Driven DNA Transport into an Asymmetric Nanometer-Scale Pore

Abstract

To understand the mechanism by which individual DNA molecules enter nanometer-scale pores, we studied the concentration and voltage dependence of polynucleotide-induced ionic-current blockades of a single alpha-hemolysin ion channel. We find that the blockade frequency is proportional to the polymer concentration, that it increases exponentially with the applied potential, and that DNA enters the pore more readily through the entrance that has the larger vestibule. We also measure the minimum value of the electrical potential that confines a modified polymer inside the pore against random diffusion and repulsive forces.

Nonequilibrium dynamics of polymer translocation and straightening

“…We should note, however, in the problem of biopolymer transport through a membrane pore, the role of specific interactions may become essentially important [9,10,13]. We neglect all the complications associated with such a factor and focused on universal aspects as a consequence of a polymeric nature, in this sense, the present analysis may be regarded as an "ideal" version in view of the relation with the problem of polymer translocation.…”

“…Our target here is the dynamical process, in which a polymer is sucked into a localized hole. This is different from the pulling the chain's one end [8], but similar in the way how the chain responds to the local force, and, in fact, relevant to the dynamics of polymer translocation through hole [9,10] and the adsorption process to a small particle. (In this case, the force f is related to the chemical potential change ∆µ due to the absorption via f = ∆µ/b.)…”

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

“…Experimental articles published since that review have furthered our knowledge about this process. For instance, Kasianowicz' group [6] has determined that the rate of entry of ssDNA into an a-hemolysin channel increases linearly with DNA concentration and exponentially with the voltage difference applied along the channel. They also found that the rate of entry is higher when the DNA enters the channel through the protein's larger vestibule rather than through the other end.…”

Controlling molecular transport through nanopores

“…This allowed determination of the minimum voltage required to keep a DNA -avidin complex trapped in an a-haemolysin nanopore to be around 70 mV [33]. A very similar approach can be used to immobilize a DNA strand and thus identify which of the four bases of DNA is located in the constriction [34,35].…”

“…Nevertheless, this can be very useful for very specific questions about the molecular structure. One of the first experiments by Henrickson et al [33] demonstrated that DNA can be stalled in a protein nanopore in 2000.…”