Capture and Translocation of Nucleic Acids into Sub-5 nm Solid-State Nanopores - Nanopores: Sensing and Fundamental Biological Interactions - page 232

Fig. 10.3 Schematic
illustration of the process of
DNA capture into solid state
nanopores. The electrical
field near the pore (shaded
area) plays a crucial role in
determining the capture
dynamics. Reproduced with
permission from Wanunu
et al. [ 50 ], copyright Nature
Publishing Group

observed for capture of dsDNA of lengths 4-6 kbp and 48 kbp ( l -phage DNA) into

large solid-state pores (diameter 5 nm) [ 17 , 36 , 37 , 52 ]. More recent studies of the

capture mechanism of dsDNA capture into sub-5 nm solid-state nanopores have
revealed two distinct steps in DNA capture, as illustrated in Fig. 10.3 [ 50 ]:
1. As a DNA coil approaches the pore from bulk (i) to some critical radius r* larger
than the coil size r g , its motion transitions from purely diffusive motion to biased
diffusive motion, driven by the decaying electric field outside the pore. This field
is maintained by the ion current through the pore, which creates a potential
profile VðrÞ outside the pore mouth that attracts the DNA coil from a distance r* ,
where r* is orders of magnitude greater than Debye screening length scales
(0.1-1 nm). Thus, a DNA coil experiencing this field is “funneled” towards the
pore mouth (ii).
2. Once the DNA coil approaches the pore to within a distance of approximately
one r g , one DNA end must be threaded into the pore, a process that involves
crossing a free-energy barrier (iii).

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10.2.1 Theoretical Considerations

The arrival of the molecules from bulk to the pore mouth and the threading of one
end into the pore involve independent physical mechanisms. The rate-limiting
step (the slower of the two steps) determines the observed capture rate in