Temperature sculpting in yoctoliter volumes

Photothermally Heated Asymmetric Thin Nanopores Suggest the Influence of Temperature on the Intermediate Conformational State of Cytochrome c in an Electric Field

Nanopore sensing is a label-free single-molecule technique that enables the study of the dynamical structural properties of proteins. Here, we detect the translocation of cytochrome c (Cyt c) through an asymmetric thin nanopore with photothermal heating to evaluate the influence of temperature on Cyt c conformation during its translocation in an electric field. Before Cyt c translocates through an asymmetric thin SiNx nanopore, ∼1 ms trapping events occur due to electric field-induced denaturation. These trapping events were corroborated by a control analysis with a transmission electron microscopy-drilled pore and denaturant buffer. Cyt c translocation events exhibited markedly greater broad current blockade when the pores were photothermally heated. Collectively, our molecular dynamics simulation predicted that an increased temperature facilitates denaturation of the α-helical structure of Cyt c, resulting in greater blockade current during Cyt c trapping. Our photothermal heating method can be used to study the influence of temperature on protein conformation at the single-molecule level in a label-free manner.

Engineering Biological Nanopore Approaches toward Protein Sequencing

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

Controlling local thermal gradients at molecular scales with Janus nanoheaters

The generation and control of heat transport with nanoparticles is an essential objective of thermoplasmonics. Janus nanoparticles consisting of dissimilar materials with contrasting interfacial Kapitza conductance provide a route to control heat transport at the nanoscale. Here we use the recently introduced Atomistic Nodal Approach to map the surface temperature and Kapitza conductance of Janus nanoparticles to individual atoms. We show that the transition in the thermal transport properties between the hydrophobic and hydrophilic interfaces is exceptionally abrupt, occurring over length scales below 1 nm. We demonstrate the generality of this result using coarse-grained and all-atom models of gold nanoparticles. Further, we show how this behaviour provides a route to sustain significant temperature differences, on the order of tens of degrees for μW heat rates, between adjacent molecular layers attached to heated gold nanoparticles. Our work provides fundamental insight into nanoscale heat transport and a principle to design heterogeneous Janus nanoparticles for thermal transport applications.

Localized Nanopore Fabrication via Controlled Breakdown

Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.

Spatial Control of Heat Flow at the Nanoscale Using Janus Particles

Janus nanoparticles (JNPs) feature heterogeneous compositions, bringing opportunities in technological and medical applications. We introduce a theoretical approach based on nonequilibrium molecular dynamics simulations and heat transfer continuum theory to investigate the temperature fields generated around heated spherical JNPs covering a wide range of particle sizes, from a few nm to 100 nm. We assess the performance of these nanoparticles to generate anisotropic heating at the nanoscale. We demonstrate that the contrasting interfacial thermal conductances of the fluid-material interfaces arising from the heterogeneous composition of the JNPs can be exploited to control the thermal fields around the nanoparticle, leading to a temperature difference between both sides of the nanoparticle (temperature contrast) that is significant for particles comprising regions with disparate hydrophilicity. We illustrate this idea using coarse-grained and atomistic models of gold nanoparticles with hydrophobic and hydrophilic coatings, in water. Furthermore, we introduce a continuum model to predict the temperature contrast as a function of the interfacial thermal conductance and nanoparticle size. We further show that, unlike homogeneous nanoparticles, the interfacial fluid temperature depends on the interfacial thermal conductance of Janus nanoparticles.

Solution Structures of Bacillus anthracis Protective Antigen Proteins Using Small Angle Neutron Scattering and Protective Antigen 63 Ion Channel Formation Kinetics

We are studying the structures of bacterial toxins that form ion channels and enable macromolecule transport across membranes. For example, the crystal structure of the Staphylococcus aureus α-hemolysin (α-HL) channel in its functional state was confirmed using neutron reflectometry (NR) with the protein reconstituted in membranes tethered to a solid support. This method, which provides sub-nanometer structural information, could also test putative structures of the Bacillus anthracis protective antigen 63 (PA63) channel, locate where B. anthracis lethal factor and edema factor toxins (LF and EF, respectively) bind to it, and determine how certain small molecules can inhibit the interaction of LF and EF with the channel. We report here the solution structures of channel-forming PA63 and its precursor PA83 (which does not form channels) obtained with small angle neutron scattering. At near neutral pH, PA83 is a monomer and PA63 a heptamer. The latter is compared to two cryo-electron microscopy structures. We also show that although the α-HL and PA63 channels have similar structural features, unlike α-HL, PA63 channel formation in lipid bilayer membranes ceases within minutes of protein addition, which currently precludes the use of NR for elucidating the interactions between PA63, LF, EF, and potential therapeutic agents.

Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues

Protein sequencing is essential to unveil the mechanism of cellular processes that govern the function of living organisms, and which play a crucial role in the field of drug design and molecular diagnostics. Nanopores have been proved to be effective tools in single molecule sensing, but the fast translocation speed of a peptide through a nanopore is one of the major obstacles that hinders the development of nanopore-based protein sequencing. In this work, by using molecular dynamics simulations (MDS) it is found that the peptide containing more hydrophobic residues permeates slower through a molybdenum disulfide nanopore, which originates from the strong interaction between the membrane surface and the hydrophobic residues. The binding affinity is remarkable especially for benzenoid residues as they contain a hydrophobic aromatic ring that is composed of relatively non-polar C-C and C-H bonds. By tuning the fraction of benzenoid residues of the peptide, the velocity of the protein translocation through the nanopore is well controlled. The peptide with all the hydrophobic residues being benzenoid residues is found to translocate through the nanopore almost ten times slower than the one without any benzenoid residues, which is beneficial for gathering adequate information for precise amino acid identification.

Nanopore sensing: A physical-chemical approach

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.

Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions

Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.

Retarded Translocation of Nucleic Acids through α-Hemolysin Nanopore in the Presence of a Calcium Flux

Electrophysiological measurement of molecular translocation through a nanopore is the fundamental basis of nanopore sensing. Free translocation of nucleic acids however is normally so fast that the identities of the compounds are not clearly resolvable. Inspired by recent progress in fluorescence imaging based nanopore sensing, we found that during electrophysiology measurements, translocation of nucleic acids is also retarded whenever a calcium flux around the pore vicinity is established. The residence time of nucleic acids has been extended to tens of milliseconds, a result of the strong coupling between nucleic acids and free calcium ions. The methodology presented here is applicable to both DNAs and RNAs and is able to clearly discriminate between different RNA homopolymers. This offers new insights for calcium imaging based nanopore sensing and suggests a new strategy of electrophysiology-based nanopore sensing aimed at a retarded motion of nucleic acids.

Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications

Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.

Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.

Optically-Monitored Nanopore Fabrication Using a Focused Laser Beam

Solid-state nanopores (ssNPs) are extremely versatile single-molecule sensors and their potential have been established in numerous biomedical applications. However, the fabrication of ssNPs remains the main bottleneck to their widespread use. Herein, we introduce a rapid and localizable ssNPs fabrication method based on feedback-controlled optical etching. We show that a focused blue laser beam irreversibly etches silicon nitride (SiN_x) membranes in solution. Furthermore, photoluminescence (PL) emitted from the SiN_x is used to monitor the etching process in real-time, hence permitting rate adjustment. Transmission electron microscopy (TEM) images of the etched area reveal an inverted Gaussian thickness profile, corresponding to the intensity point spread function of the laser beam. Continued laser exposure leads to the opening of a nanopore, which can be controlled to reproducibly fabricate nanopores of different sizes. The optically-formed ssNPs exhibit electrical noise on par with TEM-drilled pores, and translocate DNA and proteins readily. Notably, due to the localized thinning, the laser-drilled ssNPs exhibit highly suppressed background PL and improved spatial resolution. Given the total control over the nanopore position, this easily implemented method is ideally suited for electro-optical sensing and opens up the possibility of fabricating large nanopore arrays in situ.

Thermal transport across nanoparticle-fluid interfaces: the interplay of interfacial curvature and nanoparticle-fluid interactions

We investigate the general dependence of the thermal transport across nanoparticle-fluid interfaces using molecular dynamics computations. We show that the thermal conductance depends strongly both on the wetting characteristics of the nanoparticle-fluid interface and on the nanoparticle size. Strong nanoparticle-fluid interactions, leading to full wetting states in the host fluid, result in high thermal conductances and efficient interfacial transport of heat. Weak interactions result in partial drying or full drying states, and low thermal conductances. The variation of the thermal conductance with particle size is found to depend on the fluid-nanoparticle interactions. Strong interactions coupled with large interfacial curvatures lead to optimum interfacial heat transport. This complex dependence can be modelled using an equation that includes the interfacial curvature as a parameter. In this way, we rationalise the existing experimental and computer simulation results and show that the thermal transport across nanoscale interfaces is determined by the correlations of both interfacial curvature and nanoparticle-fluid interactions.

Instrumentation for low noise nanopore-based ionic current recording under laser illumination

We describe a nanopore-based optofluidic instrument capable of performing low-noise ionic current recordings of individual biomolecules under laser illumination. In such systems, simultaneous optical measurements generally introduce significant parasitic noise in the electrical signal, which can severely reduce the instrument sensitivity, critically hindering the monitoring of single-molecule events in the ionic current traces. Here, we present design rules and describe simple adjustments to the experimental setup to mitigate the different noise sources encountered when integrating optical components to an electrical nanopore system. In particular, we address the contributions to the electrical noise spectra from illuminating the nanopore during ionic current recording and mitigate those effects through control of the illumination source and the use of a PDMS layer on the SiN_x membrane. We demonstrate the effectiveness of our noise minimization strategies by showing the detection of DNA translocation events during membrane illumination with a signal-to-noise ratio of ∼10 at 10 kHz bandwidth. The instrumental guidelines for noise minimization that we report are applicable to a wide range of nanopore-based optofluidic systems and offer the possibility of enhancing the quality of synchronous optical and electrical signals obtained during single-molecule nanopore-based analysis.

Label-Free Single-Molecule Thermoscopy Using a Laser-Heated Nanopore

When light is used to excite electronic transitions in a material, nonradiative energy during relaxation is often released in the form of heat. In this work, we show that photoexcitation of a silicon nitride nanopore using a focused visible laser results in efficient localized photothermal heating, which reduces the nearby electrolyte viscosity and increases the ionic conductance. In addition, a strong localized thermal gradient in the pore vicinity is produced, evidenced by finite-element simulations and experimental observation of both ion and DNA thermophoresis. After correcting for thermophoresis, the nanopore current can be used as a nanoscale thermometer, enabling rapid force thermoscopy. We utilize this to probe thermal melting transitions in synthetic and native biomolecules that are heated at the nanopore. Our results on single molecules are validated by correspondence to bulk measurements, which paves the way to various biophysical experiments that require rapid temperature and force control on individual molecules.

Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis

Nanopore techniques offer the possibility to study biomolecules at the single-molecule level in a low-cost, label-free and high-throughput manner. By analyzing the level, duration and frequency of ionic current blockades, information regarding the structural conformation, mass, length and concentration of single molecules can be obtained in physiological conditions. Aerolysin monomers assemble into small pores that provide a confined space for effective electrochemical control of a single molecule interacting with the pore, which significantly improves the temporal resolution of this technique. In comparison with other reported protein nanopores, aerolysin maintains its functional stability in a wide range of pH conditions, which allows for the direct discrimination of oligonucleotides between 2 and 10 nt in length and the monitoring of the stepwise cleavage of oligonucleotides by exonuclease I (Exo I) in real time. This protocol describes the process of activating proaerolysin using immobilized trypsin to obtain the aerolysin monomer, the construction of a lipid membrane and the insertion of an individual aerolysin nanopore into this membrane. A step-by-step description is provided of how to perform single-oligonucleotide analyses and how to process the acquired data. The total time required for this protocol is ∼3 d.

Nanopore Sensing of Protein Folding

Single-molecule studies of protein folding hold keys to unveiling protein folding pathways and elusive intermediate folding states-attractive pharmaceutical targets. Although conventional single-molecule approaches can detect folding intermediates, they presently lack throughput and require elaborate labeling. Here, we theoretically show that measurements of ionic current through a nanopore containing a protein can report on the protein's folding state. Our all-atom molecular dynamics (MD) simulations show that the unfolding of a protein lowers the nanopore ionic current, an effect that originates from the reduction of ion mobility in proximity to a protein. Using a theoretical model, we show that the average change in ionic current produced by a folding-unfolding transition is detectable despite the orientational and conformational heterogeneity of the folded and unfolded states. By analyzing millisecond-long all-atom MD simulations of multiple protein transitions, we show that a nanopore ionic current recording can detect folding-unfolding transitions in real time and report on the structure of folding intermediates.

Thermoplasmonic Semitransparent Nanohole Electrodes

Nonradiative decay of plasmons in metallic nanostructures offers unique means for light-to-heat conversion at the nanoscale. Typical thermoplasmonic systems utilize discrete particles, while metal nanohole arrays were instead considered suitable as heat sinks to reduce heating effects. By contrast, we show for the first time that under uniform broadband illumination (e.g., the sun) ultrathin plasmonic nanohole arrays can be highly competitive plasmonic heaters and provide significantly higher temperatures than analogous nanodisk arrays. Our plasmonic nanohole arrays also heat significantly more than nonstructured metal films, while simultaneously providing superior light transmission. Besides being efficient light-driven heat sources, these thin perforated gold films can simultaneously be used as electrodes. We used this feature to develop "plasmonic thermistors" for electrical monitoring of plasmon-induced temperature changes. The nanohole arrays provided temperature changes up to 7.5 K by simulated sunlight, which is very high compared to previously reported plasmonic systems under similar conditions (solar illumination and ambient conditions). Both temperatures and heating profiles quantitatively agree with combined optical and thermal simulations. Finally, we demonstrate the use of a thermoplasmonic nanohole electrode to power the first hybrid plasmonic ionic thermoelectric device, resulting in strong solar-induced heat gradients and corresponding thermoelectric voltages.

Protein Trapping in Plasmonic Nanoslit and Nanoledge Cavities: The Behavior and Sensing

A novel plasmonic nanoledge device was presented to explore the geometry-induced trapping of nanoscale biomolecules and examine a generation of surface plasmon resonance (SPR) for plasmonic sensing. To design an optimal plasmonic device, a semianalytical model was implemented for a quantitative analysis of SPR under plane-wave illumination and a finite-difference time-domain (FDTD) simulation was used to study the optical transmission and refractive index (RI) sensitivity. In addition, total internal reflection fluorescence (TIRF) imaging was used to visualize the migration of fluorescently labeled bovine serum albumin (BSA) into the nanoslits; and fluorescence correlation spectroscopy (FCS) was further used to investigate the diffusion of BSA in the nanoslits. Transmission SPR measurements of free prostate specific antigen (f-PSA), which is similar in size to BSA, were performed to validate the trapping of the molecules via specific binding reactions in the nanoledge cavities. The present study may facilitate further development of single nanomolecule detection and new nanomicrofluidic arrays for effective detection of multiple biomarkers in clinical biofluids.

High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore

We explore the effect of temperature on the interaction of polydisperse mixtures of nonionic poly(ethylene glycol) (PEG) polymers of different average molar masses with the biological nanopore α-hemolysin. In contrast with what has been previously observed with various nanopores and analytes, we find that, for PEGs larger than a threshold molar mass (2000 g/mol, PEG 2000), increasing temperature increases the duration of the PEG/nanopore interaction. In the case of PEG 3400 the duration increases by up to a factor of 100 when the temperature increases from 5 °C to 45 °C. Importantly, we find that increasing temperature extends the polymer size range of application of nanopore-based single-molecule mass spectrometry (Np-SMMS)-type size discrimination. Indeed, in the case of PEG 3400, discrimination of individual molecular species of different monomer number is impossible at room temperature but is achieved when the temperature is raised to 45 °C. We interpret our observations as the consequence of a decrease of PEG solubility and a collapse of PEG molecules with higher temperatures. In addition to expanding the range of application of Np-SMMS to larger nonionic polymers, our findings highlight the crucial role of the polymer solubility for the nanopore detection.

Electroosmotic Trap Against the Electrophoretic Force Near a Protein Nanopore Reveals Peptide Dynamics During Capture and Translocation

We report on the ability to control the dynamics of a single peptide capture and passage across a voltage-biased, α-hemolysin nanopore (α-HL), under conditions that the electroosmotic force exerted on the analyte dominates the electrophoretic transport. We demonstrate that by extending outside the nanopore, the electroosmotic force is able to capture a peptide at either the lumen or vestibule entry of the nanopore, and transiently traps it inside the nanopore, against the electrophoretic force. Statistical analysis of the resolvable dwell-times of a metastable trapped peptide, as it occupies either the β-barrel or vestibule domain of the α-HL nanopore, reveals rich kinetic details regarding the direction and rates of stochastic movement of a peptide inside the nanopore. The presented approach demonstrates the ability to shuttle and study molecules along the passage pathway inside the nanopore, allows to identify the mesoscopic trajectory of a peptide exiting the nanopore through either the vestibule or β-barrel moiety, thus providing convincing proof of a molecule translocating the pore. The kinetic analysis of a peptide fluctuating between various microstates inside the nanopore, enabled a detailed picture of the free energy description of its interaction with the α-HL nanopore. When studied at the limit of vanishingly low transmembrane potentials, this provided a thermodynamic description of peptide reversible binding to and within the α-HL nanopore, under equilibrium conditions devoid of electric and electroosmotic contributions.

Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores

The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore. Here, we report the results of all-atom molecular dynamics simulations that elucidated the effect of temperature on the key microscopic processes governing electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperatures and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA-ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of solvent velocity at the DNA surface-slip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid.

The rich phase behavior of the thermopolarization of water: from a reversal in the polarization, to enhancement near criticality conditions

Non-equilibrium molecular dynamics simulations show that the polarization of water induced by thermal gradients depends strongly on the thermodynamic conditions, with a large enhancement near the critical point.

Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating

DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels.

Raman fingerprinting of single dielectric nanoparticles in plasmonic nanopores

Plasmonic nano-apertures are commonly used for the detection of small particles such as nanoparticles and proteins by exploiting electrical and optical techniques. Plasmonic nanopores are metallic nano-apertures sitting on a thin membrane with a tiny hole. It has been shown that plasmonic nanopores with a given geometry identify internal molecules using Surface Enhanced Raman Spectroscopy (SERS). However, label-free identification of a single dielectric nanoparticle requires a highly localized field comparable to the size of the particle. Additionally, the particle's Brownian motion can jeopardize the amount of photons collected from a single particle. Here, we demonstrate that the combination of optical trapping and SERS can be used for the detection and identification of 20 nm polystyrene nanoparticles in plasmonic nanopores. This work is anticipated to contribute to the detection of small bioparticles, optical trapping and nanotribology studies.

Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA

With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.

Analytical applications for pore-forming proteins

Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.

Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH

Cytosine (C)-rich DNA can adopt i-motif folds under acidic conditions, with the human telomere i-motif providing a well-studied example. The dimensions of this i-motif are appropriate for capture in the nanocavity of the α-hemolysin (α-HL) protein pore under an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts with α-HL identified characteristic signals that were pH dependent. These features were evaluated from pH 5.0 to 7.2, a region surrounding the transition pH of the i-motif (6.1). When the i-motif without polynucleotide tails was studied at pH 5.0, the folded structure entered the nanocavity of α-HL from either the top or bottom face to yield characteristic current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine tail allowed capture of the i-motif from the unfolded terminus, and this was used to analyze the pH dependency of unfolding. At pH values below the transition point, only folded strands were observed, and when the pH was increased above the transition pH, the number of folded events decreased, while the unfolded events increased. At pH 6.8 and 7.2 4% and 2% of the strands were still folded, respectively. The lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms, respectively, at 160 mV electrophoretic force. These lifetimes are sufficiently long to affect enzymes operating on DNA. Furthermore, these transient lifetimes are readily obtained using the α-HL nanopore, a feature that is not easily achievable by other methods.

Nanoalloy Printed and Pulse-Laser Sintered Flexible Sensor Devices with Enhanced Stability and Materials Compatibility

While conformal and wearable devices have become one of the most desired formats for printable electronics, it is challenging to establish a scalable process that produces stable conductive patterns but also uses substrates compatible with widely available wearable materials. Here, we describe findings of an investigation of a nanoalloy ink printed and pulsed-laser sintered conductive patterns as flexible functional devices with enhanced stability and materials compatibility. While nanoparticle inks are desired for printable electronics, almost all existing nanoparticle inks are based on single-metal component, which, as an electronic element, is limited by its inherent stabilities of the metal such as propensity of metal oxidation and mobility of metal ions, especially in sintering processes. The work here has demonstrated the first example in exploiting plasmonic coupling of nanoalloys and pulsed-laser energy with controllable thermal penetration. The experimental and theoretical results have revealed clear correlation between the pulsed laser parameters and the nanoalloy structural characteristics. The superior performance of the resulting flexible sensor device, upon imparting nanostructured sensing materials, for detecting volatile organic compounds has significant implications to developing stable and wearable sensors for monitoring environmental pollutants and breath biomarkers. This simple "nanoalloy printing-laser sintering-nanostructure printing" process is entirely general to many different sensor devices and nanostructured sensing materials, enabling the ability to easily construct sophisticated sensor array.

Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores

Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter's ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge, and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus α-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements.

Sorting particles with nanoscale thermophoretic devices: how efficient is it?

We investigate particle separation driven by thermal gradients across solid state nanopores using a combined molecular dynamics simulation, non-equilibrium thermodynamics theory and a kinetic model approach. The thermophoretic device, a thermal nanopump, exploits thermal gradients to sort particles of different mass, which accumulate preferentially in hot or cold reservoirs. We show that the large amount of energy dissipated by the thermal nanopump during the transport process leads in general to very low efficiencies, 0.01-0.15%. We find that the nanopump thermal conductivity and structure plays a crucial role in determining the efficiency and a route to enhance it. Doubling the pore radius, from 0.5-1 nm radius, leads to a large increase in the mass diffusion and to a 20 fold increase in the efficiency. Addition of nanoscale defects, without modification of the nanopore structure, leads to a large reduction of the nanopump thermal conductivity and to a large enhancement of the thermodynamic efficiency. We find that nanopumps with nanoscale defects are >3 times more efficient than those without defects. Finally, we identify the microscopic variables responsible for the enhancement of thermally induced transport across nanopores and discuss strategies to tune these variable in order to regulate transport efficiency.

Synchronized optical and electronic detection of biomolecules using a low noise nanopore platform

In the past two decades there has been a tremendous amount of research into the use of nanopores as single molecule sensors, which has been inspired by the Coulter counter and molecular transport across biological pores. Recently, the desire to increase structural resolution and analytical throughput has led to the integration of additional detection methods such as fluorescence spectroscopy. For structural information to be probed electronically high bandwidth measurements are crucial due to the high translocation velocity of molecules. The most commonly used solid-state nanopore sensors consist of a silicon nitride membrane and bulk silicon substrate. Unfortunately, the photoinduced noise associated with illumination of these platforms limits their applicability to high-bandwidth, high-laser-power synchronized optical and electronic measurements. Here we present a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane, for synchronized optical and electronic detection of biomolecules. Proof of principle experiments are conducted showing that the Pyrex substrates have substantially lowers ionic current noise arising from both laser illumination and platform capacitance. Furthermore, using confocal microscopy and a partially metallic pore we demonstrate high signal-to-noise synchronized optical and electronic detection of dsDNA.

Precise attoliter temperature control of nanopore sensors using a nanoplasmonic bullseye

Targeted temperature control in nanopores is greatly important in further understanding biological molecules. Such control would extend the range of examinable molecules and facilitate advanced analysis, including the characterization of temperature-dependent molecule conformations. The work presented within details well-defined plasmonic gold bullseye and silicon nitride nanopore membranes. The bullseye nanoantennae are designed and optimized using simulations and theoretical calculations for interaction with 632.8 nm laser light. Laser heating was monitored experimentally through nanopore conductance measurements. The precise heating of nanopores is demonstrated while minimizing the accumulation of heat in the surrounding membrane material.

Voltage and blockade state optimization of cluster-enhanced nanopore spectrometry

Cluster-enhanced nanopore spectrometry improves discrimination between different sized PEG molecules. This effect is analyzed as a function of the voltage and magnitude of the cluster blockade.

DNA translocations through solid-state plasmonic nanopores

Nanopores enable label-free detection and analysis of single biomolecules. Here, we investigate DNA translocations through a novel type of plasmonic nanopore based on a gold bowtie nanoantenna with a solid-state nanopore at the plasmonic hot spot. Plasmonic excitation of the nanopore is found to influence both the sensor signal (nanopore ionic conductance blockade during DNA translocation) and the process that captures DNA into the nanopore, without affecting the duration time of the translocations. Most striking is a strong plasmon-induced enhancement of the rate of DNA translocation events in lithium chloride (LiCl, already 10-fold enhancement at a few mW of laser power). This provides a means to utilize the excellent spatiotemporal resolution of DNA interrogations with nanopores in LiCl buffers, which is known to suffer from low event rates. We propose a mechanism based on plasmon-induced local heating and thermophoresis as explanation of our observations.

Modeling thermophoretic effects in solid-state nanopores

Local modulation of temperature has emerged as a new mechanism for regulation of molecular transport through nanopores. Predicting the effect of such modulations on nanopore transport requires simulation protocols capable of reproducing non-uniform temperature gradients observed in experiment. Conventional molecular dynamics (MD) method typically employs a single thermostat for maintaining a uniform distribution of temperature in the entire simulation domain, and, therefore, can not model local temperature variations. In this article, we describe a set of simulation protocols that enable modeling of nanopore systems featuring non-uniform distributions of temperature. First, we describe a method to impose a temperature gradient in all-atom MD simulations based on a boundary-driven non-equilibrium MD protocol. Then, we use this method to study the effect of temperature gradient on the distribution of ions in bulk solution (the thermophoretic effect). We show that DNA nucleotides exhibit differential response to the same temperature gradient. Next, we describe a method to directly compute the effective force of a thermal gradient on a prototypical biomolecule-a fragment of double-stranded DNA. Following that, we demonstrate an all-atom MD protocol for modeling thermophoretic effects in solid-state nanopores. We show that local heating of a nanopore volume can be used to regulate the nanopore ionic current. Finally, we show how continuum calculations can be coupled to a coarse-grained model of DNA to study the effect of local temperature modulation on electrophoretic motion of DNA through plasmonic nanopores. The computational methods described in this article are expected to find applications in rational design of temperature-responsive nanopore systems.

Nanoplasmonically-induced defects in lipid membrane monitored by ion current: transient nanopores versus membrane rupture

We have developed a nanoplasmonic-based approach to induce nanometer-sized local defects in the phospholipid membranes. Here, gold nanorods and nanoparticles having plasmon resonances in the near-infrared (NIR) spectral range are used as optical absorption centers in the lipid membrane. Defects optically induced by NIR-laser irradiation of gold nanoparticles are continuously monitored by high-precision ion conductance measurement. Localized laser-mediated heating of nanorods and nanoparticle aggregates cause either (a) transient nanopores in lipid membranes or (b) irreversible rupture of the membrane. To monitor transient opening and closing, an electrophysiological setup is assembled wherein a giant liposome is spread over a micrometer hole in a glass slide forming a single bilayer of high Ohmic resistance (so-called gigaseal), while laser light is coupled in and focused on the membrane. The energy associated with the localized heating is discussed and compared with typical elastic parameters in the lipid membranes. The method presented here provides a novel methodology for better understanding of transport across artificial or natural biological membranes.

Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores

Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4-8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.