Recent trends in nanopore polymer functionalization

Single-molecule resolution of the conformation of polymers and dendrimers with solid-state nanopores

Polymers and dendrimers are macromolecules, possessing unique and intriguing characteristics, that are widely applied in self-assembled functional materials, green catalysis, drug delivery and sensing devices. Traditional approaches for the structural characterization of polymers and dendrimers involve DLS, GPC, NMR, IR and TG, which provide their physiochemical features and ensemble information, whereas their unimolecular conformation and dispersion also are key features allowing to understand their transporting profile in confined ionic nanochannels. This work demonstrates the nanopore approach for the determination of charged homopolymers, neutral block copolymer and dendrimers under distinct bias potentials and pH conditions. The nanopore translocation properties reveal that the dispersion and transporting of PEI is pH-dependent, and its capture rate is much lower than that of PAA. The neutral block copolymer with longest molecular chain threads through with longest blockage duration, its highest capture rate was achieved in 0.5 M KCl at pH 5 with slow diffusion and high temporal resolution. The two generations of neutral dendrimers could also translocate under bias potentials, probably due to the ions adsorption on the dendrimers and driven by Brownian force. The TEG-81 with larger molecular size translocates with longer residence time and higher blockage ratio, as expected. Both of the dendrimers exhibit a higher blockage ratio at pH 7.4 than either acidic or alkalic condition, indicating a larger stretched conformation adopted under neutral condition. This work presents the analysis of unimolecular charged and neutral polymers and dendrimers, which will be insightful in understanding the self-assembly motion and transfer of synthetic macromolecules in confined space. It also provides a good indication for deciphering the macromolecule-nanopore interplay under electrophoretic condition.

Azo-PMA nanopores of sub-20 nm length for unimolecular resolution of nucleic acids and proteins

Owing to the facile fabrication and surface modification, the cost-effective polymer nanopores are widely employed in unimolecular determination of biomacromolecules and selective sensing of small molecules, nanoparticles and biomarkers. However, the documented polymer nanochannels are generally microscale in length with low spatial resolution. We herein synthesized azobenzene side-chain polymer (Azo-PMA) and spin-coated on silicon nitride membrane to obtain a polymer film of nanoscale thickness for further nanopore generation via controlled dielectric breakdown (CDB) approach. The Azo-PMA nanopores demonstrate good ions transporting activities, pH tolerance and stability in high concentration of electrolyte with low ionic current noise. In addition, the azobenzene-containing polymer nanopores exhibit photo-response upon UV/Vis. light irradiation. The Azo-PMA nanopore devices are utilized for linear and quadruple nucleic acids discrimination, sensing of proteins with distinct shapes and sizes, as well as the single amino acid resolution with good capture rate and sensitivity. We established an unimolecular sensing platform using polymer nanopores for nucleic acids and proteins detection with good spatial resolution, which will be an addition for the nanopore-carrier material exploration and applications in potential genomics and proteomics with high spatiotemporal resolution and low cost.

Solid-State Nanopores for Biomolecular Analysis and Detection

Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.

Emergence of selectivity and specificity in a coarse-grained model of the nuclear pore complex with sequence-agnostic FG-Nups

The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining the transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Furthermore, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 ≤ f ≤ 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the central role of the FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of the FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion, which resulted in enhanced translocation probability for 0.05 ≤ f ≤ 0.20. Extended brush configurations outside the pore resulted in entropic repulsion and exclusion of inert cargo in this range. Thus, our minimal NPC model exhibited a hybrid cargo translocation mechanism, with aspects of both virtual gate and selective-phase models, in this range of FG-hydrophobic fraction.

How Colloidal Lithography Limits the Optical Quality of Plasmonic Nanohole Arrays

Colloidal lithography utilizes self-assembled particle monolayers as lithographic masks to fabricate arrays of nanostructures by combination of directed evaporation and etching steps. This process provides complex nanostructures over macroscopic areas in a simple, convenient, and parallel fashion without requiring clean-room infrastructure and specialized equipment. The appeal of the method comes at the price of imperfections impairing the optical quality, especially for arrayed nanostructures relying on well-ordered lattices. Imperfections are often generically mentioned to rationalize the discrepancy between experimental and simulated resonances. Yet, little attention is given to detailed structure-property relationships connecting typical defects directly with the optical properties. Here, we use a correlative approach to connect nano- and microscopic defects occurring from the colloidal lithography process with the resulting local optical properties. We use nanohole arrays as a common plasmonic structure known to be sensitive to lattice imperfections. Correlative optical and electron microscopies reveal the individual role of packing order, organic impurities, and solid polymer bridges. Our findings show that simple cleaning processes with solvents and oxygen plasma already improve the optical quality but also highlight how well-controlled self-assembly processes are required for predictable optical properties of such nanostructures.

Automated Multi- and Block-Copolymer Writing in Mesoporous Films Using Visible-Light PET-RAFT and a Microscope

For high throughput applications, e.g., in the context of sensing especially when being combined with machine learning, large sample numbers in acceptable production time are required. This needs automated synthesis and material functionalization concepts ideally combined with high precision. To automate sensing relevant mesopore polymer functionalization while being highly precise in polymer placement, polymer amount control, and polymer sequence design, a process for polymer writing in mesoporous silica films with pore diameter in the range of 13 nm is developed. Mesoporous films are functionalized with different polymers in adjustable polymer amount including block-copolymer functionalization in an automated process using a visible-light induced, controlled photo electron/energy transfer-reversible addition-fragmentation chain-transfer (PET-RAFT) polymerization. While transferring this PET-RAFT to a commercially available microscope, direct, automated laser writing of three different polymers, as well as polymer re-initiation is demonstrated. Using a laser diameter of ≈72 µm, significantly smaller polymer spots of ≈7 µm in diameter are realized. Micrometerscale resolved polymer images including block-copolymers are written into mesoporous layers covering millimeter scale areas requiring a writing time in the range of one second per polymer spot.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Recent developments in visible light induced polymerization towards its application to nanopores

Visible light induced polymerizations are a strongly emerging field in recent years. Besides the often mild reaction conditions, visible light offers advantages of spatial and temporal control over chain growth, which makes visible light ideal for functionalization of surfaces and more specifically of nanoscale pores. Current challenges in nanopore functionalization include, in particular, local and highly controlled polymer functionalizations. Using spatially limited light sources such as lasers or near field modes for light-induced polymer functionalization is envisioned to allow local functionalization of nanopores and thereby improve nanoporous material performance. These light sources are usually providing visible light while classical photopolymerizations are mostly based on UV-irradiation. In this review, we highlight developments in visible light induced polymerizations and especially in visible light induced controlled polymerizations as well as their potential for nanopore functionalization. Existing examples of visible light induced polymerizations in nanopores are emphasized.

Recent Advances in Responsive Membrane Functionalization Approaches and Applications

In recent years, significant advances have been made in the field of functionalized membranes. With the functionalization using various materials, such as polymers and enzymes, membranes can exhibit property changes in response to an environmental stimulation, such as heat, light, ionic strength, or pH. The resulting responsive nature allows for an increased breadth of membrane uses, due to the developed functionalization properties, such as smart-gating filtration for size-selective water contaminant removal, self-cleaning antifouling surfaces, increased scalability options, and highly sensitive molecular detection. In this review, new advances in both fabrication and applications of functionalized membranes are reported and summarized, including temperature-responsive, pH-responsive, light-responsive, enzyme-functionalized, and two-dimensional material-functionalized membranes. Specific emphasis was given to the most recent technological improvements, current limitations, advances in characterization techniques, and future directions for the field of functionalized membranes.

Pore performance: artificial nanoscale constructs that mimic the biomolecular transport of the nuclear pore complex

The nuclear pore complex is a nanoscale assembly that achieves shuttle-cargo transport of biomolecules: a certain cargo molecule can only pass the barrier if it is attached to a shuttle molecule. In this review we summarize the most important efforts aiming to reproduce this feature in artificial settings. This can be achieved by solid state nanopores that have been functionalized with the most important proteins found in the biological system. Alternatively, the nanopores are chemically modified with synthetic polymers. However, only a few studies have demonstrated a shuttle-cargo transport mechanism and due to cargo leakage, the selectivity is not comparable to that of the biological system. Other recent approaches are based on DNA origami, though biomolecule transport has not yet been studied with these. The highest selectivity has been achieved with macroscopic gels, but they are yet to be scaled down to nano-dimensions. It is concluded that although several interesting studies exist, we are still far from achieving selective and efficient artificial shuttle-cargo transport of biomolecules. Besides being of fundamental interest, such a system could be potentially useful in bioanalytical devices.

Visible light induced RAFT for asymmetric functionalization of silica mesopores

One key feature for bioinspired transport design through nanoscale pores is nanolocal, asymmetric as well as multifunctional nanopore functionalization. Here, we use a visible-light induced, controlled photo electron/energy transfer-reversible addition-fragmentation chain-transfer (PET-RAFT) polymerization for asymmetric polymer placement into mesoporous silica thin films including asymmetric polymer sequence design.

DNA origami in the quest for membrane piercing

The tool kit for label-free single-molecule sensing, nucleic acid sequencing (DNA, RNA and protein) and other biotechnological applications has been significantly broadened due to the wide range of available nanopore-based technologies. Currently, various sources of nanopores, including biological, fabricated solid-state, hybrid and recently de novo chemically synthesized ion-like channels have put in use for rapid single-molecule sensing of biomolecules and other diagnostic applications. At length scales of hundreds of nanometers, DNA nanotechnology, particularly DNA origami-based devices, enables the assembly of complex and dynamic 3-dimensional nanostructures, including nanopores with precise control over the size/shape. DNA origami technology has enabled to construct nanopores by DNA alone or hybrid architects with solid-state nanopore devices or nanocapillaries. In this review, we briefly discuss the nanopore technique that uses DNA nanotechnology to construct such individual pores in lipid-based systems or coupled with other solid-state devices, nanocapillaries for enhanced biosensing function. We summarize various DNA-based design nanopores and explore the sensing properties of such DNA channels. Apart from DNA origami channels we also pointed the design principles of RNA nanopores for peptide sensing applications.

Pushing the limits of nanopore transport performance by polymer functionalization

Inspired by the design and performance of biological pores, polymer functionalization of nanopores has emerged as an evolving field to advance transport performance within the last few years. This feature article outlines developments in nanopore functionalization and the resulting transport performance including gating based on electrostatic interaction, wettability and ligand binding, gradual transport controlled by polymerization as well as functionalization-based asymmetric nanopore and nanoporous material design going towards the transport direction. Pushing the limits of nanopore transport performance and thus reducing the performance gap between biological and technological pores is strongly related to advances in polymerization chemistry and their translation into nanopore functionalization. Thereby, the effect of the spatial confinement has to be considered for polymer functionalization as well as for transport regulation, and mechanistic understanding is strongly increased by combining experiment and theory. A full mechanistic understanding together with highly precise nanopore structure design and polymer functionalization is not only expected to improve existing application of nanoporous materials but also opens the door to new technologies. The latter might include out of equilibrium devices, ionic circuits, or machine learning based sensors.

DNA sequencing: an overview of solid-state and biological nanopore-based methods

The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.

Current Fluctuations in Nanopores Reveal the Polymer-Wall Adsorption Potential

Modification of surface properties by polymer adsorption is a widely used technique to tune interactions in molecular experiments such as nanopore sensing. Here, we investigate how the ionic current noise through solid-state nanopores reflects the adsorption of short, neutral polymers to the pore surface. The power spectral density of the noise shows a characteristic change upon adsorption of polymer, the magnitude of which is strongly dependent on both polymer length and salt concentration. In particular, for short polymers at low salt concentrations no change is observed, despite the verification of comparable adsorption in these systems using quartz crystal microbalance measurements. We propose that the characteristic noise is generated by the movement of polymers on and off the surface and perform simulations to assess the feasibility of this model. Excellent agreement with experimental data is obtained using physically motivated simulation parameters, providing deep insight into the shape of the adsorption potential and underlying processes. This paves the way toward using noise spectral analysis for in situ characterization of functionalized nanopores.

Computational Design for the Damping Characteristics of Poly(ether ether ketone)

To investigate the damping characteristics of poly(ether ether ketone) (PEEK), various potential modifications of the molecular structure, including sulfonate groups, hydroxyl groups, amino groups, carboxyl groups, methyl groups, fluorines, and benzene rings, were considered. It was found that these functional groups can mediate both the storage and loss modulus of PEEK derivatives, and the loss factors of PEEK derivatives are sensitive to the content and type of functional groups, indicating an ideal designability of energy dissipation performance. The reciprocating process of H-bonds and C_π-H bonds breaking and reforming during material deformation and the available free volume in the material are critical to the energy dissipation capacities in polymers.

Smart pH-Modulated Two-Way Photoswitch Based on a Polymer-Modified Single Nanochannel

In this article, we have demonstrated a smart pH-modulated two-way photoswitch that can reversibly switch ion transport under alternating light exposure over a wide pH range. This photoswitch was prepared by functionalizing the interior of a single conical glass nanochannel with a poly-spiropyran-linked methacrylate (P-SPMA) polymer through surface-initiated atom transfer radical polymerization. The P-SPMA polymer brushes comprise functional groups that are responsive to light and pH, which can cause configuration and charge changes to affect the properties of the nanochannel wall. The SPMA polymer-modified nanochannel not only reversibly controlled ion transport under alternating light irradiation but also efficiently and flexibly regulated the direction and extent of the ion transport based on the pH. This two-way photoswitch exhibits the considerable potential of photoresponsive polymers for the advancement of "intelligent" bionic nanochannel devices for ion screening and optical sensing in various applications.

pH-Responsive Ultrathin Nanoporous SiO2 Films for Selective Ion Permeation

Ultrathin nanoporous (NP) films are an emerging field for selective and effective ion/molecular separation and electrochemical sensing applications. We describe selective ion permeation in surface-functionalized ultrathin NP SiO₂ films (NP SiO₂-NH₂). The ultrathin NP SiO₂ films with ca. 8 nm thickness were prepared from silsesquioxane-containing blend polymer Langmuir-Blodgett films (nanosheets) using the photo-oxidation method. The porous SiO₂ surface was modified with a pH-responsive amine-containing silane coupling agent. Selective ion permeation was demonstrated under acidic pH conditions (pH ≤ 6) using two equally sized redox probes: negative (Fe(CN)₆^3-/4-) and positive (Ru(NH₃)₆^2+/3+) ions. The current density for Fe(CN)₆^3-/4- decreased as the pH value increased to pH = 6, whereas it increased for Ru(NH₃)₆^2+/3+. Control measurements revealed that the probes can penetrate the pores of nonfunctionalized SiO₂ films irrespective of pH values, indicating that both the size and the surface charge response contributed to selective ion permeation. Results obtained from this study pave the way for new applications in molecular separation and sensing applications based on ultrathin nanoporous films (<10 nm) and tailored surfaces.

Simultaneous Nanolocal Polymer and In Situ Readout Unit Placement in Mesoporous Separation Layers

Bioinspired solid-state nanopores and nanochannels have attracted interest in the last two decades, as they are envisioned to advance future sensing, energy conversion, and separation concepts. Although much effort has been made regarding functionalization of these materials, multifunctionality and accurate positioning of functionalities with nanoscale precision still remain challenging. However, this precision is necessary to meet transport performance and complexity of natural pores in living systems, which are often based on nonequilibrium states and compartmentalization. In this work, a nanolocal functionalization and simultaneous localized sensing strategy inside a filtering mesoporous film using precisely placed plasmonic metal nanoparticles inside mesoporous films with pore accessibility control is demonstrated. A single layer of gold nanoparticles is incorporated into mesoporous thin films with precise spatial control along the nanoscale layer thickness. The local surface plasmon resonance is applied to induce a photopolymerization leading to a nanoscopic polymer shell around the particles and thus nanolocal polymer placement inside the mesoporous material. As near-field modes are sensitive to the dielectric properties of their surrounding, the in situ sensing capability is demonstrated using UV-vis spectroscopy. It is demonstrated that the sensing sensitivity only slightly decreases upon functionalization. The presented nanolocal placement of responsive functional polymers into nanopores offers a simultaneous filtering and nanoscopic readout function. Such a nanoscale local control is envisioned to have a strong impact onto the development of new transport and sensor concepts, especially as the system can be developed into higher complexity using different metal nanoparticles and additional design of mesoporous film filtering properties.