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Gene knockdown in HaCaT cells by small interfering RNAs entrapped in grapefruit-derived extracellular vesicles using a microfluidic device. Sci Rep 2023; 13:3102. [PMID: 36813850 PMCID: PMC9947018 DOI: 10.1038/s41598-023-30180-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Small interfering RNAs (siRNAs) knockdown the expression of target genes by causing mRNA degradation and are a promising therapeutic modality. In clinical practice, lipid nanoparticles (LNPs) are used to deliver RNAs, such as siRNA and mRNA, into cells. However, these artificial nanoparticles are toxic and immunogenic. Thus, we focused on extracellular vesicles (EVs), natural drug delivery systems, for the delivery of nucleic acids. EVs deliver RNAs and proteins to specific tissues to regulate various physiological phenomena in vivo. Here, we propose a novel method for the preparation siRNAs encapsulated in EVs using a microfluidic device (MD). MDs can be used to generate nanoparticles, such as LNPs, by controlling flow rate to the device, but the loading of siRNAs into EVs using MDs has not been reported previously. In this study, we demonstrated a method for loading siRNAs into grapefruit-derived EVs (GEVs), which have gained attention in recent years for being plant-derived EVs developed using an MD. GEVs were collected from grapefruit juice using the one-step sucrose cushion method, and then GEVs-siRNA-GEVs were prepared using an MD device. The morphology of GEVs and siRNA-GEVs was observed using a cryogenic transmission electron microscope. Cellular uptake and intracellular trafficking of GEVs or siRNA-GEVs to human keratinocytes were evaluated by microscopy using HaCaT cells. The prepared siRNA-GEVs encapsulated 11% of siRNAs. Moreover, intracellular delivery of siRNA and gene suppression effects in HaCaT cells were achieved using these siRNA-GEVs. Our findings suggested that MDs can be used to prepare siRNA-EV formulations.
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Niu M, Chen Y, Chen F, Zhao C, Yang Y, Xu Y, Feng J. Light-Driven Ion Transport through Single-Heterojunction Nanopores. NANO LETTERS 2023; 23:1010-1016. [PMID: 36693172 DOI: 10.1021/acs.nanolett.2c04507] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Inspired by natural photosynthesis, light has become an emerging ionic behavior regulator and ion-pumping source. Nanoprocessing technology has allowed the bridge between the light-regulated nanofluids and the optoelectronic properties of two-dimensional (2D) materials, which inspires applications like energy harvesting and enhances fundamental understandings in nanofluidics. However, unlike light-induced ion pumping based on densely layered membranes with multiple nanochannels, experimental implementation on atomically thin materials featuring only a single nanochannel remains challenging. Here, we report light-induced ion pumping based on a single artificial heterojunction nanopore. Under light illumination, the induced current through a single nanopore reaches tens of picoamperes. The hole-electron separation originating from the optoelectrical property of a van der Waals PN junction is proposed to capture the light-driven ion transport. Further, different methods are adopted to modify the ion behavior and response time, presenting potential applications in fluidic photoenergy harvesting, photoelectric ion transport control, and bionic artificial neurons.
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Faucher S, Kuehne M, Oliaei H, Misra RP, Li SX, Aluru NR, Strano MS. Observation and Isochoric Thermodynamic Analysis of Partially Water-Filled 1.32 and 1.45 nm Diameter Carbon Nanotubes. NANO LETTERS 2023; 23:389-397. [PMID: 36602909 DOI: 10.1021/acs.nanolett.2c00911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent measurements of fluids under extreme confinement, including water within narrow carbon nanotubes, exhibit marked deviations from continuum theoretical descriptions. In this work, we generate precise carbon nanotube replicates that are filled with water, closed from external mass transfer, and studied over a wide temperature range by Raman spectroscopy. We study segments that are empty, partially filled, and completely filled with condensed water from -80 to 120 °C. Partially filled, nanodroplet states contain submicron vapor-like and liquid-like domains and are analyzed using a Clausius-Clapeyron-type model, yielding heats of condensation of water inside closed 1.32 nm diameter carbon nanotubes (3.32 ± 0.10 kJ/mol and 3.72 ± 0.11 kJ/mol) and 1.45 nm diameter carbon nanotubes (3.50 ± 0.07 kJ/mol) that are lower than the bulk enthalpy of vaporization and closer to the bulk enthalpy of fusion. Favored partial filling fractions are calculated, highlighting the effect of subnanometer changes in confining diameter on fluid properties and suggesting the promise of molecular engineering of nanoconfined liquid/vapor interfaces for water treatment or membrane distillation.
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Tsutsui M, Yokota K, He Y, Kawai T. Ionic Signal Amplification of DNA in a Nanopore. SMALL METHODS 2022; 6:e2200761. [PMID: 36196624 DOI: 10.1002/smtd.202200761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Indexed: 06/16/2023]
Abstract
Ionic signal amplification is a key challenge for single-molecule analyses by solid-state nanopore sensing. Here, a permittivity gradient approach for amplifying ionic blockade characteristics of DNA in a nanofluidic channel is reported. The transmembrane ionic current response is found to change substantially through modifying the liquid permittivity at one side of a pore with an organic solvent. Imposing positive liquid permittivity gradients with respect to the direction of DNA electrophoresis, this study observes the resistive ionic signals to become larger due to the varying contributions of molecular counterions. On the contrary, negative gradients render adverse effects causing conductive ionic current pulses upon polynucleotide translocations. Most importantly, both the positive and negative gradients are demonstrated to be capable of amplifying the ionic signals by an order of magnitude with a 1.3-fold difference in the transmembrane liquid dielectric constants. This phenomenon allows a novel way to enhance the single-molecule sensitivity of nanopore sensing that may be useful in analyzing secondary structures and genome sequence of DNA by ionic current measurements.
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Macha M, Marion S, Tripathi M, Thakur M, Lihter M, Kis A, Smolyanitsky A, Radenovic A. High-Throughput Nanopore Fabrication and Classification Using Xe-Ion Irradiation and Automated Pore-Edge Analysis. ACS NANO 2022; 16:16249-16259. [PMID: 36153997 DOI: 10.1021/acsnano.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding membrane-wide permeation properties. In this work, we investigate Xe-ion focused ion beam as a tool for scalable, large-area nanopore fabrication on atomically thin, free-standing molybdenum disulfide. The presented irradiation protocol enables designing ultrathin membranes with tunable porosity and pore dimensions, along with spatial uniformity across large-area substrates. Fabricated nanoporous membranes are then characterized using scanning transmission electron microscopy imaging, and the observed nanopore geometries are analyzed through a pore-edge detection and analysis script. We further demonstrate that the obtained structural and statistical data can be readily passed on to computational and analytical tools to predict the permeation properties at both individual pore and membrane-wide scales. As an example, membranes featuring angstrom-scale pores are investigated in terms of their emerging water and ion flow properties through extensive all-atom molecular dynamics simulations. We believe that the combination of experimental and analytical approaches presented here will yield accurate physics-based property estimates and thus potentially enable a true function-by-design approach to fabrication for applications such as osmotic power generation and desalination/filtration.
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Levin S, Lerch S, Boje A, Fritzsche J, KK S, Ström H, Moth-Poulsen K, Sundén H, Hellman A, Westerlund F, Langhammer C. Nanofluidic Trapping of Faceted Colloidal Nanocrystals for Parallel Single-Particle Catalysis. ACS NANO 2022; 16:15206-15214. [PMID: 36054658 PMCID: PMC9527799 DOI: 10.1021/acsnano.2c06505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Catalyst activity can depend distinctly on nanoparticle size and shape. Therefore, understanding the structure sensitivity of catalytic reactions is of fundamental and technical importance. Experiments with single-particle resolution, where ensemble-averaging is eliminated, are required to study it. Here, we implement the selective trapping of individual spherical, cubic, and octahedral colloidal Au nanocrystals in 100 parallel nanofluidic channels to determine their activity for fluorescein reduction by sodium borohydride using fluorescence microscopy. As the main result, we identify distinct structure sensitivity of the rate-limiting borohydride oxidation step originating from different edge site abundance on the three particle types, as confirmed by first-principles calculations. This advertises nanofluidic reactors for the study of structure-function correlations in catalysis and identifies nanoparticle shape as a key factor in borohydride-mediated catalytic reactions.
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Xue P, Qu M, Shi J, Jiang Y, He N, Zhao T, Luo S, Zhou S, Zhang JJ, Luo Y, Chu G, Li H, Chen JF, Sun SG, Liao HG. In Situ TEM Observation of Stagnant Liquid Layer Activation in Nanochannel. NANO LETTERS 2022; 22:6958-6963. [PMID: 36037446 DOI: 10.1021/acs.nanolett.2c01762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The kinetics of mass transfer in a stagnant fluid layer next to an interface govern numerous dynamic reactions in diffusional micro/nanopores, such as catalysis, fuel cells, and chemical separation. However, the effect of the interplay between stagnant liquid and flowing fluid on the micro/nanoscopic mass transfer dynamics remains poorly understood. Here, by using liquid cell transmission electron microscopy (TEM), we directly tracked microfluid unit migration at the nanoscale. By tracking the trajectories, an unexpected mass transfer phenomenon in which fluid units in the stagnant liquid layer migrated two orders faster during gas-liquid interface updating was identified. Molecular dynamics (MD) simulations indicated that the chemical potential difference between nanoscale liquid layers led to convective flow, which greatly enhanced mass transfer on the surface. Our study opens up a pathway toward research on mass transfer in the surface liquid layers at high spatial and temporal resolutions.
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Zhang X, Wu F, Lv X, Xu L, Huang R, Chen R, Li L. Achieving Sustainable and Stable Potassium-Ion Batteries by Leaf-Bioinspired Nanofluidic Flow. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204370. [PMID: 35973233 DOI: 10.1002/adma.202204370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/02/2022] [Indexed: 06/15/2023]
Abstract
In nature, living systems have evolved integrated structures, matching optimized nanofluidics to adapt to external conditions. In rechargeable batteries, high-capacity electrodes are often plagued by the crucial and universal bottleneck of dissolution and shuttle of active substance into electrolyte, posing obstacles of inevitable capacity degradation. Introducing the concept of intelligent nanofluidics to electrodes, a leaf-bioinspired electrode configuration with hierarchical architecture to tackle this problem is proposed. This integrated structure with fine-tuned surface pores and unobstructed interior porous media, can spatially control the anisotropic nanofluidic flux, in an efficient and self-protectable way: tailoring the outflow across the electrode's surface and free transport in interior, to ensure speedy and stable energy conversion. As proofs of concept, applications of sustainable electrodes rejuvenated from fallen leaf and spent commercial batteries, are designed with leaf-bioinspired architecture. Both KCoS2 and KS battery systems show advanced steady cycling with effectively mitigated shuttle issues in this smart architecture (0.15% and 0.21% capacity decay per cycle), even at high areal mass loading, when compared with open porous structure (0.60% and 0.39%). This work may pave a new way from a biomimetic view to integrated electrode engineering with regulated surface shielding to conquer the universal dissolution-shuttle problems facing high-capacity materials.
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Zhang G, Lin L, Shen W, Wang X, Wang Y, Cao L, Liu F. A New Strategy for Highly Efficient Separation between Monovalent Cations by Applying Opposite-Oriented Pressure and Electric Fields. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203396. [PMID: 35906891 DOI: 10.1002/smll.202203396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Biological ion channels exhibit excellent ion selectivity, but it has been challenging to design their artificial counterparts, especially for highly efficient separation of similar ions. Here, a new strategy to achieve high selectivity between alkali metal ions with artificial nanostructures is reported. Molecular dynamics (MD) simulations and experiments are combined to study the transportation of monovalent cations through graphene oxide (GO) nanoslits by applying pressure or/and electric fields. It is found that the ionic transport selectivity under the pressure driving reverses compared with that under the electric field driving. Moreover, MD simulations show that different monovalent cations can be separated with unprecedentedly high selectivity by applying opposite-oriented pressure and electric fields. This highly efficient separation originates from two distinctive ionic transporting modes, that is, hydration shells drive ions under pressure, but drag ions under the electric field. Hence, ions with different hydration strengths can be efficiently separated by tuning the net mobility induced by the two types of driving forces when the selected ions are kept moving while the other ones are immobilized. And nanoconfinement is confirmed to enhance the separation efficacy. This discovery paves a new avenue for separating similar ions without elaborately designing biomimetic nanostructures.
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Thiemann F, Schran C, Rowe P, Müller EA, Michaelides A. Water Flow in Single-Wall Nanotubes: Oxygen Makes It Slip, Hydrogen Makes It Stick. ACS NANO 2022; 16:10775-10782. [PMID: 35726839 PMCID: PMC9331139 DOI: 10.1021/acsnano.2c02784] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Experimental measurements have reported ultrafast and radius-dependent water transport in carbon nanotubes which are absent in boron nitride nanotubes. Despite considerable effort, the origin of this contrasting (and fascinating) behavior is not understood. Here, with the aid of machine learning-based molecular dynamics simulations that deliver first-principles accuracy, we investigate water transport in single-wall carbon and boron nitride nanotubes. Our simulations reveal a large, radius-dependent hydrodynamic slippage on both materials, with water experiencing indeed a ≈5 times lower friction on carbon surfaces compared to boron nitride. Analysis of the diffusion mechanisms across the two materials reveals that the fast water transport on carbon is governed by facile oxygen motion, whereas the higher friction on boron nitride arises from specific hydrogen-nitrogen interactions. This work not only delivers a clear reference of quantum mechanical accuracy for water flow in single-wall nanotubes but also provides detailed mechanistic insight into its radius and material dependence for future technological application.
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Perez Sirkin YA, de Maio MV, Tagliazucchi M. Mechanisms of Enzymatic Transduction in Nanochannel Biosensors. Chem Asian J 2022; 17:e202200588. [PMID: 35831237 DOI: 10.1002/asia.202200588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/08/2022] [Indexed: 11/09/2022]
Abstract
The immobilization of enzymes in solid-state nanochannels is a new avenue for the design of biosensors with outstanding selectivity and sensitivity. This work reports the first theoretical model of an enzymatic nanochannel biosensor. The model is applied to the system previously experimentally studied by Lin, et al. (Anal. Chem. 2014, 86, 10546): a hourglass nanochannel modified by glucose oxidase for the detection of glucose. Our predictions are in good agreement with experimental observations as a function of the applied potential, pH and glucose concentration. The sensing mechanism results from the combination of three processes: i) the establishment of a steady-state proton concentration gradient due to a reaction-diffusion mechanism, ii) the effect of that gradient on the charge of the adsorbed enzymes and native surface groups, and iii) the effect of the resulting surface charge on the ionic current. Strategies to improve the sensor performance based on this mechanism are identified and discussed.
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Di Muccio G, Morozzo della Rocca B, Chinappi M. Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores. ACS NANO 2022; 16:8716-8728. [PMID: 35587777 PMCID: PMC9245180 DOI: 10.1021/acsnano.1c03017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.
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Gao Y, Yin M, Zhang H, Xu B. Electrically Suppressed Outflow of Confined Liquid in Hydrophobic Nanopores. ACS NANO 2022; 16:9420-9427. [PMID: 35658431 DOI: 10.1021/acsnano.2c02240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Confining liquid in a hydrophobic nanoenvironment has enabled a broad spectrum of applications in biomedical sensors, mechanical actuators, and energy storage and converters, where the outflow of confined liquid is spontaneous and fast due to the intrinsic hydrophobic nature of nanopores with extremely low interfacial friction, challenging design capacity and control tolerance of structures and devices. Here, we present a facile approach of suppressing the outflow of water confined in hydrophobic nanopores with an electric field. Extensive molecular dynamics simulations show that the presence of an electric field could significantly strengthen hydrogen bonds and retard degradations of the associated networks during the outflow. The outflow deformation and strength are extracted to quantitatively characterize the electrical suppression to outflow and agree well with simulations. This study proposes a practical means of impeding the fast liquid outflow in hydrophobic nanopores, potentially useful for devising nanofluidics-based functional structures and devices with controllable performance.
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Zhang M, Harms ZD, Greibe T, Starr CA, Zlotnick A, Jacobson SC. In-Plane, In-Series Nanopores with Circular Cross Sections for Resistive-Pulse Sensing. ACS NANO 2022; 16:7352-7360. [PMID: 35500295 PMCID: PMC9626396 DOI: 10.1021/acsnano.1c08680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Resistive-pulse sensing with solid-state nanopores is a sensitive, label-free technique for analyzing single molecules in solution. To add functionality to resistive-pulse measurements, direct coupling of the nanopores to other pores and nanoscale fluidic elements, e.g., reactors, separators, and filters, in the same device is an important next step. One approach is monolithic fabrication of the fluidic elements in the plane of the substrate, but methods to generate pores with circular cross sections are needed to improve sensing performance with in-plane devices. Here, we report a fabrication method that directly patterns nanopores with circular cross sections in series and in plane with the substrate. A focused ion beam instrument is used to mill a lamella in a nanochannel and, subsequently, bore a nanopore through the lamella. The diameter and geometry of the nanopore are controlled by the current and dose of the ion beam and by the tilt angle and thickness of the lamella. We fabricated devices with vertical and tilted lamellae and nanopores with diameters from 40 to 90 nm in cylindrical and conical geometries. To test device performance, we conducted resistive-pulse measurements of hepatitis B virus capsids. Current pulses from T = 3 capsids (∼31 nm diameter) and T = 4 capsids (∼35 nm diameter) were well resolved and exhibited relative pulse amplitudes (Δi/i) up to 5 times higher than data obtained on nanopores with rectangular cross sections. For smaller pore diameters (<45 nm), which approach the diameters of the capsids, a dramatic increase in the pulse amplitude was observed for both T = 3 and T = 4 capsids. Two and three pores fabricated in series further improved the resolution between the relative pulse amplitude distributions for the T = 3 and T = 4 capsids by up to 2-fold.
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Mateus JC, Weaver S, van Swaay D, Renz AF, Hengsteler J, Aguiar P, Vörös J. Nanoscale Patterning of In Vitro Neuronal Circuits. ACS NANO 2022; 16:5731-5742. [PMID: 35404570 DOI: 10.1021/acsnano.1c10750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methods for patterning neurons in vitro have gradually improved and are used to investigate questions that are difficult to address in or ex vivo. Though these techniques guide axons between groups of neurons, multiscale control of neuronal connectivity, from circuits to synapses, is yet to be achieved in vitro. As studying neuronal circuits with synaptic resolution in vivo poses significant challenges, we present an in vitro alternative to validate biophysical and computational models. In this work we use a combination of electron beam lithography and photolithography to create polydimethylsiloxane (PDMS) structures with features ranging from 150 nm to a few millimeters. Leveraging the difference between average axon and dendritic spine diameters, we restrict axon growth while allowing spines to pass through nanochannels to guide synapse formation between small groups of neurons (i.e., nodes). We show this technique can be used to generate large numbers of isolated feed-forward circuits where connections between nodes are restricted to regions connected by nanochannels. Using a genetically encoded calcium indicator in combination with fluorescently tagged postsynaptic protein, PSD-95, we demonstrate functional synapses can form in this region.
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Sharma V, Farajpour N, Lastra LS, Freedman KJ. DNA Coil Dynamics and Hydrodynamic Gating of Pressure-Biased Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106803. [PMID: 35266283 DOI: 10.1002/smll.202106803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are ideally suited for the analysis of long DNA fragments including chromosomal DNA and synthetic DNA with applications in genome sequencing and DNA data storage, respectively. Hydrodynamic fluid flow has been shown to slow down DNA transit time within the pore, however other influences of hydrodynamic forces have yet to be explored. In this report, a broad analysis of pressure-biased nanopores and the impact of hydrodynamics on DNA transit time, capture rate, current blockade depth, and DNA folding are conducted. Using a 10 nm pore, it is shown that hydrodynamic flow inhibits the early stages of linearization of DNA and produces predominately folded events which are initiated by folded DNA (2-strands) entering the pore. Furthermore, utilizing larger pores (30 nm) leads to unique DNA gating behavior in which DNA events can be switched on and off with the application of pressure. A computational model, based on combining electrophoretic drift velocities with fluid velocities, accurately predicts the pore size required to observe DNA gating. Hydrodynamic fluid flow generated by a pressure bias, or potentially more generally by other mechanisms like electroosmotic flow, is shown to have significant effects on DNA sensing and can be useful for DNA sensing technologies.
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Montes de Oca JM, Dhanasekaran J, Córdoba A, Darling SB, de Pablo JJ. Ionic Transport in Electrostatic Janus Membranes. An Explicit Solvent Molecular Dynamic Simulation. ACS NANO 2022; 16:3768-3775. [PMID: 35230815 PMCID: PMC8945361 DOI: 10.1021/acsnano.1c07706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Janus, or two-sided, charged membranes offer promise as ionic current rectifiers. In such systems, pores consisting of two regions of opposite charge can be used to generate a current from a gradient in salinity. The efficiency of nanoscale Janus pores increases dramatically as their diameter becomes smaller. However, little is known about the underlying transport processes, particularly under experimentally accessible conditions. In this work, we examine the molecular basis for rectification in Janus nanopores using an applied electric field. Molecular simulations with explicit water and ions are used to examine the structure and dynamics of all molecular species in aqueous electrolyte solutions. For several macroscopic observables, the results of such simulations are consistent with experimental observations on asymmetric membranes. Our analysis reveals a number of previously unknown features, including a pronounced local reorientation of water molecules in the pores, and a segregation of ionic species that had not been anticipated by previously reported continuum analyses of Janus pores. Using these insights, a model is proposed for ionic current rectification in which electric leakage at the pore entrance controls net transport.
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Katsikis G, Hwang IE, Wang W, Bhat VS, McIntosh NL, Karim OA, Blus BJ, Sha S, Agache V, Wolfrum JM, Springs SL, Sinskey AJ, Barone PW, Braatz RD, Manalis SR. Weighing the DNA Content of Adeno-Associated Virus Vectors with Zeptogram Precision Using Nanomechanical Resonators. NANO LETTERS 2022; 22:1511-1517. [PMID: 35148107 DOI: 10.1021/acs.nanolett.1c04092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying the composition of viral vectors used in vaccine development and gene therapy is critical for assessing their functionality. Adeno-associated virus (AAV) vectors, which are the most widely used viral vectors for in vivo gene therapy, are typically characterized using PCR, ELISA, and analytical ultracentrifugation which require laborious protocols or hours of turnaround time. Emerging methods such as charge-detection mass spectroscopy, static light scattering, and mass photometry offer turnaround times of minutes for measuring AAV mass using optical or charge properties of AAV. Here, we demonstrate an orthogonal method where suspended nanomechanical resonators (SNR) are used to directly measure both AAV mass and aggregation from a few microliters of sample within minutes. We achieve a precision near 10 zeptograms which corresponds to 1% of the genome holding capacity of the AAV capsid. Our results show the potential of our method for providing real-time quality control of viral vectors during biomanufacturing.
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Zhou J, Zlotnick A, Jacobson SC. Disassembly of Single Virus Capsids Monitored in Real Time with Multicycle Resistive-Pulse Sensing. Anal Chem 2022; 94:985-992. [PMID: 34932317 PMCID: PMC8784147 DOI: 10.1021/acs.analchem.1c03855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Virus assembly and disassembly are critical steps in the virus lifecycle; however, virus disassembly is much less well understood than assembly. For hepatitis B virus (HBV) capsids, disassembly of the virus capsid in the presence of guanidine hydrochloride (GuHCl) exhibits strong hysteresis that requires additional chemical energy to initiate disassembly and disrupt the capsid structure. To study disassembly of HBV capsids, we mixed T = 4 HBV capsids with 1.0-3.0 M GuHCl, monitored the reaction over time by randomly selecting particles, and measured their size with resistive-pulse sensing. Particles were cycled forward and backward multiple times to increase the observation time and likelihood of observing a disassembly event. The four-pore device used for resistive-pulse sensing produces four current pulses for each particle during translocation that improves tracking and identification of single particles and increases the precision of particle-size measurements when pulses are averaged. We studied disassembly at GuHCl concentrations below and above denaturing conditions of the dimer, the fundamental unit of HBV capsid assembly. As expected, capsids showed little disassembly at low GuHCl concentrations (e.g., 1.0 M GuHCl), whereas at higher GuHCl concentrations (≥1.5 M), capsids exhibited disassembly, sometimes as a complex series of events. In all cases, disassembly was an accelerating process, where capsids catastrophically disassembled within a few 100 ms of reaching critical stability; disassembly rates reached tens of dimers per second just before capsids fell apart. Some disassembly events exhibited metastable intermediates that appeared to lose one or more trimers of dimers in a stepwise fashion.
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Noh Y, Aluru NR. Phonon-Fluid Coupling Enhanced Water Desalination in Flexible Two-Dimensional Porous Membranes. NANO LETTERS 2022; 22:419-425. [PMID: 34935387 DOI: 10.1021/acs.nanolett.1c04155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Water purification using 2D nanoporous membranes has been drawing significant attention for over a decade because of fast water transport in ultrathin membranes. We perform a comprehensive study using molecular dynamics (MD) simulations on water desalination using 2D flexible membranes where the coupling between the fluid dynamics and mechanics of the membrane plays an important role. We observe that a considerable deformation and fluctuation in the 2D membrane results in an enhanced water permeability (up to 122%) along with a slight decrease in the salt rejection rate (less than 11%). Simulations on harmonically vibrating membranes indicate that the vibrational match at the membrane-water interface can significantly increase the permeance. We conduct mechanical stability tests and discuss the maximum endurable pressure of 2D porous membranes for water desalination. These findings will contribute to advances in applications using ultrathin membranes, such as energy harvesting and molecular separation.
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Zheng S, Tang J, Lv D, Wang M, Yang X, Hou C, Yi B, Lu G, Hao R, Wang M, Wang Y, He H, Yao X. Continuous Energy Harvesting from Ubiquitous Humidity Gradients using Liquid-Infused Nanofluidics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2106410. [PMID: 34715720 DOI: 10.1002/adma.202106410] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Indexed: 05/24/2023]
Abstract
Humidity-based power generation that converts internal energy of water molecules into electricity is an emerging approach for harvesting clean energy from nature. Here it is proposed that intrinsic gradient within a humidity field near sweating surfaces, such as rivers, soil, or animal skin, is a promising power resource when integrated with liquid-infused nanofluidics. Specifically, capillary-stabilized ionic liquid (IL, Omim+ Cl- ) film is exposed to the above humidity field to create a sustained transmembrane water-content difference, which enables asymmetric ion-diffusion across the nanoconfined fluidics, facilitating long-term electricity generation with the power density of ≈12.11 µW cm-2 . This high record is attributed to the nanoconfined IL that integrates van der Waals and electrostatic interactions to block movement of Omim+ clusters while allowing for directional diffusion of moisture-liberated Cl+ . This humidity gradient triggers large ion-diffusion flux for power generation indicates great potential of sweating surfaces considering that most of the earth is covered by water or soil.
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Pattanaik MS, Varma VB, Cheekati SK, Chaudhary V, Ramanujan RV. Optimal ferrofluids for magnetic cooling devices. Sci Rep 2021; 11:24167. [PMID: 34921195 PMCID: PMC8683428 DOI: 10.1038/s41598-021-03514-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
Superior passive cooling technologies are urgently required to tackle device overheating, consequent performance degradation, and service life reduction. Magnetic cooling, governed by the thermomagnetic convection of a ferrofluid, is a promising emerging passive heat transfer technology to meet these challenges. Hence, we studied the performance metrics, non-dimensional parameters, and thermomagnetic cooling performance of various ferrite and metal-based ferrofluids. The magnetic pressure, friction factor, power transfer, and exergy loss were determined to predict the performance of such cooling devices. We also investigated the significance of the magnetic properties of the nanoparticles used in the ferrofluid on cooling performance. γ-Fe2O3, Fe3O4, and CoFe2O4 nanoparticles exhibited superior cooling performance among ferrite-based ferrofluids. FeCo nanoparticles had the best cooling performance for the case of metallic ferrofluids. The saturation magnetization of the magnetic nanoparticles is found to be a significant parameter to enhance heat transfer and heat load cooling. These results can be used to select the optimum magnetic nanoparticle-based ferrofluid for a specific magnetic cooling device application.
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Wang R, Chai J, Luo B, Liu X, Zhang J, Wu M, Wei M, Ma Z. A review on slip boundary conditions at the nanoscale: recent development and applications. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2021; 12:1237-1251. [PMID: 34868800 PMCID: PMC8609245 DOI: 10.3762/bjnano.12.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The slip boundary condition for nanoflows is a key component of nanohydrodynamics theory, and can play a significant role in the design and fabrication of nanofluidic devices. In this review, focused on the slip boundary conditions for nanoconfined liquid flows, we firstly summarize some basic concepts about slip length including its definition and categories. Then, the effects of different interfacial properties on slip length are analyzed. On strong hydrophilic surfaces, a negative slip length exists and varies with the external driving force. In addition, depending on whether there is a true slip length, the amplitude of surface roughness has different influences on the effective slip length. The composition of surface textures, including isotropic and anisotropic textures, can also affect the effective slip length. Finally, potential applications of nanofluidics with a tunable slip length are discussed and future directions related to slip boundary conditions for nanoscale flow systems are addressed.
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Nagai R, Sugimachi A, Tanimoto Y, Suzuki KGN, Hayashi F, Weikert D, Gmeiner P, Kasai RS, Morigaki K. Functional Reconstitution of Dopamine D2 Receptor into a Supported Model Membrane in a Nanometric Confinement. Adv Biol (Weinh) 2021; 5:e2100636. [PMID: 34761565 DOI: 10.1002/adbi.202100636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 10/22/2021] [Indexed: 11/07/2022]
Abstract
Dopamine D2 receptor (D2R), a G-protein-coupled receptor (GPCR), plays critical roles in neural functions and represents the target for a wide variety of drugs used to treat neurological diseases. However, its fundamental physicochemical properties, such as dimerization and affinity to different lipid environments, remain unknown. Here, reconstitution and characterization of D2R in a supported model membrane in nanometric confinement are reported. D2R is expressed in Chinese hamster ovary (CHO) cells and transferred into the supported model membrane as cell membrane blebs. D2R molecules are reconstituted with an elevated density in the cleft between the substrate and poly(dimethylsiloxane) (PDMS) elastomer. Reconstituted D2R retains the physiological functions, as evaluated from its binding to an antagonist and dimerization lifetime. The transient dimer formation of D2R, similar to the live cell, suggests that it is an innate property that does not depend on the cellular structures such as actin filaments. Although the mechanism of this unique reconstitution process is currently not fully understood, the finding points to a new possibility of using a nanometric space (<100 nm thick) as a platform for reconstituting and studying membrane proteins under the quasi-physiological conditions, which are difficult to be created by other methods.
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Morikawa K, Kazumi H, Tsuyama Y, Ohta R, Kitamori T. Surface Patterning of Closed Nanochannel Using VUV Light and Surface Evaluation by Streaming Current. MICROMACHINES 2021; 12:mi12111367. [PMID: 34832779 PMCID: PMC8623798 DOI: 10.3390/mi12111367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022]
Abstract
In nanofluidics, surface control is a critical technology because nanospaces are surface-governed spaces as a consequence of their extremely high surface-to-volume ratio. Various surface patterning methods have been developed, including patterning on an open substrate and patterning using a liquid modifier in microchannels. However, the surface patterning of a closed nanochannel is difficult. In addition, the surface evaluation of closed nanochannels is difficult because of a lack of appropriate experimental tools. In this study, we verified the surface patterning of a closed nanochannel by vacuum ultraviolet (VUV) light and evaluated the surface using streaming-current measurements. First, the C18 modification of closed nanochannels was confirmed by Laplace pressure measurements. In addition, no streaming-current signal was detected for the C18-modified surface, confirming the successful modification of the nanochannel surface with C18 groups. The C18 groups were subsequently decomposed by VUV light, and the nanochannel surface became hydrophilic because of the presence of silanol groups. In streaming-current measurements, the current signals increased in amplitude with increasing VUV light irradiation time, indicating the decomposition of the C18 groups on the closed nanochannel surfaces. Finally, hydrophilic/hydrophobic patterning by VUV light was performed in a nanochannel. Capillary filling experiments confirmed the presence of a hydrophilic/hydrophobic interface. Therefore, VUV patterning in a closed nanochannel was demonstrated, and the surface of a closed nanochannel was successfully evaluated using streaming-current measurements.
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