Biomedical Engineering Reference
In-Depth Information
during polymer passage to its local structure and properties. Since solid-state
nanopores were first reported in 2001, the vast majority of publications have been
focused on DNA translocation through large nanopores (10-20 nm), in which
typical transport times correspond to average DNA speeds of 10-50 ns / bp, largely
governed by hydrodynamics of the DNA polymer [
7
,
13
,
26
,
45
]. Here we focus on
the dynamics of DNA translocation through nanopores with sub-5 nm diameters,
where dsDNA transport must be linear (folded molecules cannot enter small pores).
In this regime, interactions of the DNA with the pore walls significantly slow down
its average translocation speed, (0.1-1
s/bp) [
2
,
12
,
16
], thus enhancing the
resolution of the method (electrical measurements of low ion current levels are
not practical below ~1
m
s due to noise), allowing the investigation of a broader
range of DNA lengths.
As shown in Fig.
10.1
, our system consists of a single solid-state nanopore in a SiN
membrane [
23
,
25
,
44
]. DNA translocation is characterized by recording ion current
as a function of time, and by analysis of the distributions of two main parameters,
t
D
and
I
B
, which are the transport time and fractional pore current, respectively
(
I
B
¼ ihi ihi
m
, where
i
b
is the mean blocked current and
i
o
is the mean open pore
current). In Fig.
10.11
, we display
I
B
vs.
t
D
scatter plots measured for 8,000 bp
DNA through nanopores with two indicated diameters (
V ¼
=
21
C)
[
49
]. Three salient features emerge upon decreasing the pore size from 8 to 4 nm:
(1) An increase in the contrast of the signal in the 4 nm pore (highlighted by
decreasing values of
I
B
from 0.9 to 0.5). (2) For the 8 nm pore, DNA can enter in
both folded and unfolded configurations, whereas in the 4 nm pore, only unfolded
events are observed. The ion current distributions of the 8 nm pore exhibit multiple
peaks, whereas the 4 nm pore exhibits a single peak (Fig.
10.11
right-hand panel).
300 mV,
T ¼
Fig. 10.11 Translocation scatter plots of 8 kbp dsDNA through 8 and 4 nm solid-state nanopores
(
V ¼
300 mV). The
I
B
histograms are given on the
right hand panel
, where for the 8 nm pore, both
folded (F) and unfolded (U) events are shown. Reproduced with permission from Wanunu et al.
[
49
], Copyright Elsevier Inc
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