Biomedical Engineering Reference
In-Depth Information
Fig. 11.26 Schematic of the
reverse DNA translocation
using magnetic tweezers.
Two reservoirs, filled with
ionic buffer, are separated by a
nanopore chip (shown in
gray
). Avoltage bias is applied
across the chip. DNAs (shown
as
wiggly lines
) attach to the
magnetic bead via standard
streptavidin-biotin bonds.
Electrical force
F
E
on the
DNA and magnetic force
F
M
on the magnetic bead are
drawn as thick
solid arrows
.
Adapted from [
41
]
nanopores. The basic concept of the magnetic tweezers approach [
41
] is shown in
Figure
11.26
. DNA molecules are attached to magnetic beads via the standard
streptavidin-biotin bonds. The free end of the DNA can be captured into the
nanopore by the applied electric field. Subsequently, one can apply a precisely
controlled magnetic force on the magnetic bead to balance the electrical force on
the trapped DNA, i.e., the DNA is in a tug-of-war between the magnetic bead and
the nanopore. By increasing the magnetic force further, or reducing the bias
voltage, until the magnetic force exceeds the electrical force, the DNA can be
pulled out of the nanopore from the
cis
side of the nanopore. In this way, the
minimized net force on the DNA and the hydrodynamic drag on the micron-sized
bead will slow down the motion of DNA while it is pulled out from the nanopore.
Since one can construct a magnetic field gradient over a large space, this technique
is inherently applicable to large number of addressable nanopores. By ramping the
magnetic field slowly, the DNAs in all the nanopores can be pulled out slowly
during one ramping step.
The experiment reported in [
41
] was done on a 12 nm size nanopore at 0.1 M
KCl in Tris-EDTA buffer at pH 8. Tween 20 was used to prevent the sticking of
magnetic bead to the surface of a nanopore chip. It is known [
42
-
44
] that the
presence of a DNA in a nanopore has two competing effects for the nanopore
conductance: the physical volume of the DNA leads to a reduction in total ion
population in the nanopore, thereby reducing nanopore conductance; the negatively
charged DNA brings in extra counterions, leading to a conductance enhancement.
The net effect of a translocating DNA on the nanopore conductance depends on the
ionic strength of the buffer solution. In the case of 0.1 M KCl that was used in
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