Capture and Translocation of Nucleic Acids into Sub-5 nm Solid-State Nanopores - Nanopores: Sensing and Fundamental Biological Interactions - page 248

We observed that for the longer DNA molecules, the increased Arrhenius slopes
for increasing DNA lengths in the t 2 regime can be qualitatively explained by
considering the environment outside the pore [ 49 ]. Recall that the potential outside
the pore exerts a significant force on the DNA coil outside the pore, effectively
squeezing it towards the membrane. The force on the coil results in stronger
interactions with the membrane that grow with the biopolymer length, increasing
the effective barrier for DNA translocation. We note, however, that although this
qualitative explanation is consistent with empirical observations, it has yet to be
modeled theoretically.
In addition to interactions with the interior walls of the pore, another important
factor which alters DNA dynamics arises from hydrodynamic interactions of
the confined DNA with counterion electroosmotic flow. The same field which
electrophoretically drives negatively-charged DNA through the pore also produces
cation flow in the opposite direction, which exerts a drag force on the biomolecule.
Luan and Aksimentiev have recently employed molecular dynamics (MD)
simulations to address this question [ 28 ]. The main features of their MD studies
are schematically shown in Fig. 10.17 . In bulk electrolyte solution, as well as in
nanopores, motion and forces of DNA are modeled by considering 20 bp DNA
[poly(dA)20-poly(dT)20] in 0.1 M KCl solution under an applied electric field.
The electrical force applied to the DNA was balanced by connecting the DNA to a
weak harmonic spring with a known spring constant, simulating optical tweezers.
Bead displacement was used to estimate the overall force, revealing that force
varied linearly with the applied electric field, with a proportionality constant
of 0.25 e .
Fig. 10.17 Molecular dynamics simulation of DNA in nanopore under applied electric field.
Water flow profile in three types of nanopores as a function of distance from the centre of DNA.
Circles : 2.25 nm radius pore, triangles : 3 nm radius pore with rough surface, and rhombus :3nm
radius pore with smooth walls. Open and closed symbols are simulations done at external electric
field values of 0.125 and 0.5 V/6.4 nm respectively. Reproduced with permission from Luan and
Aksimentiev [ 28 ], Copyright (2008) by the American Physical Society