Electro-osmotic screening of the DNA charge in a nanopore

Abstract

Extensive all-atom molecular dynamics simulations were performed to characterize the microscopic origin of the force experienced by DNA in a bulk electrolyte and a solid-state nanopore when subject to an external electrostatic field E. The effective screening of the DNA charge was found to originate from the hydrodynamic drag of the electroosmotic flow that is driven by the motion of counterions along the surface of DNA. We show that the effective driving force F in a nanopore obeys the same law as in a bulk electrolyte: F = ξμE, where ξ and μ are the friction coefficient and electrophoretic mobility of DNA, respectively. Using this relationship, we suggest a method for determining the effective driving force on DNA in a nanopore that does not require a direct force measurement.

Event distributions of polymer translocation

“…If one uses Manning condensation leading to drastic charge reduction [19,20] to relate this to experiments, in the α-HL pore a typical pore potential of ≈ 120 mV would correspond tof tot ≈ 5 pN. In the light of recent computer simulations the reduction of the effective force inside the α-HL pore is not predominantly caused by the Manning condensation but by electro-osmotic flow that is driven by the motion of counterions along the surface of DNA [21,22]. However, experiments indicate that the estimate based on Manning condensation is in the right order of magnitude [23].…”

Translocation of short and long polymers through an interacting pore

“…Depending on the charge of the pore walls, there might exist an electro-osmotic flow which can either help or resist the polymer translocation. This effect is expected to be an important effect in synthetic pores 15,16 , which may be highly charged, but the relea) Electronic mail: damien.foster@u-cergy.fr vance to biological pores, such as α-hemolysin, is still debated [17][18][19] . Since the electro-osmotic flow depends on the external-field strength, it is difficult to isolate the effect of electro-osmosis when translocating charged polymers in an external field.…”

Reluctance of a neutral nanoparticle to enter a charged pore

“…This will also be justified by our later finding that the neutral particle is repelled by the uniformly charged membrane and pore surfaces and hence the energetically most favorable translocation path (e.g. driven by thermal noise) will be along the pore axis [19,[25][26][27][28]. Second, we restrict ourselves to steady state (time-independent) situations, and we assume, similarly as in Refs.…”

“…Second, we restrict ourselves to steady state (time-independent) situations, and we assume, similarly as in Refs. [6,25,27,28], that the particle itself does not to exhibit any notable proper motion within the relaxation time of its environment. In other words, the particle position is a model parameter rather than a dynamical variable.…”