Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 276

Fig. 11.25 (a) Water flow velocity profiles between DNA and pore (3-nm-radius) surfaces, when
E ¼ 0.02 ( open triangles ) and 0.08 ( filled triangles ) V/nm. The pore surface is neutral. (b) DNA
translocation through a solid-state nanopore coated with a single-wall carbon nanotube

driving force was reduced by the hydrodynamic drag of the electro-osmotic flow
along the DNA surface. Simulations further demonstrate that the effective electric
driving force is

the mobility. This
proposed hydrodynamic effect was confirmed in experiments that showed different
effective driving forces on DNA in pores with different sizes [ 38 ], indicating a
hydrodynamic effect.
Besides the pore size, the hydrodynamic drag force on DNA could be affected by
other boundary conditions of the flow, such as surface charge density and rough-
ness. It was shown in simulations that the effective driving force decreases when the
surface charge density of a pore changes from a negative to a positive value [ 39 ]
and increases when the surface becomes rougher [ 37 ]. More importantly, micro-
scopic interactions between DNA and a nanopore surface could result in irregular
motion of DNA or even immobilize DNA. However, a steady and controllable
motion of DNA inside a nanopore is critical for the ultimate success of the
nanopore-based DNA sequencing method. To avoid or reduce such an unfavorable
interaction, a solid-state nanopore might be coated with a single-walled carbon
nanotube (SWCNT) that provides a smooth surface, reducing surface imperfections
of a solid (Fig. 11.25b ). Potentially, SWCNT modification of a pore surface could
reduce the adhesive and frictional forces between DNA and a nanopore, yielding a
steadier translocation of DNA. Note that DNA translocation through a SWCNT has
been demonstrated experimentally [ 40 ], but the dynamics of that motion is still not
clear and deserves further study.

xm ,where x is the friction coefficient and m

11.2.3 Magnetic Tweezers

Although optical tweezers can drive DNA through a solid-state nanopore at an
arbitrarily slow speed [ 36 ], it is difficult to scale such assay to large number of