progress in pore-based sensing in the nanoscale range. A detailed analysis of three new types of pore sensors - in-series, parallel, and size-tunable pores - has been included. These pores offer improved measurement sensitivity over a wider particle size range. The fundamental physical chemistry of these techniques, which is still evolving, will be reviewed.

Techniques for recording reconstituted ion channels

This review describes and discusses techniques useful for monitoring the activity of protein ion channels in vitro. In the first section the biological importance and the classification of ion channels are outlined in order to justify the strong motivation for dealing with this important class of membrane proteins. The expression, reconstitution and integration of recombinant proteins into lipid bilayers are crucial steps to obtain consistent data when working with ion channels. In the second section recording techniques used in research are presented. Since this review focuses on analytical systems bearing reconstituted ion channels the industrial most important patch-clamp techniques of cells are only briefly mentioned. In section three, artificial systems developed in the last decades are described while the emerging technologies using nanostructured supports or microfluidic systems are presented in section four. Finally, the remaining challenges of membrane protein analysis and its potential applications are briefly outlined.