Stereoselective detection of amino acids with protein-modified single asymmetric nanopores

Identification and Detection of a Peptide Biomarker and Its Enantiomer by Nanopore

Until now, no fast, low-cost, and direct technique exists to identify and detect protein/peptide enantiomers, because their mass and charge are identical. They are essential since l- and d-protein enantiomers have different biological activities due to their unique conformations. Enantiomers have potential for diagnostic purposes for several diseases or normal bodily functions but have yet to be utilized. This work uses an aerolysin nanopore and electrical detection to identify vasopressin enantiomers, l-AVP and d-AVP, associated with different biological processes and pathologies. We show their identification according to their conformations, in either native or reducing conditions, using their specific electrical signature. To improve their identification, we used a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used the Monte Carlo prediction to assign each event type to a specific l- or d-AVP enantiomer.

Narrowing Signal Distribution by Adamantane Derivatization for Amino Acid Identification Using an α-Hemolysin Nanopore

The rapid progress in nanopore sensing has sparked interest in protein sequencing. Despite recent notable advancements in amino acid recognition using nanopores, chemical modifications usually employed in this process still need further refinements. One of the challenges is to enhance the chemical specificity to avoid downstream misidentification of amino acids. By employing adamantane to label proteinogenic amino acids, we developed an approach to fingerprint individual amino acids using the wild-type α-hemolysin nanopore. The unique structure of adamantane-labeled amino acids (ALAAs) improved the spatial resolution, resulting in distinctive current signals. Various nanopore parameters were explored using a machine-learning algorithm and achieved a validation accuracy of 81.3% for distinguishing nine selected amino acids. Our results not only advance the effort in single-molecule protein characterization using nanopores but also offer a potential platform for studying intrinsic and variant structures of individual molecules.

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.

Electricity-Wettability Controlled Fast Transmission of Dopamine in Nanochannels

Achieving fast transmembrane transmission of molecules in organisms is a challenging problem. Inspired by the transport of Dopmine (DA) in organisms, the DA transporter (DAT) binds to DA in a way that has a ring recognition (the recognition group is the tryptophan group). Herein, D-Tryptophan-pillar[5]arene (D-Trp-P5) functionalized conical nanochannel is constructed to achieve fast transmission of DA. The D-Trp-P5 functionalized nanochannel enables specific wettability recognition of DA molecules and has great cycle stability. With the controlling of voltage to wettability, the transport flux of DA is up to 499.73 nmol cm^-2 h^-1 at -6 V, 16.88 times higher than that under positive voltages. In response to these results, a high-throughput DA transport device based on controlled electricity-wettability is provided.

Inner Wall and Outer Surface Distinguished Solid-State Nanopores for Sensing

Solid-state nanopores, inspired by biological nanopores, have the advantages of good mechanical properties, stability, and easy modification. They have attracted wide attention in the fields of sequencing, sensing, molecular sieving, nanofluidic devices, nanoelectrochemistry, and energy conversion. Because of the ion/molecule transport characteristic of the pore, the research on solid-state nanopores mainly focuses on the functional modification of its inner wall. In recent years, the outer surface of nanopores has also attracted the attention of researchers, and the functional elements on the outer surface have the functions of anti-interference and ionic signal enhancement. In this perspective, we review research progress of inner wall and outer surface distinguished solid-state nanopores, highlight their processing and advantages, summarize their functions and applications in sensing, and give insight into further research.

Bio-inspired Track-Etched Polymeric Nanochannels: Steady-State Biosensors for Detection of Analytes

Bio-inspired polymeric nanochannel (also referred as nanopore)-based biosensors have attracted considerable attention on account of their controllable channel size and shape, multi-functional surface chemistry, unique ionic transport properties, and good robustness for applications. There are already very informative reviews on the latest developments in solid-state artificial nanochannel-based biosensors, however, which concentrated on the resistive-pulse sensing-based sensors for practical applications. The steady-state sensing-based nanochannel biosensors, in principle, have significant advantages over their counterparts in term of high sensitivity, fast response, target analytes with no size limit, and extensive suitable range. Furthermore, among the diverse materials, nanochannels based on polymeric materials perform outstandingly, due to flexible fabrication and wide application. This compressive Review summarizes the recent advances in bio-inspired polymeric nanochannels as sensing platforms for detection of important analytes in living organisms, to meet the high demand for high-performance biosensors for analysis of target analytes, and the potential for development of smart sensing devices. In the future, research efforts can be focused on transport mechanisms in the field of steady-state or resistive-pulse nanochannel-based sensors and on developing precisely size-controlled, robust, miniature and reusable, multi-functional, and high-throughput biosensors for practical applications. Future efforts should aim at a deeper understanding of the principles at the molecular level and incorporating these diverse pore architectures into homogeneous and defect-free multi-channel membrane systems. With the rapid advancement of nanoscience and biotechnology, we believe that many more achievements in nanochannel-based biosensors could be achieved in the near future, serving people in a better way.

Solid-state and polymer nanopores for protein sensing: A review

In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.

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.

Tunable Current Rectification and Selectivity Demonstrated in Nanofluidic Diodes through Kinetic Functionalization

The possibility of tuning the current rectification and selectivity in nanofluidic diodes is demonstrated both experimentally and theoretically through dynamically functionalizing a conical nanopore with poly-l-lysine. We identified an optimum functionalization time equivalent to optimum modification depth that assures the highest rectification degrees. Results showed that the functionalization time-dependent rectification behavior of nanofluidic diodes is dominated by the properties of current at positive voltages that in our electrode configuration indicate the "on" state of the diode and accumulation of ions in the nanopore. The functionalization time also tunes the ion selectivity of the diode. If the functionalization time is sufficiently short, an unusual depletion of counterions near the bipolar interface results in a cation-selective nanopore. However, a further increase in the duration of functionalization renders a nanopore that is an anion-selective nanopore. The dynamic functionalization presented in this Letter enables tuning ion selectivity of nanopores.

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Molecular Design of Solid-State Nanopores: Fundamental Concepts and Applications

Solid-state nanopores are fascinating objects that enable the development of specific and efficient chemical and biological sensors, as well as the investigation of the physicochemical principles ruling the behavior of biological channels. The great variety of biological nanopores that nature provides regulates not only the most critical processes in the human body, including neuronal communication and sensory perception, but also the most important bioenergetic process on earth: photosynthesis. This makes them an exhaustless source of inspiration toward the development of more efficient, selective, and sophisticated nanopore-based nanofluidic devices. The key point responsible for the vibrant and exciting advance of solid nanopore research in the last decade has been the simultaneous combination of advanced fabrication nanotechnologies to tailor the size, geometry, and application of novel and creative approaches to confer the nanopore surface specific functionalities and responsiveness. Here, the state of the art is described in the following critical areas: i) theory, ii) nanofabrication techniques, iii) (bio)chemical functionalization, iv) construction of nanofluidic actuators, v) nanopore (bio)sensors, and vi) commercial aspects. The plethora of potential applications once envisioned for solid-state nanochannels is progressively and quickly materializing into new technologies that hold promise to revolutionize the everyday life.

Metal-organic complex-functionalized protein nanopore sensor for aromatic amino acids chiral recognition

Chiral recognition at single-molecule level for small active molecules is important, as exhibited by many nanostructures and molecular assemblies in biological systems, but it presents a significant challenge. We report a simple and rapid sensing strategy to discriminate all enantiomers of natural aromatic amino acids (AAA) using a metal-organic complex-functionalized protein nanopore, in which a chiral recognition element and a chiral recognition valve were equipped. A trifunctional molecule, heptakis-(6-deoxy-6-amino)-β-cyclodextrin (am₇βCD), was non-covalently lodged within the nanopore of an α-hemolysin (αHL) mutant, (M113R)₇-αHL. Copper(ii) ion reversibly bonds to the amino group of am₇βCD to form an am₇βCD-Cu^II complex, which allowed chiral recognition for each enantiomer in the mixture of AAA by distinct current signals. The Cu^II plugging valve plays a crucial rule that holds chiral molecules in the nanocavity for a sufficient registering time. Importantly, six enantiomers of all nature AAA could be simultaneously recognized at one time. Enantiomeric excess (ee) could also be accurately detected by this approach. It should be possible to generalize this approach for sensing of other chiral molecules.

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.

Discrimination of supramolecular chirality using a protein nanopore

Supramolecular chirality may emerge from self-assembly processes to yield architectures that differ only in the topological arrangement of their constituent parts. Since the properties of the resulting enantiomeric assemblies are identical, purification and characterisation can be challenging. Here, we have examined the hypothesis that the intrinsic chirality of a protein nanopore can be exploited to detect supramolecular chirality. Transient blockages in the ion current flowing through a single membrane-spanning α-haemolysin nanopore were shown to discriminate between M4L6 tetrahedral coordination cages of opposing chiralities. The single-molecule nature of the approach facilitated direct access to the rates of association and dissociation with the nanopore, which allowed the concentrations of the enantiomeric supramolecular assemblies to be determined in situ. Thus, we have established that a protein nanopore can be used to discriminate the chiral topologies of supramolecular assemblies, even when they are too large to fully enter the nanopore.