Pushing the limits of nanopore transport performance by polymer functionalization

Orientational Pathways during Protein Translocation through Polymer-Modified Nanopores

Protein translocation through nanopores holds significant promise for applications in biotechnology, biomolecular analysis, and medicine. However, the interpretation of signals generated by the translocation of the protein remains challenging. In this way, it is crucial to gain a comprehensive understanding on how macromolecules translocate through a nanopore and to identify what are the critical parameters that govern the process. In this study, we investigate the interplay between protein charge regulation, orientation, and nanopore surface modifications using a theoretical framework that allows us to explicitly take into account the acid-base reactions of the titrable amino acids in the proteins and in the polyelectrolytes grafted to the nanopore surface. Our goal is to thoroughly characterize the translocation process of different proteins (GFP, β-lactoglobulin, lysozyme, and RNase) through nanopores modified with weak polyacids. Our calculations show that the charge regulation mechanism exerts a profound effect on the translocation process. The pH-dependent interactions between proteins and charged polymers within the nanopore lead to diverse free energy landscapes with barriers, wells, and flat regions dictating translocation efficiency. Comparison of different proteins allows us to identify the significance of protein isoelectric point, size, and morphology in the translocation behavior. Taking advantage of these insights, we propose pH-responsive nanopores that can load proteins at one pH and release them at another, offering opportunities for controlled protein delivery, separation, and sensing applications.

Ultrashort Peptide Grafting on Mesoporous Films and Its Impact on Ionic Mesopore Accessibility

An approach for direct in-pore solid-phase ultrashort peptide synthesis on mesoporous films using the amino acids arginine, leucine, and glycine is presented. Although the number of grafted amino acids remains low, the ionic mesopore accessibility can be gradually adjusted. The addition of arginine in up to five reaction cycles leads to a progressive increase in positive mesopore charge density, which gradually increases the anionic mesopore accessibility at acidic pH. At basic pH, the remaining silanol groups at the pore wall still dominate counter-charged cation mesopore accessibility. Thus, specific peptide sequence design is demonstrated to be a sensitive tool for molecular transport control in nanoscale pores. Overall, the direct in-pore solid-phase ultrashort peptide synthesis on mesoporous films using the sequences of different amino acids opens up exciting opportunities for the development of innovative materials with precisely tailored properties and functions based on specific peptide sequence design.

Electropolymerization of Polydopamine at Electrode-Supported Insulating Mesoporous Films

Bioinspired, stimuli-responsive, polymer-functionalized mesoporous films are promising platforms for precisely regulating nanopore transport toward applications in water management, iontronics, catalysis, sensing, drug delivery, or energy conversion. Nanopore technologies still require new, facile, and effective nanopore functionalization with multi- and stimuli-responsive polymers to reach these complicated application targets. In recent years, zwitterionic and multifunctional polydopamine (PDA) films deposited on planar surfaces by electropolymerization have helped surfaces respond to various external stimuli such as light, temperature, moisture, and pH. However, PDA has not been used to functionalize nanoporous films, where the PDA-coating could locally regulate the ionic nanopore transport. This study investigates the electropolymerization of homogeneous thin PDA films to functionalize nanopores of mesoporous silica films. We investigate the effect of different mesoporous film structures and the number of electropolymerization cycles on the presence of PDA at mesopores and mesoporous film surfaces. Our spectroscopic, microscopic, and electrochemical analysis reveals that the amount and location (pores and surface) of deposited PDA at mesoporous films is related to the combination of the number of electropolymerization cycles and the mesoporous film thickness and pore size. In view of the application of the proposed PDA-functionalized mesoporous films in areas requiring ion transport control, we studied the ion nanopore transport of the films by cyclic voltammetry. We realized that the amount of PDA in the nanopores helps to limit the overall ionic transport, while the pH-dependent transport mechanism of pristine silica films remains unchanged. It was found that (i) the pH-dependent deprotonation of PDA and silica walls and (ii) the insulation of the indium-tin oxide (ITO) surface by increasing the amount of PDA within the mesoporous silica film affect the ionic nanopore transport.

Molecular transport and water condensation inside mesopores with wettability step gradients

The wettabilities of nanoscale porous surfaces play important roles in the context of molecular and fluid transport or oil-water separation. The wettability pattern along a nanopore strongly influences fluid distribution throughout the membrane. Mesoporous silica thin films with gradually adjusted wettabilities were fabricated via cocondensation. With consecutive mesoporous layer depositions, double-layer mesoporous silica films with asymmetric or so-called Janus wettability patterns were generated. The effects of these wetting gradients on mass transport, water imbibition, and water vapor condensation were investigated with ellipsometry, cyclic voltammetry (CV), drop friction force instrument (DoFFIs), fluorescence microscopy and interferometry. By increasing the film thickness of the hydrophobic mesoporous silica top layer deposited on a hydrophilic mesoporous silica layer up to 205 nm, molecular transport through both the layers was prevented. However, water was observed to condense onto the bottom layer, and transport occurred for thinner top layers.

Surface Chain-Transfer Ring-Opening Metathesis Polymerization

Ring-opening metathesis polymerization (ROMP) is a powerful method to graft various types of polymer chains to a given surface. While surface-initiated ROMP (SI-ROMP) serves as an efficient tool for surface modification and is therefore widely reported, the method requires grafting (1) the olefin substrate and (2) the metathesis catalyst to the surface prior to the polymerization with multiple synthetic and work up steps. To overcome this difficulty, we proposed the use of the chain-transfer reaction as an alternative method for surface modification. Terminal olefins are grafted to the surface without the need to graft the metathesis catalysts, and polymers with olefin backbones are polymerized and grafted simultaneously via both ROMP and chain transfer (cross-metathesis between olefins from backbones and surfaces). Compared to SI-ROMP, this surface-chain transfer ROMP (SC-ROMP) method avoids grafting the catalyst and growing polymer chains from the surface and could be achieved in a single step. Various types of surfaces like carbon nanotubes, carbon fibers, graphene nanosheets, and silica microspheres are used for demonstration. We envision that this work could bring a convenient and effective solution to surface modification via ROMP.

Engineering Biological Nanopore Approaches toward Protein Sequencing

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

Semiconducting Polymer Nanoporous Thin Films as a Tool to Regulate Intracellular ROS Balance in Endothelial Cells

The design of soft and nanometer-scale photoelectrodes able to stimulate and promote the intracellular concentration of reactive oxygen species (ROS) is searched for redox medicine applications. In this work, we show semiconducting polymer porous thin films with an enhanced photoelectrochemical generation of ROS in human umbilical vein endothelial cells (HUVECs). To achieve that aim, we synthesized graft copolymers, made of poly(3-hexylthiophene) (P3HT) and degradable poly(lactic acid) (PLA) segments, P3HT-g-PLA. In a second step, the hydrolysis of sacrificial PLA leads to nanometer-scale porous P3HT thin films. The pore sizes in the nm regime (220-1200 nm) were controlled by the copolymer composition and the structural arrangement of the copolymers during the film formation, as determined by atomic force microscopy (AFM) and transmission electron microscopy (TEM). The porous P3HT thin films showed enhanced photofaradaic behavior, generating a higher concentration of ROS in comparison to non-porous P3HT films, as determined by scanning electrochemical microscopy (SECM) measurements. The exogenous ROS production was able to modulate the intracellular ROS concentration in HUVECs at non-toxic levels, thus affecting the physiological functions of cells. Results presented in this work provide an important step forward in the development of new tools for precise, on-demand, and non-invasive modulation of intracellular ROS species and may be potentially extended to many other physiological or pathological cell models.

Nanoscale pores introduced into paper via mesoporous silica coatings using sol-gel chemistry

Mesopores, with diameters between 2 and 50 nm, not only increase the specific surface area, but also generate hierarchically porous materials with specific properties such as capillary fluid transport, ion specific pore accessibility, or size exclusion. Paper is a strongly hierarchical, porous material with specific properties, such as capillary force-driven fluid transport. However, paper fibers change their morphology during the initial step of wood disintegration. This results in changes of the porous fiber structure. In particular paper fibers loose their mesopores during the final drying step in the fabrication process. Here, we investigate silica mesopore formation in paper by sol-gel chemistry and evaporation induced self-assembly to specifically introduce and rationally design mesopore formation and distribution in cotton linter and eucalyptus sulfate paper sheets. We demonstrate the importance of synchronizing the solvent evaporation rate and capillary fluid velocity to ensure mesopore formation as well as the influence of the fiber type and sol-gel solution composition. The combination of argon and krypton sorption, SAXS, TEM and CLSM provides systematic analysis of the porous structure and the silica distribution along the cellulose paper fiber length and cross-section. These results provide a deeper understanding of mesopore formation in paper and how the latter is influenced by paper fluidic properties.

Solid-State Nanopore/Nanochannel Sensing of Single Entities

Solid-state nanopores/nanochannels, with their high stability, tunable geometry, and controllable surface chemistry, have recently become an important tool for constructing biosensors. Compared with traditional biosensors, biosensors constructed with solid-state nanopores/nanochannels exhibit significant advantages of high sensitivity, high specificity, and high spatiotemporal resolution in the detection single entities (such as single molecules, single particles, and single cells) due to their unique nanoconfined space-induced target enrichment effect. Generally, the solid-state nanopore/nanochannel modification method is the inner wall modification, and the detection principles are the resistive pulse method and the steady-state ion current method. During the detection process, solid-state nanopore/nanochannel is easily blocked by single entities, and interfering substances easily enter the solid-state nanopore/nanochannel to generate interference signals, resulting in inaccurate measurement results. In addition, the problem of low flux in the detection process of solid-state nanopore/nanochannel, these defects limit the application of solid-state nanopore/nanochannel. In this review, we introduce the preparation and functionalization of solid-state nanopore/nanochannel, the research progress in the field of single entities sensing, and the novel sensing strategies on solving the above problems in solid-state nanopore/nanochannel single-entity sensing. At the same time, the challenges and prospects of solid-state nanopore/nanochannel for single-entity electrochemical sensing are also discussed.

Tunable nanochannel resistive pulse sensing device using a novel multi-module self-assembly

Nanochannel-based resistive pulse sensing (nano-RPS) system is widely used for the high-sensitive measurement and characterization of nanoscale biological particles and biomolecules due to its high surface to volume ratio. However, the geometric dimensions and surface properties of nanochannel are usually fixed, which limit the detections within particular ranges or types of nanoparticles. In order to improve the flexibility of nano-RPS system, it is of great significance to develop nanochannels with tunable dimensions and surface properties. In this work, we proposed a novel multi-module self-assembly (MS) strategy which allows to shrink the geometric dimensions and tune surface properties of the nanochannels simultaneously. The MS-tuned nano-RPS device exhibits an enhanced signal-to-noise ratio (SNR) for nanoparticle detections after shrunk the geometric dimensions by MS strategy. Meanwhile, by tuning the surface charge, an enhanced resolution for viral particles detection was achieved with the MS-tuned nano-RPS devices by analyzing the variation of pulse width due the tuned surface charge. The proposed MS strategy is versatile for various types of surface materials and can be potentially applied for nanoscale surface reconfiguration in various nanofluidic devices.

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.

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.