Nanopore sensing: A physical-chemical approach

Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores

Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.

The Role of MXene Surface Terminations on Peptide Transportation in Nanopore Sensing

Nanopores with two-dimensional materials have various advantages in sensing, but the fast translocation of molecules hinders their scale-up applications. In this work, we investigate the influence of -F, -O, and -OH surface terminations on the translocation of peptides through MXene nanopores. We find that the longest dwell time always occurs when peptides pass through the Ti3C2O2 nanopores. This elongated dwell time is induced by the strongest interaction between peptides and the Ti3C2O2 membrane, in which the van der Waals interactions dominate. Compared to the other two MXene nanopores, the braking effect is indicated during the whole translocation process, which evidence the advantage of Ti3C2O2 in nanopore sensing. Our work demonstrates that membrane surface chemistry has a great influence on the translocation of peptides, which can be introduced in the design of nanopores for a better performance.

Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores

DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.

Ready-to-use nanopore platform for label-free small molecule quantification: Ethanolamine as first example

In recent decades, nanopores have become a promising diagnostic tool. Protein and solid-state nanopores are increasingly used for both RNA/DNA sequencing and small molecule detection. The latter is of great importance, as their detection is difficult or expensive using available methods such as HPLC or LC-MS. DNA aptamers are an excellent detection element for sensitive and specific detection of small molecules. Herein, a method for quantifying small molecules using a ready-to-use sequencing platform is described. Taking ethanolamine as an example, a strand displacement assay is developed in which the target-binding aptamer is displaced from the surface of magnetic particles by ethanolamine. Non-displaced aptamer and thus the ethanolamine concentration are detected by the nanopore system and can be quantified in the micromolar range using our in-house developed analysis software. This method is thus the first to describe a label-free approach for the detection of small molecules in a protein nanopore system.

Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings

Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as "silent translocation." By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.

Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity

The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.

Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores

Mass spectrometry (MS) is widely used in proteomic analysis but cannot differentiate between molecules with the same mass-to-charge ratio. Nanopore technology might provide an alternative method for the rapid and cost-effective analysis and sequencing of proteins. In this study, we demonstrate that nanopore currents can distinguish between diastereomeric and enantiomeric differences in l- and d-peptides, not observed by conventional MS analysis, down to individual d-amino acids in small opioid peptides. Molecular dynamics simulations suggest that similar to chiral chromatography the resolution likely arises from multiple chiral interactions during peptide transport across the nanopore. Additionally, we used nanopore recordings to rapidly assess 4- and 11-amino acid ring formation in lanthipeptides, a process used in the synthesis of pharmaceutical peptides. The cyclization step requires distinguishing between constitutional isomers, which have identical MS signals and typically involve numerous tedious experiments to confirm. Hence, nanopore technology offers new possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.

Maintaining Single-Channel Recordings on a Silver Nanoneedle through Probe Design and Feedback Tip Positioning Control

Ion channel proteins showed great promise in the field of nanopore sensing and molecular flux imaging applications due to the atomic-level precision of the pore size and a high signal-to-noise ratio. More specifically, ion channel probes, where the protein channels are integrated at the end of a solid probe, can achieve highly localized detection. Metal probe materials such as gold and silver have been developed to support lipid bilayers and enable the use of smaller probes, or nanoneedles, compared to more traditional glass micropipette ion channel probes. Silver probes are preferable because they support sustained DC stable channel current due to the AgCl layer formed around the tip during the fabrication process. However, one of the current challenges in ion channel measurements is maintaining a single-channel recording. Multiple protein insertions complicate data analysis and destabilize the bilayer. Herein, we combine the promising probe material (Ag/AgCl) with an approach based on current feedback-controlled tip positioning to maintain long-term single-channel recordings for up to 3 h. We develop a hybrid positioning control system, where the channel current is used as feedback to control the vertical movement of the silver tip and, subsequently, control the number of protein channels inserted in the lipid membrane. Our findings reveal that the area of the lipid bilayer decreases with moving the silver tip up (i.e., decreasing the displacement in the z-direction). By reducing the bilayer area around the fine silver tip, we minimize the probability of multiple insertions and remove unwanted proteins. In addition, we characterize the effect of lipid properties such as fluidity on the lipid membrane area. We believe that the use of silver nanoneedles, which enables DC stable channel current, coupled with the developed tip displacement mechanism will offer more opportunities to employ these probes for chemical imaging and mapping different surfaces.

Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing

It was recently demonstrated that one can monitor ligand-induced structure fluctuations of individual thiolate-capped gold nanoclusters using resistive-pulse nanopore sensing. The magnitude of the fluctuations scales with the size of the capping ligand, and it was later shown one can observe ligand exchange in this nanopore setup. We expand on these results by exploring the different types of current fluctuations associated with peptide ligands attaching to tiopronin-capped gold nanoclusters. We show here that the fluctuations can be used to identify the attaching peptide through either the magnitude of the peptide-induced current jumps or the onset of high-frequency current fluctuations. Importantly, the peptide attachment process requires that the peptide contains a cysteine residue. This suggests that nanopore-based monitoring of peptide attachments with thiolate-capped clusters could provide a means for selective detection of cysteine-containing peptides. Finally, we demonstrate the cluster-based protocol with various peptide mixtures to show that one can identify more than one cysteine-containing peptide in a mixture.

Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

This paper describes a method for detecting microRNA (miRNA) expression patterns using the nanopore-based DNA computing technology. miRNAs have shown promise as markers for cancer diagnosis due to their cancer type specificity, and therefore simple strategies for miRNA pattern recognition are required. We propose a system for pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore analysis. With this system, we succeeded in the label-free detection of miRNA expression patterns from the plasma of BDC patients. Moreover, our dgDNA-miRNA complexes can be detected at subfemtomolar concentrations, which is a significant improvement compared to previously reported limits of detection (∼10^-12 M) for similar analytical platforms. Nanopore decoding of dgDNA-encoded information represents a promising tool for simple and early cancer diagnosis.

Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding

Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg²⁺). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.

Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products

Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.

Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions

Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.

Biological nanopores for single-molecule sensing

Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.

On possible trypsin-induced biases in peptides analysis with Aerolysin nanopore

Nanopore-based single-molecule analysis technique is a promising approach in the field of proteomics. In this Technical Brief, the interaction between the biological nanopore of Aerolysin (AeL) and peptides is investigated, focusing on potential biases depending on the AeL activation protocol. Our results reveal that residual trypsin, which may be unintentionally introduced in analyte solution when using a classical AeL activation protocol, can induce a significant formation of shorter peptides by enzymatic degradation of longer ones, which may lead to unwanted effects and/or misinterpretations. AeL free-trypsin activation protocol eliminates this bias and appears more appropriate for peptide/proteins analysis, specifically in the perspective of nanopore-based molecular fingerprinting or of low-abundance species characterization. This article is protected by copyright. All rights reserved.

Modifying the pH sensitivity of OmpG nanopore for improved detection at acidic pH

The outer membrane protein G (OmpG) nanopore is a monomeric β-barrel channel consisting of seven flexible extracellular loops. Its most flexible loop, loop 6, can be used to host high-affinity binding ligands for the capture of protein analytes, which induces characteristic current patterns for protein identification. At acidic pH, the ability of OmpG to detect protein analytes is hampered by its tendency toward the closed state, which renders the nanopore unable to reveal current signal changes induced by bound analytes. In this work, critical residues that control the pH-dependent gating of loop 6 were identified, and an OmpG nanopore that can stay predominantly open at a broad range of pHs was created by mutating these pH-sensitive residues. A short single-stranded DNA was chemically tethered to the pH-insensitive OmpG to demonstrate the utility of the OmpG nanopore for sensing complementary DNA and a DNA binding protein at an acidic pH.

Current and Future Methodology for Quantitation and Site-Specific Mapping the Location of DNA Adducts

Formation of DNA adducts is a key event for a genotoxic mode of action, and their presence is often used as a surrogate for mutation and increased cancer risk. Interest in DNA adducts are twofold: first, to demonstrate exposure, and second, to link DNA adduct location to subsequent mutations or altered gene regulation. Methods have been established to quantitate DNA adducts with high chemical specificity and to visualize the location of DNA adducts, and elegant bio-analytical methods have been devised utilizing enzymes, various chemistries, and molecular biology methods. Traditionally, these highly specific methods cannot be combined, and the results are incomparable. Initially developed for single-molecule DNA sequencing, nanopore-type technologies are expected to enable simultaneous quantitation and location of DNA adducts across the genome. Herein, we briefly summarize the current methodologies for state-of-the-art quantitation of DNA adduct levels and mapping of DNA adducts and describe novel single-molecule DNA sequencing technologies to achieve both measures. Emerging technologies are expected to soon provide a comprehensive picture of the exposome and identify gene regions susceptible to DNA adduct formation.

Probing Protein Nanopores with Poly(ethylene glycol)s

Neutral water-soluble poly(ethylene glycol)s (PEGs) have been extensively explored in protein nanopore research for the past several decades. The principal use of PEGs is to investigate the membrane protein ion channel physical characteristics and transport properties. In addition, protein nanopores are used to study polymer-protein interactions and polymer physicochemical properties. In this review, we focus on the biophysical studies on probing protein ion channels with PEGs, specifically on nanopore sizing by PEG partitioning. We discuss the fluctuation analysis of ion channel currents in response to the PEGs moving within their confined geometries. The advantages, limitations, and recent developments of the approach are also addressed. This article is protected by copyright. All rights reserved.

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis

Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.