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Gate Voltage Controlled Threading DNA into Transistor Nanopores Yuta Kato, Naoto Sakashita, Kentaro Ishida, and Toshiyuki Mitsui J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.7b06932 • Publication Date (Web): 11 Sep 2017 Downloaded from http://pubs.acs.org on September 14, 2017

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The Journal of Physical Chemistry

Gate Voltage Controlled Threading DNA into Transistor Nanopores Yuta Kato, Naoto Sakashita, Kentaro Ishida and Toshiyuki Mitsui* Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan * To whom correspondence should be addressed. E-mail: [email protected] ABSTRACT We present a simple method for DNA translocation driven by applying AC voltages, such as square and sawtooth waves, on an embedded thin film as a gate electrode inside of a dielectric nanopore, without applying a conventional bias voltage externally across the pore membrane. Square waveforms on a gate can drive a single DNA molecule into a nanopore, which often returns from the pore, causing an oscillation across the membrane. An optimized sawtooth-like negative voltage pulse on the gate can thread a fraction of a DNA molecule into a pore after a single pulse. This trapped DNA molecule continues to finish its translocation slowly through the pore. The DNA’s slow speed was comparable to previous findings of the escaping DNA speed from a nanopore estimated by the Smoluchowski equation with excluded-volume interactions of a long chain molecule and electrophoresis by extremely low electric fields. This simple scheme, controlling DNA molecules only by gate potential modulation at a nanopore, will

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provide an additional method to thread, translocate, or oscillate a single biomolecule at a gated nanopore. INTRODUCTION Solid-state nanopores have demonstrated the ability to gain the geometrical conditions of a single biomolecule as it passes through the pore by measuring the ionic current profile generated by a bias voltage across the pore membrane.1-3 This bias voltage is provided by a pair of Ag/AgCl electrodes, each immersed in trans and cis reservoirs, and generates an electrophoretic force to drive the charged biomolecule, such as a DNA molecule, through a pore. Initially, the typical materials of the pore membrane were dielectrics, such as SiN,4 SiO,5 and Al2O3.5-6 However, recent trends include the integration of conductive thin films on or into a nanopore. This can add a better sensing method to modulate electric potential at the nanopores; however, an especially promising tool is the fabrication of a pair of electrodes with a nanogap at the nanopore mouth. These electrodes can provide not only the compositions of single biopolymers, but also of single chemical events by reading the tunneling current, and are a step toward a novel probing tool beyond single DNA sequencing.7-9 In addition, a conductive nanopore for a site of surface-enhanced resonance Raman spectroscopy (SERRS) was demonstrated.10 Several nanopores with conductive elements, conductive nanopores, or conductive thin films such as graphene11-13 or Au14-15 or films16-17 or electrodes9, 18 incorporated into the pore have been introduced and tested for the translocation of biomolecules such as DNA molecules. These conductive pores can modulate the charge density, resulting in an electric field at or near the conductive surface of a gate, similar to a field effect transistor (FET) in semiconductors. The conductive nanopores are called ionic field effect transistors, or simply nanopore transistors.7,


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19-20

These charge modulations introduce a fluidic flow, electro-osmosis, through a nanopore.

Under such conditions, cations and anions have different mobility values or different concentrations. Especially, K+ and Cl- having similar mobility values is an exception to the general case.21 A recent study using nanopore transistors reported that translocation rates of DNA vary by the gate voltage with bias voltages across the pore membrane.17 A nanopore transistor is a three-electrode system, which can induce complex physics phenomena that affect the motion of biomolecules.22 One may explore simple schemes to manipulate a single DNA molecule, in particular by modulating the pore gate potential, to introduce to, thread in, translocate, or continuously recapture23-24 through a pore in order to probe single molecules. However, to measure the real-time DNA translocation rate, this gate potential modulation is not desirable because it reduces signal to noise ratios of ionic current to detect the translocation signals. Here, we have directly observed DNA molecules microscopically, by using fluorescent dyes while applying various voltage waveforms on a nanopore gate with both trans and cis reservoir potentials grounded, and observed the effects of the gate potential modulation. We then optimized the waveforms for the DNA translocation, oscillation, and partial threading into a gated pore. Previously, we used fluorescents microscopy to investigate the DNA dynamics directly near both dielectric25 and conductive26 (Au-coated) nanopore, especially before entry into a pore. Near an Au-coated nanopore, the unique flows, caused by electro-osmosis, were recognized by tracing individual DNA motions when a voltage difference between the Au and bulk ionic solution was applied in addition to the standard bias voltage across the nanopore membrane. These flows out of or into a pore, depending on the polarities of the voltage difference, were


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reasonably estimated numerically by the finite element method (FEM). We have also found a higher rate of undesirable DNA clogging at higher bias voltages on dielectric pores.25 In this article, we demonstrate the manipulation of DNA molecules near nanopore transistors on a geometrically symmetric membrane, SiO (200 nm)-Au (50 nm)-SiN (200 nm), by gate potential modulation by applying AC voltages on the Au while grounding both ionic solutions. Threading and leaving a DNA molecule in the middle of its translocation without AFM27-28, optical tweeter29 or high-speed electronics30 is an especially attractive scheme to attain the slowest DNA translocation speed, which provides an ideal condition to test the other sensing methods, e.g., using a tunneling current to probe the molecule. Analogous to the previous estimation to “escape” single DNA molecules from a nanopore30, we have also applied the Smoluchowski equation to estimate the electric fields needed at the nanopore to drive a DNA molecule into the nanopore using only the gate voltage modulations. We also found the cause of the generated weak pulsed electric fields, which is the different time constants of the capacitive coupling of each ion solution in trans or cis reservoirs to an Au layer embedded in the pore membrane. The area exposed to the ionic solutions, the geometry of the solution reservoirs, and the membrane materials, SiO2 or SiN, are different between the trans and cis side in our experimental setup on the stage of an optical microscope (See Figure 1a and S1). Translocation by this scheme rarely caused DNA clogging, which frequently occurs at high bias voltages across the pore membrane.25 Accordingly, this simple method, applying AC voltage modulations at a pore gate, can provide an additional method to manipulate a biomolecule, especially threading partially into a pore and then translocating slowly. This translocation method is ideal for electrode sensing because no bias voltages are applied across the pore membrane.


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EXPERIMENTAL METHODS Fabrication of gated nanopore

a

SiO2 Au SiN

200 nm 50 nm 200 nm

b

Figure 1. (a) Schematic illustration of the experimental setup. Both sides of KCl solutions, trans and cis were electrically ground by Ag/AgCl. electrodes. A cis chamber where DNA molecules are introduced is under the nanopore located on a cover slip of a fluorescent microscope. Inset figure features the three layers of membrane, SiO2 (200 nm)-Au (50 nm)-SiN (200 nm). As a gate voltage, Vgate is applied to the Au layer, electrically isolated from KCl solutions except inside of a pore. (b) A TEM image of a SiO-Au-SiN nanopore. The contrast variations along pore periphery indicates the slight cone shape of the pore, the cone angle < 5° narrower for the cis side.

A 40 µm × 40 µm freestanding membrane of 200-nm-thick SiN, supported by a 500-µm-thick Si(100) was created by conventional optical photolithography followed by anisotropic wet etching of silicon in a KOH solution.4, 31 A 50-nm-thick Au film with a 5-nm Cr


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film as an adhesion layer was deposited by thermal evaporation on the SiN membrane for a gate electrode. A 200-nm-thick SiO2 film was deposited by RF sputtering. A nanopore was then milled through the three-layer membrane using a focused ion beam (FIB) from the pit side, resulting in a minimum diameter of ~100 nm in a truncated cone with a 5° vertex. This angle was estimated by the contrast image produced by transmission electron microscopy (TEM). A typical TEM image of a nanopore is shown in Figure 1b. The quantity of ionic current flowing through the nanopores allows us to confirm the diameters of nanopores.6

DNA observation and experimental setup A fluorescent molecule dye, YOYO-1 (Molecular Probes), was used to visualize lambda phage DNA molecules. The dye-to-base pair ratio was 1:10, so that the mechanical and electrical property changes by attaching the YOYO-1 dyes are negligible for our study.32-34 The final DNA concentration was 1 ng/mL in 0.01 M KCl solution, which contained 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA. The DNA concentration was low enough not to cause DNA-DNA interaction in the KCl solution. The estimated ionic strength of the solution was 16 mM for 0.01 M KCl, and this value was confirmed by the linear I–V characteristic plots of 100 nm diameter pores.35 As illustrated in Figure 1, the electric potentials of ionic KCl solutions were set to Vcis = Vtrans = 0 V by the Ag/AgCl electrodes inserted into each reservoir. As a gate voltage, Vgate, the voltage differences from the electrically grounded Vcis and Vtrans, and Vgate were kept less than 0.5 V, since the Au gate electrodes are directly exposed to the ionic solutions inside the pore, which may electrochemically etch off the Au. It is known that the electrochemical etching of Au rarely occurs at voltage differences less than 1.0 V.36-37 A gate voltage, Vgate was applied to the Au film


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via an Au wire, carefully kept out of contact with the KCl solutions. Details of this experimental set up containing wiring to the Au film are described in Supplemental Information.

Imaging and Analysis Sequential images showing the DNA dynamics at 14 Hz were taken using a highly sensitive charge-coupled device camera (ORCA-ER Hamamatsu Photonics). The focusing plane for the optical microscope was the membrane surface on the cis side, where DNA molecules are imaged sharply when they pass through a pore.25-26 The synchronization between optical and electrical signals has confirmed by different groups.38-39 Because of the non-transparent Au film inside the pore membrane, the DNA molecules on the trans side were not observed.26 To define the center location of a single DNA molecule, geometric means were calculated from the DNA’s outlines. The fluorescence intensity of a DNA molecule was the summation of the 9 pixel values of the center location pixel and its 8-neighbor pixels. We have developed MATLAB code to find the DNA locations automatically.

RESULTS AND DISCUSSION Before investigating the influence of the AC gate voltages on Au thin film electrodes inside of a nanopore, DC gate voltages, Vgate from −0.4 to +0.4 V relative to grounded KCl solutions in both trans and cis reservoirs were examined, and as expected, no DNA molecule was captured for its translocation (See Figure S2). In contrast, the change of the gate voltage from positive to negative captured single DNA molecules, when the diffusing DNA molecule was located within


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2 µm from the pore location, and then translocated them through the pore to the trans side (See Figure S3).

Square wave VPP = 0.8 V, Voffset = 0 V, duty cycle 50%, Vcis = Vtrans = 0 V

Figure 2. Single DNA molecule oscillation through a nanopore by applying a 3 Hz square wave with 0.8 Vpp and 0 V offset on Vgate relative to both Vcis and Vtrans in 0.01M KCl. (a)–(f) Selected image frames with a nanopore, marked in a yellow circle, between 71.35 s and 72.14 s from sequence frames at 14 Hz. Fluorescence intensity of a DNA molecule blinks at the nanopore between the images. (g) A plot of the fluorescence intensity and the square wave in time during the oscillation. Synchronization between them can be identified. See also SI Movie S1. (h) A plot of the average number of DNA oscillations vs. square wave frequency. One oscillation indicates a round trip of a DNA molecule, translocating through a pore twice, between cis and trans reservoirs. ACS Paragon Plus Environment

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Square waves on Vgate relative to Vcis and Vtrans were applied with frequencies from 0.5 to 10 Hz. As expected, single DNA molecules were not only captured for translocation toward the trans side, but also immediately returned from the trans to the cis side by the sequential alternation of the polarity of the gate voltages in square wave forms. This consequently induced DNA oscillation via a nanopore. In Figure 2, a typical example of DNA oscillation and synchronization with the applied square wave is presented. In the fluorescence microscopy images, Figure 2a–f, a yellow circle indicates the location of a nanopore, inside of which the fluorescence intensity of a DNA molecule blinks between the images. The form of the square wave was 3 Hz with 0.8 VPP and 0 V offset (see Supporting Information Supplementary Movie S1). Since the concentration of DNA molecules near the nanopore was low, this blinking is caused by the repeated translocation of a single DNA molecule through a pore between the trans and cis side of reservoirs.26 By plotting the blinked fluorescence DNA intensity at the nanopore and the applied AC square wave with respect to time, their synchronicity was recognized, as shown in Figure 2g. This plot displays that the voltage drops from 0.4 V to −0.4 V drive a DNA molecule to translocate from the cis to the trans side of the reservoirs, and the voltage rises drive it to return. This indicates that AC electric fields, synchronized to the applied square wave, occur in the vicinity of and inside the pore to induce the DNA oscillation. The electric fields are likely attributed to the electrical properties of the pore membrane, SiO (200 nm)-Au (50 nm)-SiN (200 nm), facing the ionic solutions either the trans or cis side of reservoirs, forming parallel plate capacitors across the SiO or SiN as dielectric thin films in our experimental setup. We will discuss the capacitive coupling between the Au layer and each reservoir later. Figure 2h shows that the number of DNA oscillations increased with the frequency of square wave, as a 5 Hz square wave oscillated a DNA molecule more than 6 times on average.


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One oscillation indicates a round trip of a DNA molecule, translocating through a pore twice, between cis and trans reservoirs. This indicates the DNA can be repeatedly recaptured 12 times in a row for translocation. In addition, this number would likely rise more by further increasing the square wave frequency. This experiment was limited to 5 Hz by the image recording rate of 14 Hz for reasonable identification of a single DNA molecule oscillation between image frames. This DNA oscillation across a membrane through a nanopore, or DNA recapturing, has been demonstrated by Gershow, et al.23 Their nanopores were milled on dielectric membranes without any gate electrode, and standard bias voltages were used for the DNA manipulation, specifically reversing a bias voltage, triggered after detection of an ionic current “blockade” within a few tens of milliseconds. Their advanced fast electronic system with real time feedback can measure the time between the DNA capture as fast as 2–4 ms and the capture probability was near 0.7, so the oscillation frequency exceeds 300 Hz in principle. The capture probability decreases with the oscillation period, for example at 30 Hz the recapture probability was near 0.4.23 In our simple system, the oscillation frequency and synchronization with a square wave below 5 Hz, 6 times slower than Gershow’s recapturing time scales, was able to oscillate a DNA molecule approximately 6 times on average. As we discuss later, the slowed translocation speed allows low frequency oscillations in our system. Toward the goal of sequencing, slowing down the translation speed is crucial to lower the bandwidth requirement. 2, 40-43

Sawtooth wave VPP = 0.4 V, Voffset = −0.2 V, Vcis = Vtrans = 0 V, 1 Hz In the previous section, we describe DNA oscillation by applying square waves, fast rise and fast fall, on a gate electrode at the nanopore without a bias voltage, as Vcis and Vtrans are set to ground. In this section, we describe the DNA motion near a nanopore while applying voltages


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in various sawtooth waveforms on a gate electrode, which provides slow rise or fall in addition to fast fall or rise, respectively, in the sawtooth voltage waveforms. First, a waveform, with fast fall from 0.4 V to −0.4 V, followed by a slow rise back to 0.4 V in a frequency range from 1–5 Hz was tested. As expected, the DNA translocation occurred at the fast voltage fall, but the slow voltage rise did not recapture the DNA molecule, resulting in a standard one-way translocation.


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Figure 3. DNA translocation of gate voltage in Sawtooth waveform, fast fall followed by slow rise of VPP = 0.4 V, Voffset = −0.2 V, Vcis = Vtrans = 0 at 1 Hz. (a)–(c), (d)–(g) Selected image frames with a nanopore, marked in a yellow circle, from sequence frames at 14 Hz. A DNA molecule near the nanopore translocated into the nanopore before (c) and before (g). (h), (i) DNA fluorescence intensity at the nanopore in time with overlied the voltage in Sawtooth waveform applied to the nanopore gate for (a)–(c) and (d)–(g), respectively. In each image sequence, a DNA molecule translocated into a nanopore after the fast voltage fall instantaneously within 71 ms of one frame period after (b), or gradually within 7 frame periods, 0.5 s, after (d). See also SI Movies S2 and S3. (j) Translocation time distribution by measuring the fluorescence intensity of a DNA molecule at a nanopore. Two peaks, near 0.2 s and near 0.5 s, are recognized. To investigate the voltage polarity dependence of the DNA translocation, offset voltages were applied to the gate. In Figure 3a-c and Figure 3d-g, the DNA fluorescence intensity at the nanopore again shows the fast voltage fall, from 0 V to −0.4 V, at the gate induced DNA translocation to the trans side as the DNA intensity disappeared at the nanopore in Figure 3c and 3g, but again the reverse translocation did not occur during the slow voltage rise (see Supporting


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Information Supplementary Movies S2 and S3). Throughout of the observation of 236 DNA translocations under this condition, no DNA molecule returned from the other side of the membrane. The most unique feature of the translocation is the slow speed. Assuming the translation time is the number of frames before the DNA intensity vanishes after the voltage changes,25, 44 the distribution of the translocation time is plotted in Figure 3j and reveals two peaks at 0.21 s and 0.50 s. In particular, the translation time near 0.50 s would be the slowest, which may be achieved without DNA manipulation instruments, such as AFM or optical tweezer. Previously, D.P. Hoogerheide, et al., achieved such slow translocation times without these instruments. They nearly turned off a bias voltage immediately after a nanopore captured a DNA molecule within a millisecond by high speed electronics. This left a DNA molecule halfway through the pore. By weakly modulating the bias voltage below 1 mV and the entropic force contribution to move a DNA molecule out of a pore, the range of the translocation time for 23.46 kbp dsDNA was from 0.1 s to 0.8 s. Our results of the translocation time were in the same range, therefore similar driving force was expected. We will discuss the driving force with an analytical model in the next section. In contrast, DNA translocation was not observed with a gate voltage offset of +0.2 V with the same waveform generating fast fall from 0.4 V to 0 V while Vcis and Vtrans are 0 V. The instant voltage difference between the pore gate and ionic solutions may be essential to induce DNA translocation. Further investigations are necessary to explain this offset difference. However, the reducing the translocation speed, ideally lower the order of 106 bases/s, will increase the signal to noise ratio for the ionic or tunneling current measurements at the picoampere level to scrutinize a single biomolecule, therefore as a simple method, which can


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achieve such slow speed, to drive DNA translocation, this AC voltages on a pore gate electrode is desirable.

Simulation of DNA translocation by pulse electric field and entropic force To analyze the translocation time distribution of a DNA molecule by sawtooth waveforms of a gate voltage, a 1D Smoluchowski drift-diffusion equation was used.30, 45 This equation successfully evaluates the time evolution of the probability density P(x,t) of the site of a long chain molecule located inside a nanopore, as a schematic in Figure 4a shows. ∂(, ) () (, ) ∂ (, ) = + (1) ∂

∂ ∂ 2 1 − () = ∆ + (2) 1 − F(x) is the net force acting on the site inside the nanopore. With γ, the drag coefficient,

()

becomes the drift velocity. D is the diffusion coefficient, holding the fluctuation-dissipation relation D = kBT/γ. The net force, F(x), of Eq. (2) has two terms, contributions from electrophoretic and entropic forces. The electrophoretic force is estimated by the strength of an electric field inside a nanopore multiplied by a net linear charge density, σ, and the pore length which becomes σ∆V.31, 46 The entropic force is driven from the entropic free energy of a long polymer proportional to kBT, which induces excluded volume effects and v, the Flory exponent ~0.59, for a long polymer in a good solvent.30, 45, 47 This Smoluchowski drift-diffusion equation successfully describes the DNA dynamics, when the electrophoretic force is extremely low and


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the escape time is on the same scale as our results.30 As discussed later, we evaluate the ∆V, shown in Figure 4b, by assuming a pulsed electric field, induced by a voltage step inside a nanopore, instantaneously pulls a DNA molecule in Brownian motion toward the nanopore and threads it in halfway, and then the damped electric field in addition to the entropic force, pulls the long DNA molecule to complete the translocation. By assuming an initial condition as a Gaussian as Eq. (3) with σ’= 0.4(L/2) = 0.2L,30 Smoluchowski drift-diffusion equation deduces the translocation distribution shown in Figure 4b by calculating the flux, Eq. (4), assuming that the reduction of the space integral of P(x,t) between t and t + ∆t is proportional to the number of DNA molecules leaving across x = 0 because the ∆V transfers the P(x,t) toward x = 0 (see details in Figure S4a).

(, 0) =

1

"2# $

exp (−

− 2 2 $

) (3)

.

+,(, ∆) = - (, ) − (, + ∆)0 (4) /


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Figure 4. Estimation of the translocation time (a) Schematic of DNA halfway through a pore. The site of DNA inside of the pore is L/2 as the molecular length, L. (b) ∆V for Eq. (2) and transaction time distribution estimated by the Smoluchowski drift-diffusion equation. Two peaks of the translocation time are recognized.

Although there are two peaks, near 0.01 s and near 0.40 s, in the time distribution as we observed experimentally, they are quantitatively 0.19 s and 0.1 s shorter than 0.2 s and 0.5 s peaks, respectively shown in Figure 3j. There is a factor for this peak time shift. We set the center of the Gaussian, an initial condition, at x = L/2, meaning that DNA molecules have already been nearly halfway through a pore, for the estimation (see details in Figure S4) while t = 0 is the time to start pulling a DNA molecule after a gate voltage changes in experiment. This shifts the peaks toward right because of the duration for threading a DNA molecules into a pore halfway. For example, the modifications of the initial conditions or the pulsed electric field shape in Smoluchowski drift-diffusion equation shift both peaks toward right but the same amount. Next, we discuss the origin of the pulse electric field generated when the gate voltage changes. To translocate a DNA molecule from cis to trans or vice versa, the direction of an


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electric field has to be trans to cis or the opposite, respectively, across the layer of Au film even though Vcis and Vtrans are both grounded. The freestanding nanopore membrane itself, SiO2(200 nm)-Au(50 nm)-SiN(200 nm), is geometrically symmetric around the Au layer but not electrically. First, the dielectric constants are 3.9 and 7.5 for SiO2 and SiN, respectively. Secondly, the surface areas constructing the capacitances, between this Au gate layer vs. ionic solutions in the trans or cis side of the reservoirs, are different in our experimental setup. In addition, the trans and cis reservoirs have different shapes. Particularly, the height of the cis reservoir under the Si chip was made as thin as 20 µm to observe the membrane surface with high magnification by the optical microscope. This thin reservoir gives higher solution resistance for the cis side than the trans side. Together all, the capacitive coupling, determined by its resister-capacitor (RC) time constant, are expected to be different between the tran and cis side as the Au layer at center. The RC time constants were estimated by using the fitting method of exponential decay functions by measuring the current response at both electrodes due to an applied voltage step in the trans or cis reservoirs, and are presented in Figure S6.20, 48 The capacitances, 4.3 nF for Au-cis and 1.0 nF for Au-trans, were experimentally measured, and the values are supported by analytical calculations(see details in Figure S5). These capacitance values with their RC time constants give the solution resistances for the trans and cis side (see details in Figure S6). This different capacitive coupling of the trans and cis ionic solutions to Au layer embedded in a nanopore membrane generates the different shape of current pulses between the surfaces of the trans and cis electrodes when the voltage changes at the Au layer relative to the ground reservoirs by these electrodes. This would likely create an electric potential difference generating an electric field through a pore across the membrane in the time scale of the current


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pulse and its relaxation. The pulse width of the potential difference would be determined by the RC time constant of the cis side, 3.8 ms, since the constant of the trans side, 0.12 ms, was much shorter (see details in Figure S6). We estimated the ∆V waveform as an exponential function with the decay time constant of 3.8 ms for the simulation above as shown in Figure 4b. Furthermore, the potential profiles, instantaneously after a gate voltage changes and after the potential profile reaches the steady state, were numerically calculated by the finite element method using COMSOL Multiphysics 4.4.26 As presented in Figure S7, a voltage difference across the membrane is expected if the relaxation RC time constants of the potential profiles in the trans and cis reservoirs are not the same. Taken together, the electric field at vicinity and inside of a nanopore would be generated to induce DNA translocation before reaching a steady state after a gate voltage changes so that these relaxation times are different. Generally, this relaxation time can be varied not only by geometrical conditions, such as film thickness of dielectric materials or electrode surface areas, but also by changing ion concentrations. Future quantitative investigation and numerical simulation will be necessary to confirm this explanation. CONCLUSIONS We demonstrated DNA translocation by modulating the gate voltage at a nanopore without a bias voltage applied to a pair of Ag/AgCl electrodes immersing into each trans and cis reservoir. The DNA translocation into a nanopore was observed directly by using fluorescent microscopy. A square wave gate voltage at higher than 1 Hz can synchronize DNA oscillation across a pore, with the return probability increasing at higher rates. In contrast, a sawtooth wave gate voltage exhibits DNA translocation only from one side to the other, and the extremely slow translocation speed can be predicted by the Smoluchowski drift-diffusion equation with electric


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field pulse with entropic force pulling a DNA molecule. By carefully analyzing the current passing through each Ag/AgCl electrode in trans and cis reservoirs, the different values of the capacitive coupling between the ionic solutions in the reservoirs via these electrodes to an Au gate layer when the gate voltage changes can be determined. This can generate a pulse like the electric field inside a nanopore and its vicinity for threading a DNA molecule completely or halfway through the pore. We consider DNA translocation by a gate voltage modulation, particularly in threading partially a DNA molecule, beneficial to transfer a DNA molecule to a pore for testing advanced sensing methods, such as tunneling for future nanopore-based biomolecular sensor devices.

ASSOCIATED CONTENT Supporting Information Available Figure S1-S7 and Supplementary Movies S1-S3. This material is available free of charge via the Internet at http://pubs.acs.org.

AUTHOR INFORMATION Corresponding Author * E-mail: (T.M.) mitsui @phys.aoyama.ac.jp. Fax: +81 427596285. Telephone: +81 427596285. Notes The authors declare no competing financial interests.


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Acknowledgements T.M. acknowledges support from the Ministry of Education, Culture, Sports, Science and Technology - Supported Program for the Strategic Research Foundation at Private Universities, 2013-2017. T.M is grateful to Dr. Hashiguchi at KESCO Co. for suggestions related to COMSOL Multiphysics. Thin SiN film is fabricated in part at the Cornell Nano Scale Facility. Finally, T.M. would like to thank Professor Miquel Salmeron for his kindness and patience to wait for my slow STM imaging at LBL.

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