skip to main content


Title: Chemically tailoring nanopores for single-molecule sensing and glycomics
A nanopore can be fairly—but uncharitably—described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.  more » « less
Award ID(s):
1808344 1150085
NSF-PAR ID:
10160211
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Analytical and Bioanalytical Chemistry
ISSN:
1618-2642
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    In this review, recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health, are highlighted. Protein pores use three stochastic sensing‐based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nanochannel. Second, large molecules such as nucleic acids and especially peptides can be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion–ligand chelation/coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady‐state analysis, synthetic nanopores mainly use two strategies (modification and modification‐free) to detect metals. Given the advantages of high sensitivity and selectivity, and label‐free detection, nanopore‐based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.

     
    more » « less
  2. Abstract

    In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid’s acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.

     
    more » « less
  3. Electro-osmotic flow (EOF) is a phenomenon where fluid motion occurs in porous materials or micro/nano-channels when an external electric field is applied. In the particular example of single-molecule electrophoresis using single nanopores, the role of EOF on the translocation velocity of the analyte molecule through the nanopore is not fully understood. The complexity arises from a combination of effects from hydrodynamics in restricted environments, electrostatics emanating from charge decorations and geometry of the pores. We address this fundamental issue using the Poisson–Nernst–Planck and Navier–Stokes (PNP–NS) equations for cylindrical solid-state nanopores and three representative protein nanopores (α-hemolysin, MspA, and CsgG). We present the velocity profiles inside the nanopores as a function of charge decoration and geometry of the pore and applied electric field. We report several unexpected results: (a) The apparent charges of the protein nanopores are different from their net charge and the surface charge of the whole protein geometry, and the net charge of inner surface is consistent with the apparent charge. (b) The fluid velocity depends non-monotonically on voltage. The three protein nanopores exhibit unique EOF and velocity–voltage relations, which cannot be simply deduced from their net charge. Furthermore, effective point mutations can significantly change both the direction and the magnitude of EOF. The present computational analysis offers an opportunity to further understand the origins of the speed of transport of charged macromolecules in restricted space and to design desirable nanopores for tuning the speed of macromolecules through nanopores. 
    more » « less
  4. Structurally regular nanopore arrays fabricated to contain independently controllable annular electrodes represent a new kind of architecture capable of electrochemically addressing small collections of matter—down to the single entity (molecule, particle, and biological cell) level. Furthermore, these nanopore electrode arrays (NEAs) can also be interrogated optically to achieve single entity spectroelectrochemistry. Larger entities such as nanoparticles and single bacterial cells are investigated by dark-field scattering and potential-controlled single-cell luminescence experiments, respectively, while NEA-confined molecules are probed by single molecule luminescence. By carrying out these experiments in arrays of identically constructed nanopores, massively parallel collections of single entities can be investigated simultaneously. The multilayer metal–insulator design of the NEAs enables highly efficient redox cycling experiments with large increases in analytical sensitivity for chemical sensing applications. NEAs may also be augmented with an additional orthogonally designed nanopore layer, such as a structured block copolymer, to achieve hierarchically organized multilayer structures with multiple stimulus-responsive transport control mechanisms. Finally, NEAs constructed with a transparent bottom layer permit optical access to the interior of the nanopore, which can result in the cutoff of far-field mode propagation, effectively trapping radiation in an ultrasmall volume inside the nanopore. The bottom metal layer may be used as both a working electrode and an optical cladding layer, thus, producing bifunctional electrochemical zero-mode waveguide architectures capable of carrying out spectroelectrochemical investigations down to the single molecule level. 
    more » « less
  5. Atomically precise and highly selective surface reactions are required for advancing microelectronics fabrication. Advanced atomic processing approaches make use of small molecule inhibitors (SMI) to enable selectivity between growth and nongrowth surfaces. The selectivity between growth and nongrowth substrates is eventually lost for any known combinations, because of defects, new defect formation, and simply because of a Boltzmann distribution of molecular reactivities on surfaces. The selectivity can then be restored by introducing etch-back correction steps. Most recent developments combine the design of highly selective combinations of growth and nongrowth substrates with atomically precise cycles of deposition and etching methods. At that point, a single additional step is often used to passivate the unwanted defects or selected surface chemical sites with SMI. This step is designed to chemically passivate the reactive groups and defects of the nongrowth substrates both before and/or during the deposition of material onto the growth substrate. This approach requires applications of the fundamental knowledge of surface chemistry and reactivity of small molecules to effectively block deposition on nongrowth substrates and to not substantially affect deposition on the growth surface. Thus, many of the concepts of classical surface chemistry that had been developed over several decades can be applied to design such small molecule inhibitors. This article will outline the approaches for such design. This is especially important now, since the ever-increasing number of applications of this concept still rely on trial-and-error approaches in selecting SMI. At the same time, there is a very substantial breadth of surface chemical reactivity analysis that can be put to use in this process that will relate the effectiveness of a potential SMI on any combination of surfaces with the following: selectivity; chemical stability of a molecule on a specific surface; volatility; steric hindrance, geometry, packing, and precursor of choice for material deposition; strength of adsorption as detailed by interdisplacement to determine the most stable SMI; fast attachment reaction kinetics; and minimal number of various binding modes. The down-selection of the SMI from the list of chemicals that satisfy the preliminary criteria will be decided based on optimal combinations of these requirements. Although the specifics of SMI selection are always affected by the complexity of the overall process and will depend drastically on the materials and devices that are or will be needed, this roadmap will assist in choosing the potential effective SMIs based on quite an exhaustive set of “SMI families” in connection with general types of target surfaces. 
    more » « less