The translocation dynamics of the polymer through a conical pore: Non-stuck, weak-stuck, and strong-stuck modes

Abstract

The external voltage-driven polymer translocation through a conical pore (with a large opening at the entry and a small tip at the exit) is studied by using the Langevin dynamics simulation in this paper. The entire translocation process is divided into an approaching stage and a threading stage. First, the approaching stage starts from the polymer entering the large opening and ends up at a terminal monomer reaching the pore tip. In this stage, the polymer will undergo the conformation adjustment to fit the narrowed cross-sectional area of the pore, leading to three approaching modes: the non-stuck mode with a terminal monomer arriving at the pore tip smoothly, the weak-stuck mode for the polymer stuck inside the pore for a short duration with minor conformational adjustments, and the strong-stuck mode with major conformational changes and a long duration. The approaching times (the duration of the approaching stage) of the three approaching modes show different behavior as a function of the pore apex angle. Second, the threading stage describes that the polymer threads through the pore tip with a linear fashion. In this stage, an increase in the apex angle causes the reduction of the threading time (the duration of the threading stage) due to the increase in the driving force with the apex angle at the tip. Moreover, we also find that with the increase in the apex angle or the polymer length, the polymer threading dynamics will change from the quasi-equilibrium state to the non-equilibrium state.

Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions

“…As the apex angle (see Fig. 1 a) is varied, the translocation time shows non-monotonic features, consistent with earlier reports 41 , 60 – 63 . We comment on the detailed behavior of the waiting time distribution with varying force strengths and .…”

“…Further, the passage time is a non-monotonic function of the apex angle of the cone for a given length of the channel. Langevin dynamics studies of flexible polymer translocation through conical channels have shown that translocation is dependent on channel structure and interactions of the polymer with the channel 41 , 62 , 63 . Most biopolymers and proteins are however semiflexible with an energy cost associated in bending, characterized by the bending rigidity of the polymer.…”

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

“…Having a high voltage applied across the pore might result in false translocation events. Furthermore, as mentioned earlier, a cone-like shape only allows a few nucleotides around the one that is translocating due to the narrow constriction at the end [ 181 , 182 ], which enhances the accuracy of the current measurement.…”

Translocation, Rejection and Trapping of Polyampholytes

“…If a sequence remains engaged in the channel for a long time, we consider it to be trapped [37] and it has to escape through energy barriers opposing both translocation and rejection. The distribution of sojourn times under a random uncorrelated force (the time distributions discussed here are not self-averaging) is discussed in [32].…”