Translocation Of DNA Molecules Research Articles

Computational Study on the Interaction and Moving of ssDNA through Nanosheets

The adsorption characteristics and moving through nanopores of a single-stranded deoxyribonucleic acid (ssDNA) molecule on monolayers, such ashexagonal boron nitride and graphene nanosheets, were studied using the continuous approach with the 6–12 Lennard–Jones potential function. The ssDNA molecule is assumed to be at a distance l above the sheet, and the relation between the minimum energy location and the perpendicular distance of the ssDNA molecule from the nanosheet surface is found. In addition, by assuming that there is a hole in the surface of the nanosheet as a pore, the interaction energies for the ssDNA molecule moving through the pore in the surface of the nanosheet (used to calculate the radius p of the hole) are obtained, which provides the minimum energies. Furthermore, a comparative study with graphene was performed in order to compare with hexagonal boron nitride nanosheets. Our results indicate that the binding energies of the ssDNA onto graphene and hexagonal boron nitride nanosheets are approximately 15.488 and 17.582 (kcal/mol), corresponding to perpendicular distances of l=20.271 and l=20.231 Å, respectively. In addition, we observe that the ssDNA molecule passes through graphene and hexagonal boron nitride nanopores when the gap radius p>7.5 Å. Our results provide critical insights to understand and develop the interactions and translocation of DNA molecules with and through nanosheets.

Investigating the Effect of Charged Components on Translocation of DNA Molecules in Track-Etched Nanopores

To understand and improve the translocation dynamics of nanopore based sensors, we studied theoretically the translocation of DNA molecules and compared them with experimental results. In our experimental studies, we used conically shaped track-etched polymer (i.e., PET) membrane and built our model based on its physical properties. Simulations were conducted by varying the surface charges of the nanopore and the particle, particle (i.e., DNA) position and applied potential to examine the translocational behavior of DNA and its effect on current-pulse shape. Our results showed that variations in surface and DNA charge density cause conductive distortions indicating the interaction between the surface and the DNA. It also confirmed that the DNA charge density does not remain in its native form in the solution as well as the pore charge during the translocation.

Scalable fabrication of sub-10\u2009nm polymer nanopores for DNA analysis

We present the first fabrication of sub-10 nm nanopores in freestanding polymer membranes via a simple, cost-effective, high-throughput but deterministic fabrication method. Nanopores in the range of 10 nm were initially produced via a single-step nanoimprinting process, which was further reduced to sub-10 nm pores via a post-NIL polymer reflow process. The low shrinkage rate of 2.7 nm/min obtained under the conditions used for the reflow process was the key to achieving sub-10 nm pores with a controllable pore size. The fabricated SU-8 nanopore membranes were successfully employed for transient current measurements during the translocation of DNA molecules through the nanopores.

The temporal resolution and single-molecule manipulation of a solid-state nanopore by pressure and voltage

The translocation of DNA molecules through nanopores has attracted wide interest for single-molecule detection. However, the multiple roles of electric fields fundamentally constrain the deceleration and motion control of DNA translocation. In this paper, we show how a single anchored DNA molecule can be manipulated for repeated capture using a transmembrane pressure gradient. Continuously and slowly changing the magnitude of the pressure provided two opposite directions for the force field inside a nanopore, and we observed an anchored DNA molecule entering the nanopore throughout the process from tentative to total entry. The use of both voltage and pressure across a nanopore provides an alternative method to capture, detect and manipulate a DNA molecule at the single-molecule level.

Multilevel description of the DNA molecule translocation in solid-state synthetic nanopores

Interest of researchers in micro- and nanofluidics of polymer solutions and, in particular, DNA ionic solutions is constantly increasing. The use of DNA translocation with a controlled velocity through solid-state nanopores and pulsed X-ray beams in new sequencing schemes opens up new possibilities for studying the structure of DNA and other biopolymers. The problems related to the description of DNA molecular motion in a limited volume of nanopore are considered.

Theoretical and experimental studies on ionic currents in nanopore-based biosensors.

Novel generation of analytical technology based on nanopores has provided possibilities to fabricate nanofluidic devices for low-cost DNA sequencing or rapid biosensing. In this paper, a simplified model was suggested to describe DNA molecule's translocation through a nanopore, and the internal potential, ion concentration, ionic flowing speed and ionic current in nanopores with different sizes were theoretically calculated and discussed on the basis of Poisson-Boltzmann equation, Navier-Stokes equation and Nernst-Planck equation by considering several important parameters, such as the applied voltage, the thickness and the electric potential distributions in nanopores. In this way, the basic ionic currents, the modulated ionic currents and the current drops induced by translocation were obtained, and the size effects of the nanopores were carefully compared and discussed based on the calculated results and experimental data, which indicated that nanopores with a size of 10 nm or so are more advantageous to achieve high quality ionic current signals in DNA sensing.

Temperature effect on translocation speed and capture rate of nanopore-based DNA detection

We study the effects of electrolyte temperature on DNA molecule translocation experimentally without and with a temperature gradient across nanopore membranes. The same temperatures on both electrolyte chambers are first considered. The DNA molecule translocation time is measured to be 2.44 ms at 2°C in both chambers, which is 1.57 times longer than at 20°C. Then the temperature difference effect is characterized in both chambers. The results show that the DNA translocation speed can be slowed down as long as one side temperature is lowered, irrespective of the temperature gradient direction. This indicates that the thermophoretic driving force generated by a temperature gradient has no obvious effect on the threading speed of DNA molecules, while the main reason for the slowed DNA translocation speed is the increased viscosity. Interestingly, the capture rate of DNA molecules is enhanced under a temperature gradient condition, and the capture rate during DNA translocation from hot side at 21°C to cold one at 2°C is 1.7 times larger than that under the condition of both chambers at 20°C. Finally, an optimized configuration is proposed to acquire higher capture rates and lower DNA translocation speeds.

Integrated solid-state nanopore devices for third generation DNA sequencing

Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale pore. It is still really tough to attain the single base discrimination on a DNA strand by merely analyzing the ionic current due to speedy DNA translocation and low spatial resolution. More integrated configurations are pursued to present versatile comparative dissimilarities of the four bases by enhancing the spatial resolution within a DNA molecule translocation event, such as transverse tunneling current, local potential change, and capacitance oriented voltage resonance. In this mini review, the insight is provided into the status quo on several functionalized techniques and methodologies for DNA sequencing and furthermore concluding remark and outlook are presented. DNA sequencing, solid-state nanopore, spatial resolution, integrated sensors

Poisson-Fokker-Planck model for biomolecules translocation through nanopore driven by electroosmotic flow

A non-continuous electroosmotic flow model (PFP model) is built based on Poisson equation, Fokker-Planck equation and Navier-Stokse equation, and used to predict the DNA molecule translocation through nanopore. PFP model discards the continuum assumption of ion translocation and considers ions as discrete particles. In addition, this model includes the contributions of Coulomb electrostatic potential between ions, Brownian motion of ions and viscous friction to ion transportation. No ionic diffusion coefficient and other phenomenological parameters are needed in the PFP model. It is worth noting that the PFP model can describe non-equilibrium electroosmotic transportation of ions in a channel of a size comparable with the mean free path of ion. A modified clustering method is proposed for the numerical solution of PFP model, and ion current translocation through nanopore with a radius of 1 nm is simulated using the modified clustering method. The external electric field, wall charge density of nanopore, surface charge density of DNA, as well as ion average number density, influence the electroosmotic velocity profile of electrolyte solution, the velocity of DNA translocation through nanopore and ion current blockade. Results show that the ion average number density of electrolyte and surface charge density of nanopore have a significant effect on the translocation velocity of DNA and the ion current blockade. The translocation velocity of DNA is proportional to the surface charge density of nanopore, and is inversely proportional to ion average number density of electrolyte solution. Thus, the translocation velocity of DNAs can be controlled to improve the accuracy of sequencing by adjusting the external electric field, ion average number density of electrolyte and surface charge density of nanopore. Ion current decreases when the ion average number density is larger than the critical value and increases when the ion average number density is lower than the critical value. Our numerical simulation shows that the translocation velocity of DNA given by the PFP model agrees with the experimental, results better than that given by PNP model or PB model.

DNA Capture and Translocation through Nanoscale Pores—a Fine Balance of Electrophoresis and Electroosmosis

DNA Capture and Translocation through Nanoscale Pores—a Fine Balance of Electrophoresis and Electroosmosis

Mechanism of How Salt-Gradient-Induced Charges Affect the Translocation of DNA Molecules through a Nanopore

Experiments using nanopores demonstrated that a salt gradient enhances the capture rate of DNA and reduces its translocation speed. These two effects can help to enable electrical DNA sequencing with nanopores. Here, we provide a quantitative theoretical evaluation that shows the positive net charges, which accumulate around the pore entrance due to the salt gradient, are responsible for the two observed effects: they reinforce the electric capture field, resulting in promoted molecule capture rate; and they induce cationic electroosmotic flow through the nanopore, thus significantly retarding the motion of the anionic DNA through the nanopore. Our multiphysical simulation results show that, during the polymer trapping stage, the former effect plays the major role, thus resulting in promoted DNA capture rate, while during the nanopore-penetrating stage the latter effect dominates and consequently reduces the DNA translocation speed significantly. Quantitative agreement with experimental results has been reached by further taking nanopore wall surface charges into account.

A Device for Performing Lateral Conductance Measurements on Individual Double-Stranded DNA Molecules

A nanofluidic device is described that is capable of electrically monitoring the driven translocation of DNA molecules through a nanochannel. This is achieved by intersecting a long transport channel with a shorter orthogonal nanochannel. The ionic conductance of this transverse nanochannel is monitored while DNA is electrokinetically driven through the transport channel. When DNA passes the intersection, the transverse conductance is altered, resulting in a transient current response. In 1 M KCl solutions, this was found to be a current enhancement of 5-25%, relative to the baseline transverse ionic current. Two different device geometries were investigated. In one device, the DNA was detected after it was fully inserted into and translocating through the transport nanochannel. In the other device, the DNA was detected while it was in the process of entering the nanochannel. It was found that these two conditions are characterized by different transport dynamics. Simultaneous optical and electrical monitoring of DNA translocation confirmed that the transient events originated from DNA transport through the nanochannel intersection.

Conductance and DNA Translocation Current Blockage of Solid-State Nanopores

The current blockage during DNA molecule translocation through a solid-state nanopore is very important in DNA analysis techniques based on nanopores. We use Poisson—Nernst—Planck descriptions of electrolyte behavior in a nanopore with and without the presence of DNA molecules to simulate the nanopore conductance and current blockage of DNA molecules. Actual experimental parameters, such as pore size, length of nanopores, DNA drift velocity, and the charge issue of nanopores and DNA, are applied to evaluate the precise current blockage amplitude, which is found to agree very well with the experimental results.

Gate effects on DNA translocation through silicon dioxide nanopore

The effects of gate voltage on the translocation of DNA molecules through a nanopore are studied. A twenty-fold increase in the translocation time is observed with a positive gate voltage applied, without changing too much of the ionic current. The amplitude of the current blockage by the DNA molecules was reduced by roughly the same factor. At the same time, the number of the blocking events decreases significantly. The applied gate voltage also modulates the scatter plot of the amplitude of the current blockage against the dwell time. The observations are consistent with the recent theoretical results.

Translocation of DNA Molecules through Nanopores with Salt Gradients: The Role of Osmotic Flow

Recent experiments of translocation of double-stranded DNA through nanopores [M. Wanunu et al., Nature Nanotech. 5, 160 (2009)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoretic effects can quantitatively explain the experimental data on the salt-gradient dependence of the capture rate.

Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes.

Protein nanopores may provide a cheap and fast technology to sequence individual DNA molecules. However, the electrophoretic translocation of ssDNA molecules through protein nanopores has been too rapid for base identification. Here, we show that the translocation of DNA molecules through the α-hemolysin protein nanopore can be slowed controllably by introducing positive charges into the lumen of the pore by site directed mutagenesis. Although the residual ionic current during DNA translocation is insufficient for direct base identification, we propose that the engineered pores might be used to slow down DNA in hybrid systems, for example, in combination with solid-state nanopores.

Single-strand DNA molecule translocation through nanoelectrode gaps

Molecular dynamics simulations were performed to investigate the translocation ofsingle-strand DNA through nanoscale electrode gaps under the action of a constant drivingforce. The application behind this theoretical study is a proposal to use nanoelectrodesas a screening gap as part of a rapid genomic sequencing device. Preliminaryresults from a series of simulations using various gap widths and driving forcessuggest that the narrowest electrode gap that a single-strand DNA can pass is∼1.5 nm. The minimum force required to initiate the translocation within nanoseconds is∼0.3 nN. Simulations using DNA segments of various lengths indicate that the minimuminitiation force is insensitive to the length of DNA. However, the average threading velocityof DNA varies appreciably from short to long DNA segments. We attribute such variationto the different nature of drag force experienced by the short and long DNA segments inthe environment. It is found that DNA molecules deform significantly to fit in the shape ofthe nanogap during the translocation.

The Effect of Translocating Cylindrical Particles on the Ionic Current through a Nanopore

The electric field-induced translocation of cylindrical particles through nanopores with circular cross sections is studied theoretically. The coupled Nernst-Planck equations (multi-ion model, MIM) for the concentration fields of the ions in solution and the Stokes equation for the flow field are solved simultaneously. The predictions of the multi-ion model are compared with the predictions of two simplified models based on the Poisson-Boltzmann equation (PBM) and the Smoluchowski’s slip velocity (SVM). The concentration field, the ionic current though the pore, and the particle’s velocity are computed as functions of the particle’s size, location, and electric charge; the pore’s size and electric charge; the electric field intensity; and the bulk solution’s concentration. In qualitative agreement with experimental data, the MIM predicts that, depending on the bulk solution’s concentration, the translocating particle may either block or enhance the ionic current. When the thickness of the electric double layer is relatively large, the PBM and SVM predictions do not agree with the MIM predictions. The limitations of the PBM and SVM are delineated. The theoretical predictions are compared with and used to explain experimental data pertaining to the translocation of DNA molecules through nanopores.

Slowing DNA Translocation in a Solid-State Nanopore

Reducing a DNA molecule's translocation speed in a solid-state nanopore is a key step toward rapid single molecule identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temperature, salt concentration, viscosity, and the electrical bias voltage across the nanopore, we obtain a 3 base/micros translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diameter silicon nitride pore. Our results also indicate that the ionic conductivity inside such a nanopore is smaller than it is in bulk.