Directly Observing the Motion of DNA Molecules near Solid-State Nanopores

Abstract

We investigate the diffusion and the drift motion of λ DNA molecules near solid-state nanopores prior to their translocation though the nanopores using fluorescence microscopy. The radial dependence of the electric field near a nanopore generated by an applied voltage in ionic solution can be estimated quantitatively in 3D by analyzing the motion of negatively charged DNA molecules. We find that the electric field is approximately spherically symmetric around the nanopore under the conditions investigated. In addition, DNA clogging at the nanopore was directly observed. Surprisingly, the probability of the clogging event increases with increasing external bias voltage. We also find that DNA molecules clogging the nanopore reduce the electric field amplitude at the nanopore membrane surface. To better understand these experimental results, analytical method with Ohm’s law and computer simulation with Poisson and Nernst-Planck (PNP) equations are used to calculate the electric field near the nanopore. These results are of great interest in both experimental and theoretical considerations of the motion of DNA molecules near voltage-biased nanopores. These findings will also contribute to the development of solid-state nanopore based DNA sensing devices.

Direct observation of DNA knots using a solid-state nanopore

“…The former configuration of local folds has extremely low rates of occurrence due to the nature of the translocation process, which can be seen as follows. The nanopore can be thought of as applying a point force to the polymer at the location of the nanopore, since the electric field strength is highest in the pore and strongly decreases as 1/r 2 away from the pore 33 . A long DNA molecule coils up into a polymer blob that has a large size (many hundreds of nm) compared to the nm-size nanopore.…”

Interfacing solid‐state nanopores with gel media to slow DNA translocations

“…In order to estimate Rc, we can assume the electric field extends outwards from the nanopore in a radial fashion according to Ohm's law (assuming spherical symmetry) [92],…”

Coordination of the electrical and optical signals revealing nanochannels with an ‘onion-like’ gating mechanism and its sensing application

“…To address these limitations, the incorporation of additional measurements that supplement the electrical measurements to validate the envisaged gating process through the ion channels is indispensable. 21,22 Among many techniques, fluorescent imaging is well established in studying the behavior of molecules in a variety of confined spaces. 23 By combining ionic current signal with molecule fluorescence imaging, we will directly observe whether the decrease in ionic current does in fact correspond to the blockade of the channels by ambient stimuli.…”