Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA

Langevin Dynamics Study on the Driven Translocation of Polymer Chains with a Hairpin Structure

The hairpin structure is a common and fundamental secondary structure in macromolecules. In this work, the process of the translocation of a model polymer chain with a hairpin structure is studied using Langevin dynamics simulations. The simulation results show that the dynamics of hairpin polymer translocation through a nanopore are influenced by the hairpin structure. Hairpin polymers can be classified into three categories, namely, linear-like, unsteady hairpin, and steady hairpin, according to the interaction with the stem structure. The translocation behavior of linear-like polymers is similar to that of a linear polymer chain. The time taken for the translocation of unsteady hairpin polymers is longer than that for a linear chain because it takes a long time to unfold the hairpin structure, and this time increases with stem interaction and decreases with the driving force. The translocation of steady hairpin polymers is distinct, especially under a weak driving force; the difficulty of unfolding the hairpin structure leads to a low translocation probability and a short translocation time. The translocation behavior of hairpin polymers can be explained by the theory of the free-energy landscape.

Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.

Beta-Barrel Nanopores as Diagnostic Sensors: An Engineering Perspective

Biological nanopores are ultrasensitive and highly attractive platforms for disease diagnostics, including the sequencing of viral and microbial genes and the detection of biomarkers and pathogens. To utilize biological nanopores as diagnostic sensors, they have been engineered through various methods resulting in the accurate and highly sensitive detection of biomarkers and disease-related biomolecules. Among diverse biological nanopores, the β-barrel-containing nanopores have advantages in nanopore engineering because of their robust structure, making them well-suited for modifications. In this review, we highlight the engineering approaches for β-barrel-containing nanopores used in single-molecule sensing for applications in early diagnosis and prognosis. In the highlighted studies, β-barrel nanopores can be modified by genetic mutation to change the structure; alter charge distributions; or add enzymes, aptamers, and protein probes to enhance sensitivity and accuracy. Furthermore, this review discusses challenges and future perspectives for advancing nanopore-based diagnostic sensors.

Electro-osmotic flow in nanoconfinement: Solid-state and protein nanopores

Electro-osmotic flow (EOF) is a phenomenon where fluid motion occurs in porous materials or micro/nano-channels when an external electric field is applied. In the particular example of single-molecule electrophoresis using single nanopores, the role of EOF on the translocation velocity of the analyte molecule through the nanopore is not fully understood. The complexity arises from a combination of effects from hydrodynamics in restricted environments, electrostatics emanating from charge decorations and geometry of the pores. We address this fundamental issue using the Poisson-Nernst-Planck and Navier-Stokes (PNP-NS) equations for cylindrical solid-state nanopores and three representative protein nanopores (α-hemolysin, MspA, and CsgG). We present the velocity profiles inside the nanopores as a function of charge decoration and geometry of the pore and applied electric field. We report several unexpected results: (a) The apparent charges of the protein nanopores are different from their net charge and the surface charge of the whole protein geometry, and the net charge of inner surface is consistent with the apparent charge. (b) The fluid velocity depends non-monotonically on voltage. The three protein nanopores exhibit unique EOF and velocity-voltage relations, which cannot be simply deduced from their net charge. Furthermore, effective point mutations can significantly change both the direction and the magnitude of EOF. The present computational analysis offers an opportunity to further understand the origins of the speed of transport of charged macromolecules in restricted space and to design desirable nanopores for tuning the speed of macromolecules through nanopores.

Influence of nanopore coating patterns on the translocation dynamics of polyelectrolytes

Polyelectrolytes can electrophoretically be driven through nanopores in order to be detected. The respective translocation events are often very fast and the process needs to be controlled to promote efficient detection. To this end, we attempt to control the translocation dynamics by coating the inner surface of a nanopore. For this, different charge distributions are chosen that result in substantial variations of the pore-polymer interactions. In addition and in view of the existing detection modalities, experimental settings, and nanopore materials, different types of sensors inside the nanopore have been considered to probe the translocation process and its temporal spread. The respective transport of polyelectrolytes through the coated nanopores is modeled through a multi-physics computational scheme that incorporates a mesoscopic/electrokinetic description for the solvent and particle-based scheme for the polymer. This investigation could underline the interplay between sensing modality, nanopore material, and detection accuracy. The electro-osmotic flow and electrophoretic motion in a pore are analyzed together with the polymeric temporal and spatial fluctuations unraveling their correlations and pathways to optimize the translocation speed and dynamics. Accordingly, this work sketches pathways in order to tune the pore-polymer interactions in order to control the translocation dynamics and, in the long run, errors in their measurements.

Considerable slowdown of short DNA fragment translocation across a protein nanopore using pH-induced generation of enthalpic traps inside the permeation pathway

A pressing challenge in the realm of nanopore-based sensing technologies for nucleic acid characterization has been the cheap and efficient control of analyte translocation. To address this, a plethora of methods were tested, including mutagenesis, molecular motors, enzymes, or the optimization of experimental conditions. Herein, we present a paradigm exploiting the manipulation of electrostatic interactions between 22-mer single-stranded DNAs (22_ssDNA) and low pH-induced charges in the alpha-hemolysin (α-HL) nanopore, to efficiently control the passage of captured molecules. We discovered that in electrolytes buffered at pH = 5 and pH = 4.5 where the nanopore's vestibule and lumen become oppositely charged as compared to that at neutral pH, the electrostatic anchoring at these regions of a 22_ssDNA fragment leads to a dramatic increase of the translocation time, orders of magnitude larger compared to that at neutral pH. This pH-dependent tethering effect is reversible, side invariant, and sensitive to the ionic strength and ssDNA contour length. In the long run, our discovery has the potential to provide a simple read-out of the sequence of bases pertaining to short nucleotide sequences, thus extending the efficacy of current nanopore-based sequencers.

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

We studied the translocation of polyelectrolyte (PE) chains driven by an electric field through a pore by means of molecular dynamics simulations of a coarse-grained HP model mimicking high salt conditions. Charged monomers were considered as polar (P) and neutral monomers as hydrophobic (H). We considered PE sequences that had equally spaced charges along the hydrophobic backbone. Hydrophobic PEs were in the globular form in which H-type and P-type monomers were partially segregated and they unfolded in order to translocate through the narrow channel under the electric field. We provided a quantitative comprehensive study of the interplay between translocation through a realistic pore and globule unraveling. By means of molecular dynamics simulations, incorporating realistic force fields inside the channel, we investigated the translocation dynamics of PEs at various solvent conditions. Starting from the captured conformations, we obtained distributions of waiting times and drift times at various solvent conditions. The shortest translocation time was observed for the slightly poor solvent. The minimum was rather shallow, and the translocation time was almost constant for medium hydrophobicity. The dynamics were controlled not only by the friction of the channel, but also by the internal friction related to the uncoiling of the heterogeneous globule. The latter can be rationalized by slow monomer relaxation in the dense phase. The results were compared with those from a simplified Fokker-Planck equation for the position of the head monomer.

Translocation, Rejection and Trapping of Polyampholytes

Polyampholytes (PA) are a special class of polymers comprising both positive and negative monomers along their sequence. Most proteins have positive and negative residues and are PAs. Proteins have a well-defined sequence while synthetic PAs have a random charge sequence. We investigated the translocation behavior of random polyampholyte chains through a pore under the action of an electric field by means of Monte Carlo simulations. The simulations incorporated a realistic translocation potential profile along an extended asymmetric pore and translocation was studied for both directions of engagement. The study was conducted from the perspective of statistics for disordered systems. The translocation behavior (translocation vs. rejection) was recorded for all 220 sequences comprised of N = 20 charged monomers. The results were compared with those for 107 random sequences of N = 40 to better demonstrate asymptotic laws. At early times, rejection was mainly controlled by the charge sequence of the head part, but late translocation/rejection was governed by the escape from a trapped state over an antagonistic barrier built up along the sequence. The probability distribution of translocation times from all successful attempts revealed a power-law tail. At finite times, there was a population of trapped sequences that relaxed very slowly (logarithmically) with time. If a subensemble of sequences with prescribed net charge was considered the power-law decay was steeper for a more favorable net charge. Our findings were rationalized by theoretical arguments developed for long chains. We also provided operational criteria for the translocation behavior of a sequence, explaining the selection by the translocation process. From the perspective of protein translocation, our findings can help rationalize the behavior of intrinsically disordered proteins (IDPs), which can be modeled as polyampholytes. Most IDP sequences have a strong net charge favoring translocation. Even for sequences with those large net charges, the translocation times remained very dispersed and the translocation was highly sequence-selective.

Brownian dynamics of cylindrical capsule-like particles in a nanopore in an electrically biased solid-state membrane

We use Brownian dynamics simulations to study the motion of cylindrical capsule-like particles (capsules) as they translocate through nanopores of various radii in an electrically biased silicon membrane. We find that for all pore sizes the electrostatic interaction between the particle and the pore results in the particle localization towards the pore 's center when the membrane and the particle have charges of the same sign (case 1) while in case of the opposite sign charges, the capsule prefers to stay near and along the nanopore wall (case 2). The preferential localization leads to all capsules rotating less while inside the pore compared to the bulk solution, with a larger net charge and/or particle length resulting in a smaller range of rotational movement. It also strongly affects the whole translocation process: in the first case, the translocation is due to the free diffusion along the pore axis and is weakly dependent on the particle charge and the nanopore radius while in the second case, the translocation time dramatically increases with the particle size and charge as the capsule gets "stuck" to the nanopore surface.

Multiscale simulations of charge and size separation of nanoparticles with a solid-state nanoporous membrane

Nanoporous membranes provide an attractive approach for rapid filtering of nanoparticles at high-throughput volume, a goal useful to many fields of science and technology. Creating a device to readily separate different particles would require an extensive knowledge of particle-nanopore interactions and particle translocation dynamics. To this end, we use a multiscale model for the separation of nanoparticles by combining microscopic Brownian dynamics simulations to simulate the motion of spherical nanoparticles of various sizes and charges in a system with nanopores in an electrically biased membrane with a macroscopic filtration model accounting for bulk diffusion of nanoparticles and membrane surface pore density. We find that, in general, the separation of differently sized particles is easier to accomplish than of differently charged particles. The separation by charge can be better performed in systems with low pore density and/or smaller filtration chambers when electric nanopore-particle interactions are significant. The results from these simple cases can be used to gain insight in the more complex dynamics of separating, for example, globular proteins.

Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids

Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.

Single-molecule Study on the Interactions between Cyclic Nonribosomal Peptides and Protein Nanopore

Nonribosomal peptides (NRPs) are a type of secondary metabolites mostly originated from microorganisms such as bacteria and fungi. Their proteolytic stability, highly selective bioactivity, and microorganism-specificity have made them an attractive source of drugs for the pharmaceutical industry. Herein, with microcystins (MCs) as a NRP model, we, for the first time, proposed a sensitive method to study the interactions between NRPs and the protein nanopore. Due to the large molecular size (~3 nm diameter) of MCs and their net negative charges, MCs failed to translocate through the α-hemolysin (α-HL) protein channel. Our results demonstrated that the biomolecular interaction of MC-α-HL protein was significantly affected by the applied potential bias. The constant blockage amplitude in the voltage-dependent studies indicated that the current modulation events were dominantly contributed to the bumping interaction between MCs and the α-HL protein under the electrophoretic force. The mean residence time of the bumping events exhibited a two-stage decrease (from 1.90 ms to 1.02 ms, and from 1.02 ms to 0.69 ms) at the threshold voltages of -70 mV and -100 mV, respectively. Using our strategy (i.e., based on their electrophoretic driven interaction with the α-HL protein pore), discrimination of different MC molecules (MC-LR, MC-RR, MC-YR and linear analog) with varied branched residues could be accomplished. This work should provide an insight in developing a rapid and effective method for the identification of cyclic NRPs as valuable biomarkers for fungal infections.

Conformational fluctuations of a DNA electrophoretically translocating through a nanopore under the action of a motor protein

Single-file single-molecule electrophoresis through a nanopore has emerged as one of the successful methods in DNA sequencing. In gaining sufficient accuracy in the readout of the sequence, it is essential to position every nucleotide of the sequence with great accuracy and precision at the interrogation point of the nanopore. A combination of a ratcheting enzyme and a threaded DNA across a protein pore under an electric field is experimentally shown to be a viable method for DNA sequencing within the single-molecule electrophoresis technique. Using coarse-grained models of the enzyme and the protein nanopore, and Langevin dynamics simulations, we have characterized the conformational fluctuations of the DNA inside the nanopore. We show that the conformational fluctuations of DNA are significant for slowly operating enzymes such as phi29 DNA polymerase. Our results imply that there is considerable uncertainty in precisely positioning a nucleotide at the interrogation point of the nanopore. The discrepancy between the results of coarse-grained simulations and the experimentally successful accurate sequencing suggests that additional features of the experiments, such as explicit treatment of electrolyte ions and hydrodynamics, must be incorporated in the simulations to accurately model experimental constructs.

Coarse-grained molecular dynamics study of wettability influence on protein translocation through solid nanopores

Protein translocation through nanopores is widely involved in molecular sensing and analyzing devices, whereby nanopore surface properties are crucial. However, fundamental understanding of how these properties affect protein motion inside nanopores remains lacking. In this work, we study the influence of nanopore surface wettability on voltage-driven protein translocation through nanopores with coarse-grained molecular dynamics simulations. The results show that the electrophoretic mobility of protein translocation increases as the contact angle of nanopore surface increases from 0° to 90°, but becomes almost constant as the contact angle is above 90°. This observation can be attributed to the variation of the friction coefficient of protein translocation through the nanopores with different nanopore contact angles. We further show that the interaction between nanopore and water, rather than that between the nanopore and protein, dominates the protein transport in nanopores. These findings provide new insights into protein translocation dynamics across nanopores and will be beneficial to the design of high-efficiency nanopore devices for single molecule protein sensing.