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Transmembrane protein channels enable fast and highly sensitive electrical detection of single molecules. Nanopore sequencing of DNA was achieved using an engineered Mycobacterium smegmatis porin A (MspA) in combination with a motor enzyme. Due to its favorable channel geometry, the octameric MspA pore exhibits the highest current level as compared to other pore proteins. To date, MspA is the only protein nanopore with a published record of DNA sequencing. While widely used in commercial devices, nanopore sequencing of DNA suffers from significant base-calling errors due to stochastic events of the complex DNA-motor-pore combination and the contribution of up to five nucleotides to the signal at each position. Asymmetric mutations within subunits of the channel protein offer an enormous potential to improve nucleotide resolution and sequencing accuracy. However, random subunit assembly does not allow control of the channel composition of MspA and other oligomeric protein pores. In this study, we showed that it is feasible to convert octameric MspA into a single-chain pore by connecting eight subunits using peptide linkers. We constructed single-chain MspA trimers, pentamers, hexamers and heptamers to demonstrate that it is feasible to alter the subunit stoichiometry and the MspA pore diameter. All single-chain MspA proteins formed functional channels in lipid bilayer experiments. Importantly, we demonstrated that single-chain MspA discriminated all four nucleotides identical to MspA produced from monomers. Thus, single-chain MspA constitutes a new milestone in its development and adaptation as a biosensor for DNA sequencing and many other applications.STATEMENT OF SIGNFICANCENanopore sequencing of DNA is a fast and cheap technology that uniquely delivers multi-kilobase reads. It is currently used world-wide in many applications such as genome sequencing, epigenetics, and surveillance of viral and bacterial pathogens and has started to revolutionize human lives in medicine, agriculture and environmental studies. However, the high base-calling error rates prevent nanopore DNA sequencing from reaching its full potential. In this study, we converted octameric MspA into a single-chain pore enabling asymmetric mutations to fine-tune the pore geometry and chemistry and address the shortcomings of nanopores. Thus, single-chain MspA constitutes a new milestone in its development and adaptation as a biosensor for DNA sequencing and many other applications.

RNA fibers are a class of biomaterials that can be assembled using HIV-like kissing loop interactions. Because of the programmability of molecular design and low immunorecognition, these structures present an interesting opportunity to solve problems in nanobiotechnology and synthetic biology. However, the experimental tools to fully characterize and discriminate among different fiber structures in solution are limited. Herein, we utilize solid-state nanopore experiments and Brownian dynamics simulations to characterize and distinguish several RNA fiber structures that differ in their degrees of branching. We found that, regardless of the electrolyte type and concentration, fiber structures that have more branches produce longer and deeper ionic current blockades in comparison to the unbranched fibers. Experiments carried out at temperatures ranging from 20–60 °C revealed almost identical distributions of current blockade amplitudes, suggesting that the kissing loop interactions in fibers are resistant to heating within this range.

Two-dimensional (2D) heterostructured electrodes built from vertical stacking of different 2D materials are among the most promising electrode architectures for electrochemical energy storage devices. These materials offer interesting opportunities for energy storage applications such as versatility in the structural design of electrode, and the possibility to integrate individual 2D building blocks with different properties into heterostructures. These features can potentially enable new materials with improved or new electrochemical features. Here, we report on large-scale liquid phase self-assembly of 2D heterostructures built from two different 2D transition metal carbides (MXenes), Ti3C2Tx and V2CTx. A cation-driven self-assembly process was used to assemble the negatively-charged flakes of the two MXenes into heterolayered flakes. The freestanding and binder-free MXene heterostructure films could deliver a high volumetric capacitance of ~1473 F cm−3 and showed no capacitance loss after 50,000 charge-discharge cycles in 3 M H2SO4 electrolyte. Due to coupling of redox reactions of Ti3C2Tx and V2CTx, the heterostructure electrodes showed a nearly constant current over their entire potential window, which is reminiscent of traditional pseudocapacitive materials. This electrochemical behavior differs from individual MXene electrodes or most other emerging pseudocapacitive materials whose maximum performance is usually achieved in a narrow potential range.

Synthesis of RNA molecules that contain an internal site-specific modification is important for RNA research and therapeutics. While solid-state synthesis is attainable for such RNA in the range of 100 nucleotides (nts), it is currently impossible with kilobase (kb)-long RNA. Instead, long RNA with an internal modification is usually assembled in an enzymatic 3-part splint ligation to join a short RNA oligonucleotide, containing the site-specific modification, with both a left-arm and a right-arm long RNA that are synthesized by in vitro transcription. However, long RNAs have structural heterogeneity and those synthesized by in vitro transcription have 3’-end sequence heterogeneity, which together substantially reduce the yield of 3-part splint ligation. Here we describe a method of 3-part splint ligation with an enhanced efficiency utilizing a ribozyme cleavage reaction to address the 3’-end sequence heterogeneity and involving DNA disruptors proximal to the ligation sites to address the structural heterogeneity. The yields of the synthesized kb-long RNA are sufficiently high to afford purification to homogeneity for practical RNA research. We also verify the sequence accuracy at each ligation junction by nanopore sequencing.

The application of nanopores as label-free, single-molecule biosensors for electrical or optical probing of structural features in biomolecules has been widely explored. While biological nanopores (membrane proteins and bacteriophage portal proteins) and solid-state nanopores (thin films and two-dimensional materials) have been extensively employed, the third class of nanopores known as hybrid nanopores, where an artificial membrane substitutes the organic support membrane of proteins, has been only sparsely studied, due to challenges in implementation. G20c portal protein contains a natural DNA pore that is used by viruses for filling their capsid with viral genomic DNA. We have previously developed a lipid-free hybrid nanopore by “corking” the G20c portal protein into a SiNx nanopore. Herein, we demonstrate that through chemical functionalization of the synthetic nanopore, covalent linkage between the solid-state pore and the G20c portal protein considerably improves the hybrid pore stability, lifetime, and voltage resilience. Moreover, we demonstrate electric-field-driven and motor protein-mediated transport of DNA molecules through this hybrid pore. Our integrated protein/solid-state hybrid nanopore can serve as a robust and durable framework for sensing and sequencing at high voltages, potentially providing higher resolution, higher signal-to-noise ratio, and higher throughput compared to the more conventional membrane-embedded protein platforms.

Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine these implications for both liquid chromatography-tandem mass spectrometry (LC-MS/MS) and single-molecule counting and provide estimates on how many molecules are routinely measured in proteomics experiments by LC-MS/MS. We review strategies that have been helpful for counting billions of protein molecules by LC-MS/MS and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges of the wide dynamic range of the proteome. We also examine the theoretical possibilities for scaling up single-molecule and mass spectrometry proteomics approaches to quantifying the billions of protein molecules that make up the proteomes of our cells., Recorded presentation: https://youtu.be/w0IOgJrrvNM

Developing techniques for the high-quality synthesis of mono and few-layered two-dimensional (2D) materials with lowered complexity and cost continues to remain an important goal, both for accelera...

Conformational transitions of proteins are governed by chemical kinetics, often toggled by passage through an activated state separating two conformational ensembles. The passage time of a protein through the activated state can be too fast to be detected by single-molecule experiments without the aid of viscogenic agents. Here, we use high-bandwidth nanopore measurements to resolve microsecond-duration transitions that occur between conformational states of individual protein molecules partly blocking pore current. We measure the transition state passage time between folded and unfolded states of a two-state λ

Nanopore sequencing is one of only a few methods that can potentially determine the amino acid sequence of individual protein molecules as these are passed through a pore sensor. However, mechanisms for unfolding and translocation of proteins are still unavailable to date. Here we describe a general approach for realizing unidirectional transport of full-length proteins through nanopores. We combine a chemically resistant biological nanopore platform with a high concentration guanidinium chloride buffer to achieve unidirectional, single-file protein transport that is propelled by a giant electro-osmotic effect, as revealed by molecular dynamics simulations and confirmed experimentally. Remarkably, we observed that protein velocities are uniform regardless of the protein sequence, which allows the identification and discrimination among proteins based on their electrical signatures, as well as to distinguish protein signatures by their threading orientation (N-to-C vs. C-to-N terminus). With average transport velocities of 10 µs per amino acid, our method can enable direct, enzyme-free protein fingerprinting and protein sequencing when combined with a high-resolution pore and high-speed nanopore readout.

Enzyme-mediated chemical modifications to mRNA are important for fine-tuning gene expression, but they are challenging to quantify due to low copy number and limited tools for accurate detection. Existing studies have typically focused on the identification and impact of adenine modifications on mRNA (m6A and inosine) due to the availability of analytical methods. The pseudouridine (Ψ) mRNA modification is also highly abundant but difficult to detect and quantify because there is no available antibody, it is mass silent, and maintains canonical basepairing with adenine. Nanopores may be used to directly identify Ψ sites in RNAs using a systematically miscalled base, however, this approach is not quantitative and highly sequence dependent. In this work, we apply supervised machine learning models that are trained on sequence-specific, synthetic controls to endogenous transcriptome data and achieve the first quantitative Ψ occupancy measurement in human mRNAs. Our supervised machine learning models reveal that for every site studied, different signal parameters are required to maximize Ψ classification accuracy. We show that applying our model is critical for quantification, especially in low-abundance mRNAs. Our engine can be used to profile Ψ-occupancy across cell types and cell states, thus providing critical insights about physiological relevance of Ψ modification to mRNAs.

Nanopore-based sensors have established themselves as a prominent tool for solution-based, single-molecule analysis of the key building blocks of life, including nucleic acids, proteins, glycans and a large pool of biomolecules that have an essential role in life and healthcare. The predominant molecular readout method is based on measuring the temporal fluctuations in the ionic current through the pore. Recent advances in materials science and surface chemistries have not only enabled more robust and sensitive devices but also facilitated alternative detection modalities based on field-effect transistors, quantum tunnelling and optical methods such as fluorescence and plasmonic sensing. In this Review, we discuss recent advances in nanopore fabrication and sensing strategies that endow nanopores not only with sensitivity but also with selectivity and high throughput, and highlight some of the challenges that still need to be addressed. Nanopore sensors enable the solution-based analysis of nucleic acids, proteins and other biomolecules at the single-molecule level. This Review discusses new fabrication and sensing strategies — including field-effect transistors, quantum tunnelling and optical methods — that enhance the sensitivity and selectivity of nanopores.

Two-dimensional membranes have gained enormous interest due to their potential to deliver precision filtration of species with performance that can challenge current desalination membrane platforms. Molybdenum disulfide (MoS2) laminar membranes have recently demonstrated superior stability in aqueous environment to their extensively-studied analogs graphene-based membranes; however, challenges such as low ion rejection for high salinity water, low water flux, and low stability over time delay their potential adoption as a viable technology. Here, we report composite laminate multilayer MoS2 membranes with stacked heterodimensional one- to two-layer-thick porous nanosheets and nanodisks. These membranes have a multimodal porous network structure with tunable surface charge, pore size, and interlayer spacing. In forward osmosis, our membranes reject more than 99% of salts at high salinities and, in reverse osmosis, small-molecule organic dyes and salts are efficiently filtered. Finally, our membranes stably operate for over a month, implying their potential for use in commercial water purification applications., Molybdenum disulfide membranes are attractive for filtration of nanoscale species but should be optimized for application. Here, the authors report composite membranes with tunable surface charge, pore size and interlayer spacing, achieving efficient filtration of small-molecule dyes and osmosis.

Two-dimensional (2D) materials, owing to their extremely low thickness, are ideal materials for nanopores with optimal detection sensitivity and resolution. Among 2D materials, molybdenum disulfide (MoS

Reversible electrochemical intercalation of cations into the interlayer space of 2D materials induces tunable physical and chemical properties in them. In MXenes, a large class of recently developed 2D carbides and nitrides, low intercalation energy, high storage capacitance, and reversible intercalation of various cations have led to their improved performance in sensing and energy storage applications. Herein, a coupled nanopore-actuator system where an ultrathin free-standing MXene film serves as a nanopore support membrane and ionically active actuator is reported. In this system, the contactless MXene membrane in the electric field affects the cation movement in the field through their (de)intercalation between individual MXene flakes. This results in reversible swelling and contraction of the membrane monitored by ionic conductance through the nanopore. This unique nanopore coupled to a mechanical actuation system could provide new insights into designing single-molecule biosensing platforms at the nanoscale.

Enzyme-mediated chemical modifications to mRNAs have the potential to fine-tune gene expression in response to environmental stimuli. Notably, pseudouridine-modified mRNAs are more resistant to RNase-mediated degradation, more responsive to cellular stress, and have the potential to modulate immunogenicity and enhance translation in vivo. However, the precise biological functions of pseudouridine modification on mRNAs remain unclear due to the lack of sensitive and accurate tools for mapping. We developed a semi-quantitative method for mapping pseudouridylated sites with high confidence directly on mammalian mRNA transcripts via direct RNA, long-read nanopore sequencing. By analysis of a modification-free transcriptome, we demonstrate that the depth of coverage and intrinsic errors associated with specific k-mer sequences are critical parameters for accurate base-calling. We adjust these parameters for high-confidence U-to-C base-calling errors that occur at pseudouridylated sites, which are benchmarked against sites that were identified previously by biochemical methods. We also uncovered new pseudouridylated sites, many of which fall on genes that encode RNA binding proteins and on uridine-rich k-mers. Sites identified by U-to-C base calling error were verified using 1000mer synthetic RNA controls bearing a single pseudouridine in the center position, demonstrating that 1. the U-to-C base-calling error occurs at the site of pseudouridylation, and 2. the basecalling error is systematically under-calling the pseudouridylated sites. High-occupancy sites with >40% U-to-C basecalling error are classified as sites of hyper modification type I, whereas genes with more than one site of pseudouridylation are classified as having type II hyper modification which is confirmed by single-molecule analysis. We report the discovery of mRNAs with up to 7 unique sites of pseudouridine modification. Here we establish an innovative pipeline for direct identification, quantification, and detection of pseudouridine modifications and type I/II hypermodifications on native RNA molecules using long-read sequencing without resorting to RNA amplification, chemical reactions on RNA, enzyme-based replication, or DNA sequencing steps.

In contrast to sequence-specific techniques such as polymerase chain reaction, DNA sequencing does not require prior knowledge of the sample for surveying DNA. However, current sequencing technologies demand high inputs for a suitable library preparation, which typically necessitates DNA amplification, even for single-molecule sequencing methods. Here, electro-optical zero-mode waveguides (eZMWs) are presented, which can load DNA into the confinement of zero-mode waveguides with high efficiency and negligible DNA fragment length bias. Using eZMWs, highly efficient voltage-induced loading of DNA fragments of various sizes from ultralow inputs (nanogram-to-picogram levels) is observed. Rapid DNA fragment identification is demonstrated by burst sequencing of short and long DNA molecules (260 and 20 000 bp) loaded from an equimolar picomolar-level concentration mixture in just a few minutes. The device allows further studies in which low-input DNA capture is essential, for example, in epigenetics, where native DNA is required for obtaining modified base information.

Nanopore technology offers long, accurate sequencing of an DNA or RNA strand via enzymatic ratcheting of the strand through a nanopore in single nucleotide steps, producing stepwise modulations of the nanopore ion current. In contrast to nucleic acids, their daughter molecules, proteins, have neutral peptide backbones and side chains of varying charges. Further, proteins have stable secondary and higher order structures that obstruct protein linearization required for single file nanopore transport. Here, we describe a general approach for realizing unidirectional transport of proteins through a nanopore that neither requires the protein to be uniformly charged nor a pull from a biological enzyme. At high concentrations of guanidinium chloride, we find full-length proteins to translocate unidirectionally through an alpha-hemolysin nanopore in a polymer-based membrane, provided that one of the protein ends is decorated with a short anionic peptide. Molecular dynamics simulations show that such surprisingly steady protein transport is driven by a giant electro-osmotic effect caused by binding of guanidinium cations to the inner surface of the nanopore. We show that ionic current signals produced by protein passage can be used to distinguish two biological proteins and the global orientation of the same protein (N-to-C vs. C-to-N terminus) during the nanopore transport. With the average transport rate of one amino acid per 10 microseconds, our method may enable direct enzyme-free protein fingerprinting or perhaps even sequencing when combined with a high-speed nanopore reader instrument.

A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single-amino-acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA helicase Hel308. Reading the ion current signal through the nanopore enabled discrimination of single-amino-acid substitutions in single reads. Molecular dynamics simulations showed these signals to result from size exclusion and pore binding. We also demonstrate the capability to ‘rewind’ peptide reads, obtaining numerous independent reads of the same molecule, yielding an error rate

Microorganisms account for most of the biodiversity on earth. Yet while there are increasingly powerful tools for studying microbial genetic diversity, there are fewer tools for studying microorganisms in their natural environments. In this paper, we present recent advances in CMOS electrochemical imaging arrays for detecting and classifying microorganisms. These microscale sensing platforms can provide non-optical measurements of cell geometries, behaviors, and metabolic markers. We review integrated electronic sensors appropriate for monitoring microbial growth, and present measurements of single-celled algae using a CMOS sensor array with thousands of active pixels. Integrated electrochemical imaging can contribute to improved medical diagnostics and environmental monitoring, as well as discoveries of new microbial populations.

Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field–driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiN(x)) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5-nm-diameter pore, we find that, in a threshold electric-field regime of ∼30 to 100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5- and 2.0-nm-diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens avenues for exploring protein folding structures, internal contacts, and electric-field–induced deformability.

Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiNx) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5 nm diameter pore we find that, in a threshold electric field regime of ∼30-100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5 nm and 2.0 nm diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens new avenues for exploring protein folding structures, internal contacts, and electric field-induced deformability.Significance StatementCan localized electric fields drive the complete unfolding of a protein molecule? Protein unfolding prior to its translocation through a nanopore constriction is an important step in protein transport across biological membranes and also an important step in nanopore-based protein sequencing. We studied here the electric-field-driven translocation behavior of a model protein (cyt c) through nanopores of diameters ranging from 1.5 to 5.5 nm. These single molecule measurements show that electric fields at the nanopore constriction can select both partially and fully unfolded protein conformations. Zero-field free energy gaps between these conformations, found using a simple thermodynamic model, are in remarkable agreement with previously reported studies of cyt c unfolding energetics.

Bottom-up assembly of two-dimensional (2D) materials into macroscale morphologies with emergent properties requires control of the material surroundings, so that energetically favorable conditions direct the assembly process. MXenes, a class of recently developed 2D materials, have found new applications in areas such as electrochemical energy storage, nanoscale electronics, sensors, and biosensors. In this paper, we present a lateral self-assembly method for wafer-scale deposition of a mosaic-type 2D MXene flake monolayer that spontaneously orders at the interface between two immiscible solvents. ReaxFF molecular dynamics simulations elucidate the interactions of a MXene flake with the solvents and its stability at the liquid/liquid interface, the prerequisite for MXene flakes self-assembly at the interface. Moreover, facile transfer of this monolayer onto a flat substrate (Si, glass) results in high-coverage monolayer films with uniform thickness and homogeneous optical properties. Multiscale characterization of the resulting films reveals the mosaic structure and sheds light on the electronic properties of the films, which exhibit good electrical conductivity over cm-scale areas.

Use of chaotropic reagents is common in biophysical characterization of biomolecules. When the study involves transmembrane protein channels, the stability of the protein channel and supporting bilayer membrane must be considered. In this letter we show that planar bilayers composed of poly(1,2-butadiene)-b-poly(ethylene oxide) diblock copolymer are stable and leak-free at high guanidinium chloride concentrations, in contrast to diphytanoyl phosphatidylcholine bilayers which exhibit deleterious leakage under similar conditions. Further, insertion and functional analysis of channels such as α-hemolysin and MspA are straightforward in these polymer membranes. Finally, we demonstrate that α-hemolysin channels maintain their structural integrity at 2M guanidinium chloride concentrations using blunt DNA hairpins as molecular reporters.

Electrokinetic translocation of biomolecules through solid-state nanopores represents a label-free single-molecule technique that may be used to measure biomolecular structure and dynamics. Recent investigations have attempted to distinguish individual transfer RNA (tRNA) species based on the associated pore translocation times, ion-current noise, and blockage currents. By manufacturing sufficiently smaller pores, each tRNA is required to undergo a deformation to translocate. Accordingly, differences in nanopore translocation times and distributions may be used to infer the mechanical properties of individual tRNA molecules. To bridge our understanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified "structure-based" energetic model. Calculating the free-energy landscape for distinct tRNA species implicates transient unfolding of the terminal RNA helix during nanopore translocation. This provides a structural and energetic framework for interpreting current experiments, which can aid the design of methods for identifying macromolecules using nanopores.