Solid-State Nanopores: Methods of Fabrication and Integration, and Feasibility Issues in DNA Sequencing - Nanopores: Sensing and Fundamental Biological Interactions - page 192

constant of the DNA is now set by the bead, which is a lot smaller. For a 1 m

polystyrene bead in water, D ~10 5 nm 2 /s, 1,000-fold less. In this case, the required
translocation velocity v is about 200 bp/

m

s for single-base resolution. If one relaxes
the resolution to 3 bases, the desired translocation speed is ~10 bp/

m

m s, which is about

m

half what is typical for solid-state nanopores (~20-25 bp/ s at 120 mV).

The above estimates are encouraging for HANS sequencing using solid-state
nanopores: if 6-mer probes are used, one should be able to resolve the probe location
to within half its size. Combined with the known sequence information of each
probes, reconstruction of the sequence for the test DNA should be entirely feasible.
The absolutely necessary requirement here is the 1,000-fold reduction in diffusion
constant when the DNA is held under tension in the “reverse translocation” proce-
dure. It should be pointed out that the direction of translocation can still be forward,
in the direction of electric force, as long as the DNA is held under tension.

8.5 Recent Experiments on Constrained DNA
Translocation and Hybridization Detection

A key issue in the field of nanopore technology is how to control the DNA
translocation processes. Here the discussions will be on the DNA-on-bead approach
as the basic concept in controlling DNA translocation through a nanopore. One can
control the bead motion using laser trap (Keyser et al. [ 28 ]) or magnetic field (Peng
and Ling, [ 27 ]). The optical tweezers approach is more convenient, but the absorp-
tion of laser light by the buffer causes the ionic current through the pore to fluctuate
dramatically (Keyser et al. [ 28 ]). Thus it is difficult to simultaneously measure ionic
current while the DNA is being dragged in a dynamic fashion.

8.5.1 Reverse DNA Translocation Through a Solid-State
Nanopore by Magnetic Tweezers

The basic concept of the experiment by Peng and Ling [ 27 ] is shown in Fig. 8.11 .
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. Since one can construct a magnetic field gradient over a large space,
this technique is inherently applicable to large number of addressable nanopores.