Velocity of DNA during Translocation through a Solid-State Nanopore

Abstract

While understanding translocation of DNA through a solid-state nanopore is vital for exploiting its potential for sensing and sequencing at the single-molecule level, surprisingly little is known about the dynamics of the propagation of DNA through the nanopore. Here we use linear double-stranded DNA molecules, assembled by the DNA origami technique, with markers at known positions in order to determine for the first time the local velocity of different segments along the length of the molecule. We observe large intramolecular velocity fluctuations, likely related to changes in the drag force as the DNA blob unfolds. Furthermore, we observe an increase in the local translocation velocity toward the end of the translocation process, consistent with a speeding up due to unfolding of the last part of the DNA blob. We use the velocity profile to estimate the uncertainty in determining the position of a feature along the DNA given its temporal location and demonstrate the error introduced by assuming a constant translocation velocity.

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

“…Ideally, the molecule will be slowed uniformly such that every point of the molecule travels at the same rate, providing simplicity for analysis. This research may prove very difficult, as any velocity measurement [106] will have to make use of a size marker on the DNA molecule, likely in the form of a radial protrusion or a nick in the DNA, both of which would alter the movement of a DNA molecule through the tight confines of a gel. Instead, it is possible that simulations would be able to determine the velocity profile of a translocating molecule.…”

Direct observation of DNA knots using a solid-state nanopore

“…Note that such a small knot size indicates that the DNA knots in these long DNA polymers are remarkably tight. The numbers may underestimate the size of the knots somewhat, especially for those which occur at the end of the translocation process where we know that the velocity is higher than average 41,42 . Measurements on circular versions of the same molecules in the same conditions reveal similar distributions of very tight knots (Supplementary Section 6).…”

Graphene nanodevices for DNA sequencing

“…Also, the DNA molecule's movement is not completely confined, leading to positional fluctuations and variation in translocation velocity [40]. As temporal signals are interpreted into spatial information, this could be a serious problem for ionic current detection.…”