Velocity of DNA during Translocation through a Solid-State
Nanopore
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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