Capture and Translocation of Nucleic Acids into Sub-5 nm Solid-State Nanopores - Nanopores: Sensing and Fundamental Biological Interactions - page 230

receiving chamber (“ trans ”). This process dictates the ultimate sensitivity of nanopore
detection; an extremely fast translocation speed may result in poor spatial resolution
and the inability to detect fine details of any biopolymer side-groups [ 5 ]. In contrast, a
sufficiently slow and steady translocation process would provide enough time for local
averaging over the stochastic noise associated with single molecule sensing, resulting
in superior device sensitivity.
Together, these two processes encompass the entirety of a molecule's progress to
and through the nanopore. Moreover, as our understanding of these processes
continues to develop, novel ways to manipulate and control the capture rate and
the translocation speed can be realized. Focusing on solid-state nanopores made in
inorganic membranes of silicon nitride, in this chapter we review the basic principles
affecting voltage driven DNA capture and DNA translocation. More specifically,
we focus here on nanopores roughly 5 nm in diameter, which exclusively allow
linear passage of double-stranded DNA. The capture and passage of linearized
biopolymers is distinctly different from transport of coiled or even partly folded
biopolymers, as the latter may involve multiple conformations or folded states
of the biopolymer, all of which are excluded from a purely linear passage.
This distinction is extremely important for many prominent applications of
nanopores, such as DNA sequencing, genome profiling, or mapping of DNA-bound
molecules [ 5 ].
In a typical solid-state nanopore experiment, a pair of electrodes is used to apply
an electrical potential

DV far away from the thin insulating membrane separating
the two chambers and containing the pore (Fig. 10.2a )[ 48 ]. Because the system is
suspended in a high ionic-strength electrolyte solution (e.g. physiological condi-
tions), even modest electrical potentials ( DV ~ 0.1 V) produce sufficiently large

local electrical fields in the pore (~10 5 V/cm) to overcome the free energy barrier
associated with stretching and threading extremely long, charged biopolymers into
the pore [ 17 , 37 ]. As a result, molecules like DNA and RNA will translocate from
the negatively biased cis into the trans chamber.
As a macromolecule enters the pore, its presence physically excludes a substantial
fraction of electrolytes from the pore, causing an abrupt blockade in the ionic current
flowing through the pore. Figure 10.2b displays the ionic current just before and after
the addition of 400 bp DNA molecules to the negatively biased cis chamber, using a
4 nm synthetic pore [ 49 ]. Upon addition of the DNAmolecules (see arrow) a series of
downwards spikes in the ionic current flowing through the pore are clearly visible.
Closer inspection of these current “blockades” (Fig. 10.2c ) reveals that a large
fraction of the current spikes remain at the blocked state for a relatively long
dwell-time ( t D ). This timescale was found to scale with DNA length, and to reduce
exponentially with the applied voltage [ 49 ]. Moreover, as we discuss in Sect. 10.4 ,
t D was also found to decrease exponentially with the pore diameter, d . Specifically, a
small change in pore size (e.g. 1 nm or less) results in a considerable change in dwell
time. These findings imply that t D represents the passage time (or the “translocation”
time) of each biopolymer from cis to trans . This was further confirmed by PCR
measurements of material from the trans chamber [ 49 ], similar to previous results
proving DNA translocation through protein pores [ 22 ].