Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore

We investigate the base-by-base translocation dynamics of single-stranded DNA (ssDNA) confined in a solid-state nanopore dressed with an electrostatic trap, using all-atom molecular dynamics (MD) simulation. We observe on the simulation time scale of tens of nanoseconds that ssDNA can be driven through the nanopore in a ratchetlike fashion, with a step size equal to the spacing between neighboring phosphate groups in the ssDNA backbone. A 1D-Langevin-like model is derived from atomistic dynamics which can quantitatively describe simulation results and can be used to study dynamics on longer time scales. The controlled ratcheting motion of DNA could potentially enhance the signal-to-noise ratio for nanoelectronic DNA sensing technologies.

Figure 1

Simulations of ssDNA driven through an electrostatic trap in a solid-state nanopore. (a) A cross-section view of the setup of MD simulations. The metal and dielectric regions are labeled with “$M$” and “$D$”, respectively. (b),(c) Relations between the pulling force and the ssDNA position when ssDNA is pulled at a constant velocity ($1\AA /\mathrm{ns}$) using a harmonic spring ($100\mathrm{pN}/\AA$). The trapping fields are 0 (b) and $108\mathrm{mV}/\AA$ (c), respectively.

Figure 2

Dynamics of ssDNA when pulled using a stiff ($100\mathrm{pN}/\AA$) or a weak ($10\mathrm{pN}/\AA$) spring. (a) Force-position dependence when ssDNA is pulled using the stiff spring [gray line] or the weak spring [black line]. The red curve shows the averaged (over 100 pS) pulling force in the stiff spring. (b) Force-time dependence when ssDNA is pulled using the weak spring.

Figure 3

Time-position dependence of ssDNA. (a) Simulated time-position dependence of the ssDNA molecule pulled by a harmonic spring. (b) Modeled time-position dependence of the ssDNA molecule that is pulled under the same conditions. According to the pulling velocity, data in each panel are grouped into three sets: (i) $v=1\AA /\mathrm{ns}$ and $k=10$ (red), 100 (cyan), 1000 (black) $\mathrm{pN}/\AA$; (ii) $v=3\AA /\mathrm{ns}$ and $k=33.3$ (orange) $\mathrm{pN}/\AA$; (iii) $v=10\AA /\mathrm{ns}$ and $k=10$ (green), 100 (blue) $\mathrm{pN}/\AA$. The interval of mesh lines is $d$.

Figure 4

Thermally activated ratchetlike motion of ssDNA driven by a biasing electric field. (a) Transition from a ratcheting to a steady-sliding motion of ssDNA when increasing the biasing electric field from $0.6\mathrm{mV}/\AA$ to $9.4\mathrm{mV}/\AA$, or the electric driving force on bare DNA from 20 to 300 pN. The interval of mesh lines is $d$. (b)–(d) Predictions of time-dependent force in spring from Eq. (1) at $T=0$. The spring constants are $1000\mathrm{pN}/\AA$ (b), $10\mathrm{pN}/\AA$ (c), and $0.1\mathrm{pN}/\AA$ (d), respectively. All parameters are the same as used in the simulation.