Graphene Nanopores for Protein Sequencing

Nanopore label-free detection of single-nucleotide deletion in Baxα/BaxΔ2

Baxα, a key tumor suppressor gene, will not be expressed correctly as a result of single nucleotide mutation in its microsatellite region; Instead, BaxΔ2, an isoform of Baxα, is often produced. In addition, lack of the exon 2 due to an alternative splicing, BaxΔ2 has the same sequence as Baxα except single base deletion from eight continuous guanines (G8) to G7. Most of the currently available methods for Bax∆2 detection are inefficient and time-consuming, and/or require the use of labels or dyes. In this work, we reported a label-free nanopore sensing strategy to differentiate between Baxα and BaxΔ2 with a DNA polymer as a molecular probe based on alternative spliced sequences. Two DNA molecules were designed to selectively detect Baxα and BaxΔ2, respectively. The method was rapid, accurate, and highly sensitive: picomolar concentrations of target nucleic acids could be detected in minutes. Our developed simple and fast nanopore-based detection strategy is not only useful for distinguishing between Baxα and Bax∆2, but also provides a useful tool for detection of other single-base mutations in genetic diagnosis.

Hybrid plasmonic nanostructures based on controlled integration of MoS2 flakes on metallic nanoholes

Here, we propose an easy and robust strategy for the versatile preparation of hybrid plasmonic nanopores by means of controlled deposition of single flakes of MoS2 directly on top of metallic holes. The device is realized on silicon nitride membranes and can be further refined by TEM or FIB milling to achieve the passing of molecules or nanometric particles through a pore. Importantly, we show that the plasmonic enhancement provided by the nanohole is strongly accumulated in the 2D nanopore, thus representing an ideal system for single-molecule sensing and sequencing in a flow-through configuration. Here, we also demonstrate that the prepared 2D material can be decorated with metallic nanoparticles that can couple their resonance with the nanopore resonance to further enhance the electromagnetic field confinement at the nanoscale level. This method can be applied to any gold nanopore with a high level of reproducibility and parallelization; hence, it can pave the way to the next generation of solid-state nanopores with plasmonic functionalities. Moreover, the controlled/ordered integration of 2D materials on plasmonic nanostructures opens a pathway towards new investigation of the following: enhanced light emission; strong coupling from plasmonic hybrid structures; hot electron generation; and sensors in general based on 2D materials.

Paving the way to single-molecule protein sequencing

Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.

Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.

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.

Single-File Protein Translocations through Graphene-MoS2 Heterostructure Nanopores

Successfully threading unfolded protein molecules through nanopores whose sizes are comparable to that of an amino acid is a prerequisite for the nanopore-based protein sequencing method that promises to be high-throughput and low-cost. While the electric driving method can be effective for a homogeneously charged DNA molecule, it fails to drive an unfolded protein through a nanopore because the net charge of a protein fragment inside of the pore (where the electric field exists) can be positive, negative, or neutral. Here we propose and demonstrate by molecular dynamics simulations protein transport through a nanopore in a quasi-two-dimensional heterostructure stacked together by graphene and molybdenum disulfide (MoS₂) nanosheets. Thanks to different van der Waals interactions ( U) between a protein molecule and different 2D surfaces, it is energetically favorable for protein to progressively move from the MoS₂ surface to the graphene surface (more negative U) through a nanopore in the heterostructure.

Protein sequencing via nanopore based devices: a nanofluidics perspective

Proteins perform a huge number of central functions in living organisms, thus all the new techniques allowing their precise, fast and accurate characterization at single-molecule level certainly represent a burst in proteomics with important biomedical impact. In this review, we describe the recent progresses in the developing of nanopore based devices for protein sequencing. We start with a critical analysis of the main technical requirements for nanopore protein sequencing, summarizing some ideas and methodologies that have recently appeared in the literature. In the last sections, we focus on the physical modelling of the transport phenomena occurring in nanopore based devices. The multiscale nature of the problem is discussed and, in this respect, some of the main possible computational approaches are illustrated.

Bioinspired smart asymmetric nanochannel membranes

Bioinspired smart asymmetric nanochannel membranes (BSANM) have been explored extensively to achieve the delicate ionic transport functions comparable to those of living organisms. The abiotic system exhibits superior stability and robustness, allowing for promising applications in many fields. In view of the abundance of research concerning BSANM in the past decade, herein, we present a systematic overview of the development of the state-of-the-art BSANM system. The discussion is focused on the construction methodologies based on raw materials with diverse dimensions (i.e. 0D, 1D, 2D, and bulk). A generic strategy for the design and construction of the BSANM system is proposed first and put into context with recent developments from homogeneous to heterogeneous nanochannel membranes. Then, the basic properties of the BSANM are introduced including selectivity, gating, and rectification, which are associated with the particular chemical and physical structures. Moreover, we summarized the practical applications of BSANM in energy conversion, biochemical sensing and other areas. In the end, some personal opinions on the future development of the BSANM are briefly illustrated. This review covers most of the related literature reported since 2010 and is intended to build up a broad and deep knowledge base that can provide a solid information source for the scientific community.

Dielectrophoresis-Based Protein Enrichment for a Highly Sensitive Immunoassay Using Ag/SiO2 Nanorod Arrays

A nanoscale insulator-based dielectrophoresis (iDEP) technique is developed for rapid enrichment of proteins and highly sensitive immunoassays. Dense arrays of nanorods (NDs) by oblique angle deposition create a super high electric field gradient of 2.6 × 10²⁴ V² m^-3 and the concomitant strong dielectrophoresis force successfully traps small proteins at a bias as low as 5 V. 1800-fold enrichment of bovine serum albumin protein at a remarkable rate of up to 180-fold s^-1 is achieved using oxide coated Ag nanorod arrays with pre-patterned sawtooth electrodes. Based on this system, an ultrasensitive immunoassay of mouse immunoglobulin G is demonstrated with a reduction in the limit of detection from 5.8 ng mL^-1 (37.6 pM) down to 275.3 fg mL^-1 (1.8 f M), compared with identical assays performed on glass plates. This methodology is also applied to detect a cancer biomarker prostate-specific antigen spiked in human serum with a detection limit of 2.6 ng mL^-1 . This high sensitivity results from rapid biomarker enrichment and metal enhanced fluorescence through the integration of nanostructures. The concentrated proteins also accelerate binding kinetics and enable signal saturation within 1 min. Given the easy fabrication process, this nanoscale iDEP system provides a highly sensitive detection platform for point-of-care diagnostics.

Real-Time Nanopore-Based Recognition of Protein Translocation Success

A growing number of new technologies are supported by a single- or multi-nanopore architecture for capture, sensing, and delivery of polymeric biomolecules. Nanopore-based single-molecule DNA sequencing is the premier example. This method relies on the uniform linear charge density of DNA, so that each DNA strand is overwhelmingly likely to pass through the nanopore and across the separating membrane. For disordered peptides, folded proteins, or block copolymers with heterogeneous charge densities, by contrast, translocation is not assured, and additional strategies to monitor the progress of the polymer molecule through a nanopore are required. Here, we demonstrate a single-molecule method for direct, model-free, real-time monitoring of the translocation of a disordered, heterogeneously charged polypeptide through a nanopore. The crucial elements are two "selectivity tags"-regions of different but uniform charge density-at the ends of the polypeptide. These affect the selectivity of the nanopore differently and enable discrimination between polypeptide translocation and retraction. Our results demonstrate exquisite sensitivity of polypeptide translocation to applied transmembrane potential and prove the principle that nanopore selectivity reports on biopolymer substructure. We anticipate that the selectivity tag technique will be broadly applicable to nanopore-based protein detection, analysis, and separation technologies, and to the elucidation of protein translocation processes in normal cellular function and in disease.

Protein Nanopore-Based Discrimination between Selected Neutral Amino Acids from Polypeptides

Nanopore probing of biological polymers has the potential to achieve single-molecule sequencing at low cost, high throughput, portability, and minimal sample preparation and apparatus. In this article, we explore the possibility of discrimination between neutral amino acid residues from the primary structure of 30 amino acids long, engineered peptides, through the analysis of single-molecule ionic current fluctuations accompanying their slowed-down translocation across the wild type α-hemolysin (α-HL) nanopore, and molecular dynamics simulations. We found that the transient presence inside the α-HL of alanine or tryptophan residues from the primary sequence of engineered peptides results in distinct features of the ionic current fluctuation pattern associated with the peptide reversibly blocking the nanopore. We propose that α-HL sensitivity to the molecular exclusion at the most constricted region mediates ionic current blockade events correlated with the volumes that are occluded by at least three alanine or tryptophan residues, and provides the specificity needed to discriminate between groups of neutral amino acids. Further, we find that the pattern of current fluctuations depends on the orientation of the threaded amino acid residues, suggestive of a conformational anisotropy of the ensemble of conformations of the peptide on the restricted nanopore region, related to its relative axial orientation inside the nanopore.

Aggregated Single-Walled Carbon Nanotubes Absorb and Deform Dopamine-Related Proteins Based on Molecular Dynamics Simulations

Single-walled carbon nanotubes (SWCNTs) have attracted considerable attention owing to their applications in various fields such as biotechnology and biomedicine. Recently, aggregated SWCNTs have shown more significant effects on the treatment of methamphetamine addiction (Nat. Nanotech. 2016, 11, 613). However, the mechanisms underlying these actions are unclear. By using all-atom molecular dynamics simulations, we investigate the effects of single and aggregated SWCNTs (single-(10,10)CNT, aggregated-7-(10,10)CNTs, and single-(35,35)CNT with the same diameter as that of the aggregated one) on the activity of dopamine-related proteins [tyrosine hydroxylase (TyrOH) and dopamine transporter (DAT), which are related to the synthesis and transport of dopamine, respectively]. We find that both TyrOH and DAT can adsorb onto these SWCNTs. For TyrOH, the aggregated-7-(10,10)CNTs mainly affect the conformation of the active site of the protein, and hence, they are more effective in inhibiting the expression of TyrOH. For DAT, our results suggest that the aggregated-7-(10,10)CNTs allow DAT to maintain an outward-facing conformation and hence are favorable to the reuptake of dopamine. The binding of a dopamine reuptake inhibitor, [³H]-WIN35,428, to DAT is significantly disrupted by aggregated-7-(10,10)CNTs and hence improve the ability to transport dopamine. Our results provide the dynamic interactions of proteins with single/aggregated SWCNTs, which illustrate the mechanism of aggregated SWCNTs for the treatment of drug addiction.

SDS-assisted protein transport through solid-state nanopores

Using nanopores for single-molecule sequencing of proteins - similar to nanopore-based sequencing of DNA - faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force; both characteristics being advantageous for future protein sequencing applications using solid-state nanopores.

Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore

It is now possible to create, in a thin inorganic membrane, a single, sub-nanometer-diameter pore (i.e., a sub-nanopore) about the size of an amino acid residue. To explore the prospects for sequencing protein with it, measurements of the force and current were performed as two denatured histones, which differed by four amino acid residue substitutions, were impelled systematically through the sub-nanopore one at a time using an atomic force microscope. The force measurements revealed that once the denatured protein, stabilized by sodium dodecyl sulfate (SDS), translocated through the sub-nanopore, a disproportionately large force was required to pull it back. This was interpreted to mean that the SDS was cleaved from the protein during the translocation. The force measurements also exposed a dichotomy in the translocation kinetics: either the molecule slid nearly frictionlessly through the pore or it slipped-and-stuck. When it slid frictionlessly, regardless of whether the molecule was pulled N-terminus or C-terminus first through the pore, regular patterns were observed intermittently in the force and blockade current fluctuations that corresponded to the distance between stretched residues. Furthermore, the amplitude of the fluctuations in the current blockade were correlated with the occluded volume associated with the amino acid residues in the pore. Finally, a comparison of the patterns in the current fluctuations associated with the two practically identical histones supported the conclusion that a sub-nanopore was sensitive enough to discriminate amino acid substitutions in the sequence of a single protein molecule by measuring volumes of 0.1 nm³ per read.

Large Rectification Effect of Single Graphene Nanopore Supported by PET Membrane

Graphene is an ideal candidate for the development of solid state nanopores due to its thickness at the atomic scale and its high chemical and mechanical stabilities. A facile method was adopted to prepare single graphene nanopore supported by PET membrane (G/PET nanopore) within the three steps assisted by the swift heavy ion irradiation and asymmetric etching technology. The inversion of the ion rectification effect was confirmed in G/PET nanopore while comparing with bare PET nanopore in KCl electrolyte solution. By modifying the wall charge state of PET conical nanopore with hydrochloric acid from negative to positive, the ion rectification effect of G/PET nanopore was found to be greatly enhanced and the large rectification ratio up to 190 was obtained during this work. Moreover, the high ionic flux and high ion separation efficiency was also observed in the G/PET nanopore system. By comparing the "on" and "off" state conductance of G/PET nanopore while immersed in the solution with pH value lower than the isoelectric point of the etched PET (IEP, pH = 3.8), the voltage dependence of the off conductance was established and it was confirmed that the large rectification effect was strongly dependent on the particularly low off conductance at higher applied voltage.

Graphene Nanopores for Electronic Recognition of DNA Methylation

We investigate theoretically the ability of graphene nanopore membranes to detect methylated sites along a DNA molecule by electronic sheet current along the two-dimensional (2D) materials. Special emphasis is placed on the detection sensitivity changes due to pore size, shape, position, and the presence of defects around the nanopore in a membrane with constricted geometry. Enhanced sensitivity for detecting methylated CpG sites, labeled by methyl-CpG binding domain (MBD) proteins along a DNA molecule, is obtained for electronic transport through graphene midgap states caused by the constriction. A large square deviation from the graphene conductance with respect to the open nanopore is observed during the translocation of MBD proteins. This approach exhibits superior resolution in the detection of multiple methylated sites along the DNA compared to conventional ionic current blockade techniques.

Polymer translocation through nano-pores in vibrating thin membranes

Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer can accommodate several bases at the same time, making difficult accurate sequencing applications. More recently, the use of graphene membranes has paved the way to new sequencing capabilities, with the possibility to measure transverse currents, among other advances. The reduced thickness of these new membranes poses new questions on the effect of deformability and vibrations of the membrane on the translocation process, two features which are not taken into account in the well established theoretical frameworks. Here, we make a first step forward in this direction. We report numerical simulation work on a model system simple enough to allow gathering significant insight on the effect of these features on the average translocation time, with appropriate statistical significance. We have found that the interplay between thermal fluctuations and the deformability properties of the nano-pore play a crucial role in determining the process. We conclude by discussing new directions for further work.