Gating of single synthetic nanopores by proton-driven DNA molecular motors

Sequence Context in DNA i-Motifs Can Nurture Very Stable and Persistent Kinetic Traps

I-motifs are non-canonical DNA structures with recognized biological significance and a proven utility in material engineering. Consequently, understanding and control of i-motif properties is essential to sustain progress across both disciplines. In this work, we systematically investigate how proximity to the most common form of DNA, a double-stranded duplex, influences the thermodynamic and kinetic properties of adjacent i-motifs. We demonstrate that double-stranded stems in i-motif loops promote kinetic trapping of very stable and persistent partially folded conformations. Further, we investigate pathways toward rational control over a folding topology makeup.

Photo-Driven Ion Directional Transport across Artificial Ion Channels: Band Engineering of WS2 via Peptide Modification

Biological photo-responsive ion channels play important roles in the important metabolic processes of living beings. To mimic the unique functions of biological prototypes, the transition metal dichalcogenides, owing to their excellent mechanical, electrical, and optical properties, are already used for artificial intelligent channel constructions. However, there remain challenges to building artificial bio-semiconductor nanochannels with finely tuned band gaps for accurately simulating or regulating ion transport. Here, two well-designed peptides are employed for the WS2 nanosheets functionalization with the sequences of PFPFPFPFC and DFDFDFDFC (PFC and DFC; P: proline, D: aspartate, and F: phenylalanine) through cysteine (Cys, C) linker, and an asymmetric peptide-WS2 membrane (AP-WS2M) could be obtained via self-assembly of peptide-WS2 nanosheets. The AP-WS2M could realize the photo-driven anti-gradient ion transport and vis-light enhanced osmotic energy conversion by well-designed working patterns. The photo-driven ion transport mechanism stems from a built-in photovoltaic motive force with the help of formed type II band alignment between the PFC-WS2 and DFC-WS2. As a result, the ions would be driven across the channels of the membrane for different applications. The proposed system provides an effective solution for building photo-driven biomimetic 2D bio-semiconductor ion channels, which could be extensively applied in the fields of drug delivery, desalination, and energy conversion.

Monitoring Enzymatic Reaction Kinetics and Activity Assays in Confined Nanospace

Enzyme-mediating biotransformations commonly occur in micro- and nanospace, which is crucial to maintain the essential biochemical processes and physiological functions in living systems. Probing enzyme-catalytic reactions in a biomimetic fashion remains challenging due to the lack of competent tools and methodology. Here, we show that studying enzymatic reaction kinetics can be readily achieved by a well-designed solid-state nanopore. Using tyrosine as a classical substrate, we quantitatively characterize the catalytic activity of tyrosinase (TYR) and tyrosine decarboxylase (TDC) in a nanoconfined space. Tyrosine was first immobilized in the nanopipette, wherein the active sites of tyrosine were left unoccupied. When successively exposed to TYR and TDC, a two-step cascade reaction can spontaneously take place. In this process, the surface wettability and charge of the nanopipette stemming from the catalytic products can sensitively regulate ion transport and ionic current rectification behavior, which were monitored by ionic current signal. In this biomimetic scenario, we obtained the enzymatic reaction kinetics of monophenyl oxidase that were not previously actualized in the conventional macroenvironment. Significantly, TYR showed higher enzyme activity, with a Km value of 1.59 mM, which was lower than that measured in a free and open space (with a Km of 3.01 mM). This suggests that tyrosine should be the most appropriate substrate of TYR, thus improving our understanding of tyrosine-associated biochemical reactions. This work offers an applicable technical platform to mimic enzyme-mediated biotransformations and biometabolisms.

A Portable Device for in Situ Noninvasive Monitoring of Cell Secretions and Communications with Fluorescence and Nanochannel Electrochemistry

In situ monitoring of cell secretions and communications plays a fundamental role in screening of disease diagnostic biomarkers and drugs. Quantitative detection of cell secretions and monitoring of intercellular communication have been separately reported, which often rely on target labeling or complex pretreatment steps, inevitably causing damage to the target. Simultaneous in situ noninvasive detection of cell secretions and monitoring of intercellular communication are challenging and have never been reported. Herein, we smartly developed a portable device for in situ label-free monitoring of cell secretions and communications with fluorescence and ion-transport-based nanochannel electrochemistry. Based on the dual signal mode, a series of nonelectroactive secretions were sensitively and accurately quantified. The detection limits for VEGF, MUC1, and ATP were 3.84 pg/mL, 32.7 pg/mL, and 47.4 fM (3σ/S), which were 1/3.9, 1/1.1, and 1/41 of those of commercial ELISA kits, respectively. More interestingly, under the released secretions, the gradual opening of the nanochannel connected the two cells in the left and right chambers of the device; thus, the secretion mediated intercellular communication can be monitored. The proposed platform may provide a promising tool for understanding the mechanism of intercellular communication and discovering new therapeutic targets.

Rectifying artificial nanochannels with multiple interconvertible permeability states

Transmembrane channels play a vital role in regulating the permeation process, and have inspired recent development of biomimetic channels. Herein, we report a class of artificial biomimetic nanochannels based on DNAzyme-functionalized glass nanopipettes to realize delicate control of channel permeability, whereby the surface wettability and charge can be tuned by metal ions and DNAzyme-substrates, allowing reversible conversion between different permeability states. We demonstrate that the nanochannels can be reversibly switched between four different permeability states showing distinct permeability to various functional molecules. By embedding the artificial nanochannels into the plasma membrane of single living cells, we achieve selective transport of dye molecules across the cell membrane. Finally, we report on the advanced functions including gene silencing of miR-21 in single cancer cells and selective transport of Ca2+ into single PC-12 cells. In this work, we provide a versatile tool for the design of rectifying artificial nanochannels with on-demand functions.

Functionalized nanopores based on hybridization chain reaction: Fabrication and microRNA sensing

Enzyme-free hybridization chain reaction (HCR) technology is often used as a signal amplification tool for the detection of different targets. In this study, an ultrasensitive and label-free method for detecting miRNA-21 was developed using the nanopore ionic current rectification (ICR) technology coupled with HCR technology. The probe oligonucleotide (DNA1) was combined with the gold-coated nanopore through the Au-S bond to form a DNA1-functionalized gold-coated nanopore (DNA1-Au-coated nanopore). Since miRNA-21 is partially complementary to DNA1, it can be selectively recognized by DNA1-functionalized gold-coated nanopores. The target (miRNA-21) can induce the opening of hairpin DNA and HCR reaction after the introduction of hairpin DNA H1 and H2. The concentration of miRNA-21 will affect the combination of H1 and H2 on the inner wall of the nanopore, and its surface charge will change with the internal modification, thereby changing the ion current rectification ratio. Under the condition that the concentration of H1, H2 and HCR reaction time are constant, the change of ICR ratio is linearly correlated with the logarithm of miRNA-21 concentration within a certain range, which shows that the sensing strategy we designed can achieve target miRNA-21 detection. This ultrasensitive miRNA holds great promise in the field of cancer diagnosis.

Controllable Fabrication and Rectification of Bipolar Nanofluid Diodes in Funnel-Shaped Si3 N4 Nanopores

Solid-state nanopores attract widespread interest, owning to outstanding robustness, extensive material availability, as well as capability for flexible manufacturing. Bioinspired solid-state nanopores further emerge as potential nanofluidic diodes for mimicking the rectification progress of unidirectional ionic transport in biological K+ channels. However, challenges that remain in rectification are over-reliance on complicated surface modifications and limited control accuracy in size and morphology. In this study, suspended Si3 N4 films of only 100 nm thickness are used as substrate and funnel-shaped nanopores are controllably etched on that with single-nanometer precision, by focused ion beam (FIB) equipped with a flexibly programmable ion dose at any position. A small diameter 7 nm nanopore can be accurately and efficiently fabricated in only 20 ms and verified by a self-designed mathematical model. Without additional modification, funnel-shaped Si3 N4 nanopores functioned as bipolar nanofluidic diodes achieve high rectification by simply filling each side with acidic and basic solution, respectively. Main factors are finely tuned experimentally and simulatively to enhance the controllability. Moreover, nanopore arrays are efficiently prepared to further improve rectification performance, which has great potential for high-throughput practical applications such as extended release of drugs, nanofluidic logic systems, and sensing for environmental monitoring and clinical diagnosis.

Rapid and Highly Efficient Separation of i-Motif DNA Species by CE-UV and Multivariate Curve Resolution

The i-motif is a class of nonstandard DNA structure with potential biological implications. A novel capillary electrophoresis with an ultraviolet absorption spectrophotometric detection (CE-UV) method has been developed for the rapid analysis of the i-motif folding equilibrium as a function of pH and temperature. The electrophoretic analyses are performed in reverse polarity of the separation voltage with 32 cm long fused silica capillaries permanently coated with hydroxypropyl cellulose (HPC), after an appropriate conditioning procedure was used to achieve good repeatability. However, the electrophoretic separation between the folded and unfolded conformers of the studied cytosine-rich i-motif sequences (i.e., TT, Py39WT, and nmy01) is compromised, especially for Py39WT and nmy01, which result in completely overlapped peaks. Therefore, deconvolution with multivariate curve resolution-alternating least-squares (MCR-ALS) has been required for the efficient separation of the folded and unfolded species found at different concentration levels at pH 6.5 and between 12 and 40 °C, taking advantage of the small dissimilarities in the electrophoretic mobilities and UV spectra levels. MCR-ALS has also provided quantitative information that has been used to estimate melting temperatures (Tm), which are similar to those determined by UV and circular dichroism (CD) spectroscopies. The obtained results demonstrate that CE-UV assisted by MCR-ALS may become a very useful tool to get novel insight into the folding of i-motifs and other complex DNA structures.

Functional Nanopores Enabled with DNA

Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.

Heterogeneous Electrospinning Nanofiber Membranes with pH-regulated Ion Gating for Tunable Osmotic Power Harvesting

Biological ion channels existing in organisms are critical for many biological processes. Inspired by biological ion channels, the heterogeneous electrospinning nanofiber membranes (HENM) with functional ion channels are constructed by electrospinning technology. The HENM successfully realizes ion-gating effects, which can be used for tunable energy conversions. Introduction of pyridine and carboxylic acid groups into the HENM plays an important role in generating unique and stable ion transport behaviors, in which gates become alternative states of open and close, responding to symmetric/asymmetric pH stimulations. Then we used the HENM to convert osmotic energy into electric energy which reach a maximum value up to 12.34 W m^-2 and the output power density of HENM-based system could be regulated by ion-gating effects. The properties of the HENM provide widespread potentials in application of smart nanofluidic devices, energy conversion, and water treatment.

Nanopore-based technologies beyond DNA sequencing

Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.

Solid-state nanopore: chemical modifications, interactions, and functionalities

Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.

Insight on the regulation mechanism of the nanochannels in hard and brittle materials induced by sparially shaped femtosecond laser

The efficient fabrication of nanochannels on hard and brittle materials is a difficult task in the field of micro and nano processing. We have realized nanochannel arrays on silica with characteristic scales varying from 50–230 nm using a single femtosecond Bessel beam pulse of 515 nm. By characterizing the surface openings, we found that the characteristic scales of the nanopore openings are inextricably linked to the surface energy deposition effect. We achieved not only three asymmetric channel profiles by adjusting the laser-sample interaction region, but also high aspect ratio nanochannels with characteristic scales about 50 nm and aspect ratios over 100. These results on hard and brittle materials provide a broader platform and application scenarios for smart particle rectifiers, DNA molecular sequencing, biosensors, and nanofluidic devices, which are also more suitable for future practical applications due to their low cost, good durability, and high productivity.

Construction of a pH-Mediated Single-Molecule Switch with a Nanopore-DNA Complex

A molecular switch is one of the simplest examples of artificial molecular machines. Even so, the development of molecular switches is still at its very early stage. Currently, building single-molecule switches mostly rely on the molecular junction technique, but many of their performance characteristics are device-dependent. Here, a pH-mediated single-molecule switch based on the combination of an α-hemolysin (αHL) nanopore and a hexacyclen-modified DNA strand is developed. The single-stranded DNA is suspended inside an αHL through biotin-streptavidin linkage and the hexacyclen-modified nucleobase interacts with amino acid residues at positions 111, 113, and 147 to cause current oscillations. Distinct current transitions are observed when pH is tuned back and forth in the range of 3.0-7.4, with a typical "up" level when pH > 6.5 and a "down" level when pH < 4.5. This nanopore-DNA complex possesses membrane-bound advantages and may find applications in single-cell studies where pH could be readily tuned to control ON-OFF functions.

Single Artificial Ion Channels with Tunable Ion Transport Based on the Surface Modification of pH-Responsive Polymers

Artificial ion channels with tunable ionic transport control and intelligent iontronic functions at the nanoscale have a wide application in logic computing and biosensing. Although some artificial ion channels with smart ion transport characteristics have been developed, most of them are constructed on porous membranes with undefined channel numbers. It is still challenging to achieve multiple ion transport features in single nanochannels and to control the ion flow more accurately with excellent repeatability. In this paper, a design strategy is presented to fabricate pH-responsive ion channels with various ion transport features based on a single polydimethylsiloxane (PDMS) nanochannel. The single-ion nanochannel developed by this approach can be further integrated into electronic systems on a chip. Three types of artificial ion channels are demonstrated and investigated systematically in this work. With symmetric or asymmetric pH stimuli, these ion channels can alternatively change their working states among an opened state, a closed state, and an ionic diode state. Four different ion transport features can be realized in a triple-gated ion channel system. With these advantages of the design, it is promising to build smart nanofluidic iontronic devices with widespread applicability in energy conversions, active ion transport control, and biological analysis.

SAXS data modelling for the characterisation of ion tracks in polymers

Here, we present new models to fit small angle X-ray scattering (SAXS) data for the characterization of ion tracks in polymers. Ion tracks in polyethylene terephthalate (PET), polycarbonate (PC), polyimide (PI) and polymethyl methacrylate (PMMA) were created by swift heavy ion irradiation using ¹⁹⁷Au and ²³⁸U with energies between 185 MeV and 2.0 GeV. Transmission SAXS measurements were performed at the Australian Synchrotron. SAXS data were analysed using two new models that describe the tracks by a cylindrical structure composed of a highly damaged core with a gradual transition to the undamaged material. First, we investigate the 'Soft Cylinder Model', which assumes a smooth function to describe the transition region by a gradual change in density from a core to a matrix. As a simplified and computational less expensive version of the 'Soft Cylinder Model', the 'Core Transition Model' was developed to enable fast fitting. This model assumes a linear increase in density from the core to the matrix. Both models yield superior fits to the experimental SAXS data compared with the often-used simple 'Hard Cylinder Model' assuming a constant density with an abrupt transition.

Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

Biological nanochannels which can regulate ionic transport across cell membranes intelligently play a significant role in physiological functions. Inspired by these nanochannels, numerous artificial nanochannels have been developed during recent years. The exploration of smart solid-state nanochannels can lay a solid foundation, not only for fundamental studies of biological systems but also practical applications in various fields. The basic fabrication principles, functional materials, and diverse applications based on artificial nanochannels are summarized in this review. In addition, theoretical insights into transport mechanisms and structure-function relationships are discussed. Meanwhile, it is believed that improvements will be made via computer-guided strategy in designing more efficient devices with upgrading accuracy. Finally, some remaining challenges and perspectives for developments in both novel conceptions and technology of this inspiring research field are stated.

Light-Controlled Ionic/Molecular Transport through Solid-State Nanopores and Nanochannels

Biological nanochannels perfectly operate in organisms and exquisitely control mass transmembrane transport for complex life process. Inspired by biological nanochannels, plenty of intelligent artificial solid-state nanopores and nanochannels are constructed based on various materials and methods with the development of nanotechnology. Specially, the light-controlled nanopores/nanochannels have attracted much attention due to the unique advantages in terms of that ion and molecular transport can be regulated remotely, spatially and temporally. According to the structure and function of biological ion channels, light-controlled solid-state nanopores/nanochannels can be divided into light-regulated ion channels with ion gating and ion rectification functions, and light-driven ion pumps with active ion transport property. In this review, we present a systematic overview of light-controlled ion channels and ion pumps according to the photo-responsive components in the system. Then, the related applications of solid-state nanopores/nanochannels for molecular sensing, water purification and energy conversion are discussed. Finally, a brief conclusion and short outlook are offered for future development of the nanopore/nanochannel field.

Increased ion transport and high-efficient osmotic energy conversion through aqueous stable graphitic carbon nitride/cellulose nanofiber composite membrane

Increased attention has evoked on the utilization of renewable energy, particularly osmotic power as a potential solution to the energy crisis and environmental pollution. Herein, we fabricate graphitic carbon nitride (g-C₃N₄)/cellulose nanofiber (CNF) composite membranes with tailored lamellar nanochannels for capturing osmotic energy from salinity gradients. Composite membranes exhibiting charge-governed ion conductivity were prepared via co-homogenization of g-C₃N₄ with CNF and vacuum filtration. Ion conductivity was efficiently modulated by fine-tuning the charge density through controlling the weight content of CNF in the composite membranes. Higher ion conductivity of 0.014 S cm^-1 at low concentrations (<10^-2 M KCl) was achieved due to the increased charge density of the lamellar nanochannels and the excellent aqueous stability of the membranes. We demonstrate the potential of the composite membranes in nanofluidic osmotic energy conversion, displaying thermo-enhanced power output performance. This work could inspire new designs of cellulose-based nanofluidic devices for improved osmotic energy conversion.

Photoresponsive Solid Nanochannels Membranes: Design and Applications

Light stimuli have notable advantages over other environmental stimuli, such as more precise spatial and temporal regulation, and the ability to serve as an energy source to power the system. In nature, photoresponsive nanochannels are important components of organisms, with examples including the rhodopsin channels in optic nerve cells and photoresponsive protein channels in the photosynthesis system of plants. Inspired by biological channels, scientists have constructed various photoresponsive, smart solid-state nanochannels membranes for a range of applications. In this review, the methods and applications of photosensitive nanochannels membranes are summarized. The authors believe that this review will inspire researchers to further develop multifunctional artificial nanochannels for applications in the fields of biosensors, stimuli-responsive smart devices, and nanofluidic devices, among others.

Recent advances in polymeric nanostructured ion selective membranes for biomedical applications

Nano structured ion-selective membranes (ISMs) are very attractive materials for a wide range of sensing and ion separation applications. The present review focuses on the design principles of various ISMs; nanostructured and ionophore/ion acceptor doped ISMs, and their use in biomedical engineering. Applications of ISMs in the biomedical field have been well-known for more than half a century in potentiometric analysis of biological fluids and pharmaceutical products. However, the emergence of nanotechnology and sophisticated sensing methods assisted in miniaturising ion-selective electrodes to needle-like sensors that can be designed in the form of implantable or wearable devices (smartwatch, tattoo, sweatband, fabric patch) for health monitoring. This article provides a critical review of recent advances in miniaturization, sensing and construction of new devices over last decade (2011-2021). The designing of tunable ISM with biomimetic artificial ion channels offered intensive opportunities and innovative clinical analysis applications, including precise biosensing, controlled drug delivery and early disease diagnosis. This paper will also address the future perspective on potential applications and challenges in the widespread use of ISM for clinical use. Finally, this review details some recommendations and future directions to improve the accuracy and robustness of ISMs for biomedical applications.

The Selective Transport of Ions in Charged Nanopore with Combined Multi-Physics Fields

The selective transport of ions in nanopores attracts broad interest due to their potential applications in chemical separation, ion filtration, seawater desalination, and energy conversion. The ion selectivity based on the ion dehydration and steric hindrance is still limited by the very similar diameter between different hydrated ions. The selectivity can only separate specific ion species, lacking a general separation effect. Herein, we report the highly ionic selective transport in charged nanopore through the combination of hydraulic pressure and electric field. Based on the coupled Poisson–Nernst–Planck (PNP) and Navier–Stokes (NS) equations, the calculation results suggest that the coupling of hydraulic pressure and electric field can significantly enhance the ion selectivity compared to the results under the single driven force of hydraulic pressure or electric field. Different from the material-property-based ion selective transport, this method endows the general separation effect between different kinds of ions. Through the appropriate combination of hydraulic pressure and electric field, an extremely high selectivity ratio can be achieved. Further in-depth analysis reveals the influence of nanopore diameter, surface charge density and ionic strength on the selectivity ratio. These findings provide a potential route for high-performance ionic selective transport and separation in nanofluidic systems.

Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals

Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.

Gap Confinement Effect of a Tandem Nanochannel System and Its Application in Salinity Gradient Power Generation

As an important nanofluidic device, an artificial ion nanochannel could selectively transport ions inside its nanoconfinement space and the surface charge of the pore wall. Here, confinement effects were realized by tandem nanochannel units, which kept their cascade gaps less than 500 nm. Within these gaps, ionic conductance was governed by the surface charge density of the channel unit. Cations could be sufficiently selected and enriched within this confined space, which improves the cation transfer number of the system. Therefore, the tandem nanochannel system could greatly improve the diffusion potential and energy conversion efficiency in the salinity gradient power generation process. Poisson-Nernst-Planck equations were introduced to numerically simulate the ionic transport behavior and confirmed the experimental results. Finally, the gap confinement effect was introduced in the porous cellulose acetate membrane tandem nanochannel system, and a high output power density of 4.72 W/m² and energy conversion efficiency of 42.22% were achieved under stacking seven channel units.

A surface charge governed nanofluidic diode based on a single polydimethylsiloxane (PDMS) nanochannel

HYPOTHESIS

Nanofluidic diodes have attracted intense attention recently. Commonly used materials to design these devices are membrane-based short nanopores and aligned Carbon nanotube bundles. It is highly desirable and very challenging to develop a nanofluidic diode based on a single PDMS nanochannel which is easier to be introduced into an integrated electronic system on a chip. Layer-by-layer (LBL) deposition of charged polyelectrolytes can change the size and surface properties of PDMS nanochannels that provides new possibilities to develop high-performance nanofluidic based on PDMS nanochannels.

EXPERIMENTS

A novel design of nanofluidic diode is presented by controlling the surface charges and sizes of single PDMS nanochannels by surface modification using polyelectrolytes. Polybrene (PB) and Dextran sulfate (DS) are used to reduce the PDMS nanochannel size to meet the requirement of ion gating by LBL method and generate opposite surface charges at the ends of nanochannels. The parameters of such a nanofluidic diode are investigated systematically.

FINDINGS

This nanofluidic diode developed in this work has high effective current rectification performance. The rectification ratio can be as high as 218 which is the best ever reported in PB/DS modified nanochannels. This rectification ratio reduces with high voltage frequency and ionic concentration whereas increases in shorter nanochannels.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Ferrocene-Containing DNA Monolayers: Influence of Electrostatics on the Electron Transfer Dynamics

A 153-mer target DNA was amplified using ethynyl ferrocene dATP and a tailed forward primer resulting in a duplex with a single-stranded DNA tail for hybridization to a surface-tethered probe. A thiolated probe containing the sequence complementary to the tail as well as a 15 polythimine vertical spacer with a (CH₂)₆ spacer was immobilized on the surface of a gold electrode and hybridized to the ferrocene-modified complementary strand. Potential step chronoamperometry and cyclic voltammetry were used to probe the potential of zero charge, PZC, and the rate of heterogeneous electron transfer between the electrode and the immobilized ferrocene moieties. Chronoamperometry gives three, well-resolved exponential current-time decays corresponding to ferrocene centers located within 13 Å (4 bases) along the duplex. Significantly, the apparent standard heterogeneous electron transfer rate constant, k_app^o, observed depends on the initial potential, i.e., the rate of electron transfer at zero driving force is not the same for oxidation and reduction of the ferrocene labels. Moreover, the presence of ions, such as Sr²⁺, that strongly ion pair with the negatively charged DNA backbone modulates the electron transfer rate significantly. Specifically, k_app^o = 246 ± 23.5 and 14 ± 1.2 s^-1 for reduction and oxidation, respectively, where the Sr²⁺ concentration is 10 mM, but the corresponding values in 1 M Sr²⁺ are 8 ± 0.8 and 150 ± 12 s^-1. While other factors may be involved, these results are consistent with a model in which a low Sr²⁺ concentration and an initial potential that is negative of the PZC lead to electrostatic repulsion of the negatively charged DNA backbone and the negatively charged electrode. This leads to the DNA adopting an extended configuration (concertina open), resulting in a slow rate of heterogeneous electron transfer. In contrast, for ferrocene reduction, the initial potential is positive of PZC and the negatively charged DNA is electrostatically attracted to the electrode (concertina closed), giving a shorter electron transfer distance and a higher rate of heterogeneous electron transfer. When the Sr²⁺ concentration is high, the charge on the DNA backbone is compensated by the electrolyte and the charge on the electrode dominates the electron transfer dynamics and the opposite potential dependence is observed. These results open up the possibility of electromechanical switching using DNA superstructures.

Recent Progress in DNA Motor-Based Functional Systems

The designability, functionalization, and diverse secondary structures of DNA enable the construction of DNA motors with stimuli-responsiveness. Therefore, it has been widely used to fabricate functional systems or generate mechanical power under external stimuli, such as pH, light, heat, electrical, and chemical molecular signals. Furthermore, the DNA motor has also been demonstrated to promote the applications of smart devices and materials, particularly in controllable drug delivery and reversible molecular switching. In this review, we have summarized and discussed recent progress of the construction and applications of DNA motor-based functional systems, such as responsive nanodevices, modified surfaces, and hydrogels.

DNA Walking and Rolling Nanomachine for Electrochemical Detection of miRNA

miRNAs, a class of endogenous noncoding RNAs, are involved in many crucial biological processes, which have emerged as a new set of biomarkers for disease theranostics. Exploring efficient signal amplification strategy is highly desired to pursue a highly sensitive miRNA biosensing platform. DNA nanotechnology shows great promise in the fabrication of amplified miRNA biosensors. In this work, a novel DNA walking and rolling nanomachine is developed for highly sensitive and selective detection of miRNA. Particularly, this approach programs two forms of dynamic DNA nanomachines powered by corresponding enzymes, which are well integrated. It is able to achieve a limit of detection as low as 39 × 10^-18 m, along with excellent anti-interfering performance and clinical applications. In addition, by designing pH-controlled detachable intermolecular DNA triplex, the main sensing elements can be conveniently reset, which fulfills the requirements of point-of-care profiling of miRNA. The high consistency between the proposed approach and quantitative real-time polymerase chain reaction validates the robustness and reliability. Therefore, it is anticipated that the DNA walking and rolling nanomachine has attractive application prospects in miRNA assay for biological researches and clinical diagnosis.

Bioinspired Ultrafast-Responsive Nanofluidic System for Ion and Molecule Transport with Speed Control

The design of an intelligent nanofluidic system for regulating the transport of substances such as ions and molecules is significant for applications in biological sensing, drug delivery, and energy harvesting. However, the existing nanofluidic system faces challenges in terms of an uncontrollable transport speed for molecules and ions and also a complex preparation processes, low durability, and slow response rate. Herein, we demonstrate the use of a bioinspired ferrofluid-based nanofluid that can facilitate multilevel ultrafast-responsive ion and molecule transport with speed control. Specifically, we reversibly deform bulk ferrofluids using a magnet and wet/dewet the outer surface of superhydrophilic nanochannels for building a smart transport system. By changing the direction and strength of the external magnetic field, a speed control, ultrafast-responsive molecular transport (<0.1 s), and controlled current gating ratio are achieved owing to the different pattern changes of ferrofluids on the outer surface of nanochannels. We also illustrate a practical application of this strategy for antibacterial devices to control the transport of drug molecules in a programmed manner. These results suggest that molecule transport can be further complexified and quantified through an intelligent nanofluidic system.

Analytes Triggered Conformational Switch of i-Motif DNA inside Gold-Decorated Solid-State Nanopores

The nanopore-based technique is a useful tool for single-molecule sensing and characterization. In this work, we have developed a new DNA-functionalized gold-modified nanopore, and analytes can induce the conformational switch of i-motif DNA formed on the inner surface of the nanopore. i-Motif DNA structure can be formed in the presence of silver ions (Ag⁺), which will result in the change in surface charge and structure of the nanopore tip and ion current rectification (ICR) ratio. The i-motif DNA structure on nanopore surface will be destroyed after the addition of glutathione (GSH) due to the strong interaction of Ag-S bond, which results in the recovery of surface charge, steric hindrance, and ICR ratio. This analyte-triggered conformational switch of i-motif DNA can help us deeply understand the DNA technology inside single nanopore and will benefit the possible applications in an ultrasensitive detection and biological/chemical analysis.

Construction and Characterization of a Mirror-Image l-DNA i-Motif

The first thermally stable and pH-responsive quadruplex intercalated motif (i-motif) structure formed by l-DNA is presented. Although this l-type i-motif exhibits the same physiochemical properties as its d isomer, its inverted chirality and good enzymatic resistance potentially open the way to the development of new DNA materials of pharmaceutical and biological interest.

Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles

The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif-forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif-forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.

Regulating the ionic current rectification behavior of branched nanochannels by filling polyelectrolytes

The overlapping of the electric double layer (EDL) in a nanochannel yields many interesting and significant electrokinetic phenomena such as ionic current rectification (ICR), which occurs only at a relatively low bulk salt concentration (∼1 mM) where the EDL thickness is comparable to the nanochannel size. In an attempt to raise this concentration to higher levels and the ICR performance improved appreciably, a branched nanochannel filled with polyelectrolytes (PEs) is proposed in this study. We show that these objectives can be achieved by choosing appropriate PE. For example, if the stem side of an anodic aluminun oxide nanochannel is filled with polystyrene sulfonate (PSS) an ICR ratio up to 850 can be obtained at 1 mM, which was not reported in previous studies. Taking account of the effect of electroosmotic flow, the underlying mechanisms of the ICR phenomena observed are discussed and the influences of the solution pH, the bulk salt concentration, and how the region(s) of a nanochannel is filled with PE examined. We show that the ICR behavior of a branched nanochannel can be modulated satisfactorily by filling highly charged PE and the solution pH.

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Ionic current in nanochannels grafted with pH-responsive polyelectrolyte brushes modeled using augmented strong stretching theory

In this paper, we provide a theory to quantify the ionic current ( i ion ) in nanochannels grafted with pH-responsive polyelectrolyte (PE) brushes. We consider the PE brushes to be modeled by our recently proposed augmented strong stretching theory (SST) model that improves the existing SST models by incorporating the effects of excluded volume interactions and an extended mass action law. Use of such augmented SST for this problem implies that this is the first study on computing i ion in PE brush-grafted nanochannels accounting for the appropriate coupled configuration-electrostatic description of the PE brushes. i ion is obtained as functions of PE brush grafting density, medium pH and salt concentration ( c ∞ ), and the density of polyelectrolyte chargeable sites (PECS). For large c ∞ , i ion increases linearly with c ∞ (as for such c ∞ , i ion becomes independent of the PE charge and is dominated by the bulk mobility and number density of the electrolyte ions), whereas i ion is independent of c ∞ at small c ∞ (where the electric double layer electrostatics and the total number of ions in the system is dominated by the hydrogen ions). We further witness an enhancement of i ion for smaller pH and larger grafting density at low and moderate c ∞ , while there is little to no effect of the PECS density on the ionic current except for weakly grafted brushes at low c ∞ . We anticipate that this study will serve as a theoretical foundation for a large number of applications that are based on the brush-induced modification of the ionic current in a nanochannel.

Molecular Design of Solid-State Nanopores: Fundamental Concepts and Applications

Solid-state nanopores are fascinating objects that enable the development of specific and efficient chemical and biological sensors, as well as the investigation of the physicochemical principles ruling the behavior of biological channels. The great variety of biological nanopores that nature provides regulates not only the most critical processes in the human body, including neuronal communication and sensory perception, but also the most important bioenergetic process on earth: photosynthesis. This makes them an exhaustless source of inspiration toward the development of more efficient, selective, and sophisticated nanopore-based nanofluidic devices. The key point responsible for the vibrant and exciting advance of solid nanopore research in the last decade has been the simultaneous combination of advanced fabrication nanotechnologies to tailor the size, geometry, and application of novel and creative approaches to confer the nanopore surface specific functionalities and responsiveness. Here, the state of the art is described in the following critical areas: i) theory, ii) nanofabrication techniques, iii) (bio)chemical functionalization, iv) construction of nanofluidic actuators, v) nanopore (bio)sensors, and vi) commercial aspects. The plethora of potential applications once envisioned for solid-state nanochannels is progressively and quickly materializing into new technologies that hold promise to revolutionize the everyday life.

Biomolecule-Functionalized Solid-State Ion Nanochannels/Nanopores: Features and Techniques

Solid-state ion nanochannels/nanopores, the biomimetic products of biological ion channels, are promising materials in real-world applications due to their robust mechanical and controllable chemical properties. Functionalizations of solid-state ion nanochannels/nanopores by biomolecules pave a wide way for the introduction of varied properties from biomolecules to solid-state ion nanochannels/nanopores, making them smart in response to analytes or external stimuli and regulating the transport of ions/molecules. In this review, two features for nanochannels/nanopores functionalized by biomolecules are abstracted, i.e., specificity and signal amplification. Both of the two features are demonstrated from three kinds of nanochannels/nanopores: nucleic acid-functionalized nanochannels/nanopores, protein-functionalized nanochannels/nanopores, and small biomolecule-functionalized nanochannels/nanopores, respectively. Meanwhile, the fundamental mechanisms of these combinations between biomolecules and nanochannels/nanopores are explored, providing reasonable constructs for applications in sensing, transport, and energy conversion. And then, the techniques of functionalizations and the basic principle about biomolecules onto the solid-state ion nanochannels/nanopores are summarized. Finally, some views about the future developments of the biomolecule-functionalized nanochannels/nanopores are proposed.

Electroosmotic flow velocity in DNA modified nanochannels

Electroosmotic flow (EOF) is systematically investigated in DNA grafted hard PDMS (h-PDMS) channels with size ranging from 50 nm to 2.5 μm by using the current-slope method. The effects of the DNA types, the incubation time in the process of surface modification, and the pH value, ionic concentration of electrolyte solutions, and the UV (ultraviolet) illumination on the velocity of electroosmotic flow are experimentally studied. It is found that the DNA type and the incubation time of DNAs affect the grafting density and the surface charge on the channel walls, thus influencing the EOF velocity. In the DNA modified channels, the pH effects on EOF velocity become less prominent compared with that in the pristine channels. On the contrary, UV illumination can increase the EOF velocity significantly in the DNA modified channels, whereas takes unapparent effects on EOF velocity in the pristine channels. The effects of ionic concentration on EOF are also studied in this paper. It is observed that EOF velocity is dependent on the channel size when the ionic concentration is low even without overlapped electric double layer (EDL) and is essentially independent of the channel size when the ionic concentration is high. Furthermore, with high ionic concentration and thin EDL, the EOF velocity can be enhanced by the coated DNA brushes on the channel surface.

Steady State and Dynamic Response of Voltage-Operated Membrane Gates

An electrochemical flow cell with Nafion 212, aqueous LiI/I2 redox solution, and carbon paper electrode was operated as an electro-osmotic gate based on the Electrokinetic Energy Conversion (EKEC) principle. The gate was operated in different modes. (i) In normal DC pump operation it is shown to follow the predictions from the phenomenological transport equations. (ii) Furthermore, it was also demonstrated to operate as a normally open, voltage-gated valve for microfluidic purposes. For both pump and valve operations low energy requirements (mW range) were estimated for precise control of small flows (μL range). (iii) Finally, the dynamic response of the pump was investigated by using alternating currents at a range of different frequencies.