A stimuli-responsive nanopore based on a photoresponsive host-guest system

Organic-Inorganic Artificial Ion Channel Polyvinylidene Fluoride Membranes for Controllable Selectivity Transport of Alkali Metal Cations

In this article, organic-inorganic hybrid materials with different functional groups were used to form organic-inorganic hybrid dense membranes for selective separation of mono/divalent ions by blending these materials and polyvinylidene fluoride (PVDF) in dimethylacetamide with HCl as the catalyst. The membranes prepared by 3-(ureido benzene) propyltriethoxysilane (H1), 3-(ureido-4-methoxyphenyl) propyltriethoxysilane (H2), 3-(ureido-3-chloro-4-methoxyphenyl) propyltriethoxysilane (H3), 3-(ureidoindazolyl) propyltrieth-oxysilane (H4), or 3-(ureidopentanol) propyltriethoxysilane (H5) were labeled as HM1-HM5, respectively. The transport properties of different chlorides were tested. The effects of different anions on sodium cation transport were also tested. The results showed that HM1-HM4 could transport monovalent Li+, Na+, and K+ except Ca2+ and Mg2+, and the permeability of Li+, Na+, and K+ through the hybrid membranes followed the order of PNa+ > PK+ > PLi+. Moreover, membranes with different H2 content were also prepared due to HM2 having the best ion transport performance. The ion transport performance increased accordingly with the mass ratio of H2 to PVDF, and the permeability of Na+ was twice that of Li+ and K+ when the mass ratio was 15/10. Under this condition, it was also proved that NH4+ could not transport through the hybrid membrane with various selectivity for different anions as Cl- > NO3- > HCO3- > SO42-.

Real-Time Label-Free Kinetics Monitoring of Trypsin-Catalyzed Ester Hydrolysis by a Nanopore Sensor

Trypsin is an important proteolytic enzyme in the digestive system and its activity is a major indicator for evaluating diseases such as chronic pancreatitis. Here, we present a novel label-free method to detect trypsin kinetics using a nanopore technique. A mutant α-hemolysin (M113R)₇ protein nanopore equipped with a polyamine decorated β-cyclodextrin (am₇β-CD) was employed as a sensing platform for the real-time monitoring of the process of trypsin enzymatic cleavage of a substrate Nα-benzoyl-l-arginine ethyl ester (BAEE) at the single molecule level. Significantly, this sensor can exclusively respond to the current modulation caused by the product and prevent interference from the substrate, thus improving detection sensitivity, and it provides a new scheme to detect enzyme activity for cleaving small molecules.

Investigation of hairpin DNA and chelerythrine interaction by a single bio-nanopore sensing interface

Chelerythrine (CHE) is one of the potential drugs for cancer treatments. The interaction between hairpin DNA and CHE has been investigated by spectral and mass spectrometry methods. In this paper, the stability of hairpin DNA with different loop bases and its interaction with CHE were explored with a single α-hemolysin (α-HL) nanopore sensing interface. The results showed that the characteristic current pulses not only relate to the loop composition changes of the hairpin DNA, but also provide interaction information between CHE and the hairpin DNA molecules. The dwell time of current pulses for hairpin DNA was significantly increased (hundreds of ms) due to the addition of CHE, and two characteristic current distributions were recognized for the hairpin with T₃ and C₃ loops. The two characteristic current groups could be ascribed to the hairpin DNA and the ones with CHE. This study indicates that it is possible to study the interaction between single CHE and single hairpin DNA molecules by the single-nanopore sensing interface as an alternative method to conventional spectrometric methods for therapeutic mechanism and drug screening purposes.

Counterion effect on sulfonatocalix[n]arene recognition

Sulfonatocalixarenes, like other ionic receptors, possess counterions that can affect the molecular recognition process. In the present review it is shown that the competitive effect of the alkaline cations frequently used as counterions determines not only the magnitude of the external guest association constant, but also the stoichiometry of the complexes. Experimental evidences are shown about the interaction of the counterions with sulfonatocalixarene, allowing to quantify its association equilibrium constants. The counterions recognition will be a competitive process that must be taken into account when investigating the interaction of calixarenes with an external guests. When the external guest is a neutral molecule it will be possible to form ternary complexes where the counterion shows a competitive and cooperative effect. By increasing the size of the receptor, sulfonatocalix[6] and sulfonatocalix[8]arene, the complexity of the system is increased due to the formation of counterion complexes with stoichiometries 1:1 and 1:2. In the presence of an external guest, the formation of heteroternary complexes with 1:1:1 stoichiometries including a counterion and an organic cation will be possible.

Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms

Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.

Measuring Binding Constants of Cucurbituril-Based Host-Guest Interactions at the Single-Molecule Level with Nanopores

Cucurbiturils are one type of widely used macrocyclic host compound in supramolecular chemistry. Their peculiar properties have led to applications in a wide variety of research areas such as fluorescence spectroscopy, drug delivery, catalysis, and nanotechnology. However, the solubilities of cucurbiturils are rather poor in water and many organic solvents, which may cause accuracy problems when measuring binding constants with traditional methods. In this report, we aim to develop an approach to measure the binding constants of cucurbituril-based host-guest interactions at the single-molecule level. First, we covalently attach different guest compounds to the side-chain of DNA molecules. Then, excess cucurbiturils are incubated with DNA probes to form the host-guest complexes. Next, the modified DNA hybrids are threaded through α-hemolysin nanopore to generate highly characteristic current events. Finally, statistical analyses of the obtained events afford the binding constants of cucurbiturils with various molecules. This new approach provides a simple and straightforward method to compare binding strength of different host-guest complexes and may find applications for quantifying other macrocycle-based host-guest interactions.

Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores

Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.

Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate

Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a hybrid nanopore system that allows for both a stepwise change of its conductance and a nonlinear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position (and, in a later stage, remove) the peptide gate right at the most-sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a nonlinear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.

Bacteriorhodopsin-Inspired Light-Driven Artificial Molecule Motors for Transmembrane Mass Transportation

In nature, biological machines and motors can selectively transport cargoes across the lipid membranes to efficiently perform various physiological functions via ion channels or ion pumps. It is interesting and challengeable to develop artificial motors and machines of nanodimensions to controllably regulate mass transport in compartmentalized systems. In this work, we show a system of artificial molecular motors that uses light energy to perform transmembrane molecule transport through synthetical nanochannels. After functionalizing the polymer nanochannels with azobenzene derivatives, these nanomachines exhibit autonomous selective transport behavior over a long distance upon simultaneous irradiation with UV (365 nm) and visible (430 nm) light. With new strategies or suitable materials for directed molecular movement, such device can be regarded as a precursor of artificial light-driven molecular pumps.

Controlling Interactions of Cyclic Oligosaccharides with Hetero-Oligomeric Nanopores: Kinetics of Binding and Release at the Single-Molecule Level

Controlling the molecular interactions through protein nanopores is crucial for effectively detecting single molecules. Here, the development of a hetero-oligomeric nanopore derived from Nocardia farcinica porin AB (NfpAB) is discussed for single-molecule sensing of biopolymers. Using single-channel recording, the interaction of cyclic oligosaccharides such as cationic cyclodextrins (CDs) of different symmetries and charges with NfpAB is measured. Studies of the transport kinetics of CDs reveal asymmetric geometry and charge distribution of NfpAB. The applied potential promotes the attachment of the cationic CDs to the negatively charged pore surface due to electrostatic interaction. Further, the attached CDs are released from the pore by reversing the applied potential in time-resolved blockages. Release of CDs from the pore depends on its charge, size, and magnitude of the applied potential. The kinetics of CD attachment and release is controlled by fine-tuning the applied potential demonstrating the successful molecular transport across these nanopores. It is suggested that such controlled molecular interactions with protein nanopores using organic templates can be useful for several applications in nanopore technology and single-molecule chemistry.

Label-Free Sensing of Human 8-Oxoguanine DNA Glycosylase Activity with a Nanopore

Human 8-oxoguanine DNA glycosylase (hOGG1) plays a significant role in maintaining the genomic integrity of living organisms for its capability of repairing DNA lesions. Accurate detection of hOGG1 activity would greatly facilitate the screening and early diagnosis of diseases. In this work, we report a nanopore-based sensing strategy to probe the hOGG1 activity by employing the enzyme-catalytic cleavage reaction of DNA substrate. The hOGG1 specifically catalyzed the removal of the 8-hydroxyguanine (8-oxoG) and cleaved the DNA substrates immobilized on magnetic beads, thereby releasing the output DNA which would quantitatively produce the signature current events when subjected to α-hemolysin (α-HL) nanopore test. The approach enables the sensitive detection of hOGG1 activity without the need of any labeling or signal amplification route. Furthermore, the method can be applied to assay the inhibition of hOGG1 and evaluate the activity of endogenous hOGG1 in crude cell extracts. Importantly, since DNAs with specific sequences are the catalytic substrates of a wide variety of enzymes, the proposed strategy should be universally applicable for probing the activities of different types of enzymes with nanopore sensors.

In Situ Synthetic Functionalization of a Transmembrane Protein Nanopore

Monitoring current flow through a single nanopore has proved to be a powerful technique for the in situ detection of molecular structure, binding, and reactivity. Transmembrane proteins, such as α-hemolysin, provide particularly attractive platforms for nanopore sensing applications due to their atomically precise structures. However, many nanopore applications require the introduction of functional groups to tune selectivity. To date, such modifications have required genetic modification of the protein prior to functionalization. Here we demonstrate the in situ synthetic modification of a wild-type α-hemolysin nanopore embedded in a membrane. We show that reversible dynamic covalent iminoboronate formation and the resulting changes in the ion current flowing through an individual nanopore can be used to map the reactive behavior of lysine residues within the nanopore channel. Crucially, the modification of lysine residues located outside the nanopore channel was found not to affect the stability or utility of the nanopore. Finally, knowledge of the reactivity patterns enabled the irreversible functionalization of a single, assignable lysine residue within the nanopore channel. The approach constitutes a simple, generic tool for the rapid, in situ synthetic modification of protein nanopores that circumvents the need for prior genetic modification.

Functionalization of single solid state nanopores to mimic biological ion channels: A review

In nature, ion channels are highly selective pores and act as gate to ensure selective ion transport, allowing ions to cross the membrane. By mimicking them, single solid state nanopore devices emerge as a new, powerful class of molecule sensors that allow for the label-free detection of biomolecules (DNA, RNA, and proteins), non-biological polymers, as well as small molecules. In this review, we exhaustively describe the fabrication and functionalization techniques to design highly robust and selective solid state nanopores. First we outline the different materials and methods to design nanopores, we explain the ionic conduction in nanopores, and finally we summarize some techniques to modify and functionalize the surface in order to obtain biomimetic nanopores, responding to different external stimuli.

High-bandwidth nanopore data analysis by using a modified hidden Markov model

Nanopore-based sensing is an emerging analytical technique with a number of important applications, including single-molecule detection and DNA sequencing. In this paper, we developed a Modified Hidden Markov Model (MHMM) to analyze directly the raw (unfiltered) nanopore current blockade data, which significantly reduced the filtering-induced distortion of the nanopore events. Traditionally, prior to further analysis, the measured nanopore data need to be pre-filtered to supress the strong noises. Nonetheless, this would result in the distortion of the shape of the blockade current especially for rapid translocations and bumping blockades. The HMM has been proved to be robust with respect to highly noisy data and thus ideally suitable for processing raw nanopore data directly. Unfortunately, its performance is somehow sensitive to the initial parameters usually preset arbitrarily. To overcome this problem, we use the Fuzzy c-Means (FCM) algorithm to initialize the HMM parameters automatically. Then we use the Viterbi training algorithm to optimize the HMM. Finally, the application results on both the simulated and experimental data are presented to demonstrate the practicability of the developed method for accurate detection of the nanopore current blockade events. The proposed method enables detection of the nanopore events at the highest bandwidth of the commercial instruments to extract the true useful information about the single molecules under analysis.

Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore

Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore.

Nanopore-Based Selective Discrimination of MicroRNAs with Single-Nucleotide Difference Using Locked Nucleic Acid-Modified Probes

The accurate discrimination of microRNAs (miRNAs) with highly similar sequences would greatly facilitate the screening and early diagnosis of diseases. In the present work, a locked nucleic acid (LNA)-modified probe was designed and used for α-hemolysin (α-HL) nanopore to selectively and specifically identify miRNAs. The hybridization of the LNA probe with the target miRNAs generated unique long-lived signals in the nanopore thus facilitated an accurate discrimination of miRNAs with similar sequences, even a single-nucleotide difference. Furthermore, the developed nanopore-based analysis with LNA probe could selectively detect target miRNAs in a natural serum background. This selective and sensitive approach may be highly valuable in the detection of clinically relevant biomarkers in complex samples.

Gene expression variability in clonal populations: Causes and consequences

During the last decade it has been shown that among cell variation in gene expression plays an important role within clonal populations. Here, we provide an overview of the different mechanisms contributing to gene expression variability in clonal populations. These are ranging from inherent variations in the biochemical process of gene expression itself, such as intrinsic noise, extrinsic noise and bistability to individual responses to variations in the local micro-environment, a phenomenon called phenotypic plasticity. Also genotypic variations caused by clonal evolution and phase variation can contribute to gene expression variability. Consequently, gene expression studies need to take these fluctuations in expression into account. However, frequently used techniques for expression quantification, such as microarrays, RNA sequencing, quantitative PCR and gene reporter fusions classically determine the population average of gene expression. Here, we discuss how these techniques can be adapted towards single cell analysis by integration with single cell isolation, RNA amplification and microscopy. Alternatively more qualitative selection-based techniques, such as mutant screenings, in vivo expression technology (IVET) and recombination-based IVET (RIVET) can be applied for detection of genes expressed only within a subpopulation. Finally, differential fluorescence induction (DFI), a protocol specially designed for single cell expression is discussed.

Alkyl detection facilitated by a DNA conjugate with an α-hemolysin nanopore

A novel α-hemolysin nanopore (α-HL) based strategy for the detection of an alkyl linker at the single-molecule level.

A universal strategy for aptamer-based nanopore sensing through host-guest interactions inside α-hemolysin

Nanopore emerged as a powerful single-molecule technique over the past two decades, and has shown applications in the stochastic sensing and biophysical studies of individual molecules. Here, we report a versatile strategy for nanopore sensing by employing the combination of aptamers and host-guest interactions. An aptamer is first hybridized with a DNA probe which is modified with a ferrocene⊂cucurbit[7]uril complex. The presence of analytes causes the aptamer-probe duplex to unwind and release the DNA probe which can quantitatively produce signature current events when translocated through an α-hemolysin nanopore. The integrated use of magnetic beads can further lower the detection limit by approximately two to three orders of magnitude. Because aptamers have shown robust binding affinities with a wide variety of target molecules, our proposed strategy should be universally applicable for sensing different types of analytes with nanopore sensors.

Single-molecule analysis of the self-assembly process facilitated by host–guest interactions

The self-assembly process operated by para-sulfonatocalix[6]arenes and methyl viologen was analyzed at the single-molecule level through an α-hemolysin nanopore.

An integrated system for optical and electrical detection of single molecules/particles inside a solid-state nanopore

Nanopore techniques have proven to be useful tools for single-molecule detection. The combination of optical detection and ionic current measurements enables a new possibility for the parallel readout of multiple nanopores without complex nanofluidics and embedded electrodes. In this study, we developed a new integrated system for the label-free optical and electrical detection of single molecules based on a metal-coated nanopore. The entire system, containing a dark-field microscopy system and an ultralow current detection system with high temporal resolution, was designed and fabricated. An Au-coated nanopore was used to generate the optical signal. Light scattering from a single Au-coated nanopore was measured under a dark-field microscope. A lab-built ultralow current detection system was designed for the correlated optical and electrical readout. This integrated system might provide more direct and detailed information on single analytes inside the nanopore compared with classical ionic current measurements.

Amplification of single molecule translocation signal using β-strand peptide functionalized nanopores

Changes in ionic current flowing through nanopores due to binding or translocation of single biopolymer molecules enable their detection and characterization. It is, however, much more challenging to detect small molecules due to their rapid and small signal signature. Here we demonstrate the use of de novo designed peptides for functionalization of nanopores that enable the detection of a small analytes at the single molecule level. The detection relies on cooperative peptide conformational change that is induced by the binding of the small molecule to a receptor domain on the peptide. This change results in alteration of the nanopore effective diameter and hence induces current perturbation signal. On the basis of this approach, we demonstrate here the detection of diethyl 4-nitrophenyl phosphate (paraoxon), a poisonous organophosphate molecule. Paraoxon binding is induced by the incorporation of the catalytic triad of acetylcholine esterase in the hydrophilic domain of a short amphiphilic peptide and promotes β-sheet assembly of the peptide both in solution and for peptide molecules immobilized on solid surfaces. Nanopores coated with this peptide allowed the detection of paraoxon at the single molecule level revealing two binding arrangements. This unique approach, hence, provides the ability to study interactions of small molecules with the corresponding engineered receptors at the single molecule level. Furthermore, the suggested versatile platform may be used for the development of highly sensitive small analytes sensors.

Single-cell RNA-seq: advances and future challenges

Phenotypically identical cells can dramatically vary with respect to behavior during their lifespan and this variation is reflected in their molecular composition such as the transcriptomic landscape. Single-cell transcriptomics using next-generation transcript sequencing (RNA-seq) is now emerging as a powerful tool to profile cell-to-cell variability on a genomic scale. Its application has already greatly impacted our conceptual understanding of diverse biological processes with broad implications for both basic and clinical research. Different single-cell RNA-seq protocols have been introduced and are reviewed here—each one with its own strengths and current limitations. We further provide an overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field.

Single molecule analysis by biological nanopore sensors

Nanopore sensors provide a highly innovative technique for a rapid and label-free single molecule analysis, which holds a great potential in routing applications. Biological nanopores have been used as ultra-sensitive sensors over a wide range of single molecule analysis including DNA sequencing, disease diagnosis, drug screening, environment monitoring and the construction of molecule machines. This mini review will focus on the current strategies for the identification and characterization of an individual analyte, especially based on our recent achievements in biological nanopore biosensors.

Construction of biomimetic smart nanochannels for confined water

In this review, we focus on the confined water that exists in one-dimensional micro/nano composite structures, particularly inside biological nanochannels. Using these nanochannels as inspiration, we discuss a strategy for the design and construction of biomimetic smart nanochannels. Unique features of the inner surfaces of a nanochannel's wall have similar properties to living systems. Importantly, the abiotic analogs have potential applications in, for example, sensing, energy conversion and filtering.