Translocation of links through a pore: effects of link complexity and size

Abstract

We have used Langevin dynamics to simulate the forced translocation of linked polymer rings through a narrow pore. For fixed size (i.e. fixed number of monomers) the translocation time depends on the link type and on whether the rings are knotted or unknotted. For links with two unknotted rings the crossings between the rings can slow down the translocation and are responsible for a delay as the crossings pass through the pore. The results fall on a set of relatively smooth curves for different link families with the translocation time not always increasing with crossings number within the same family. When one ring is knotted the results depend on whether the link is prime or composite and, for the composite case, they depend on whether the knotted or unknotted ring enters the pore first. We find a similar situation for 3-component links where the results depend on whether the link is prime or composite. These results contribute to our understanding of how the entanglement complexity between filaments impacts their translocation dynamics and should be useful for extending nanopore-sensing techniques to probe the topological properties of these systems.

RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration

“…Nanopore translocation is a powerful single-molecule probing technique that has been used in diverse contexts: from studying the physical response of homopolymers, − ,,, to the topological friction in chains with knots and links, ,− for sequencing and analyzing biopolymers’ secondary and tertiary structures, ,,,,− ,− , and study RNA, too. − ,− …”

RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration

“…Nanopore translocation is a powerful single-molecule probing technique that has been used in diverse contexts: from studying the physical response of homopolymers [19-21, 32, 34, 39], to the topological friction in chains with knots and links [33,[40][41][42][43][44][45][46][47][48], for sequencing and analyzing biopolymers' secondary and tertiary structures [7,11,29,41,[49][50][51][52][53][54][55][56][57], and study RNA too [1][2][3][4][6][7][8].…”

Tunable Knot Segregation in Copolyelectrolyte Rings Carrying a Neutral Segment

“…Convergent theoretical and experimental advancements have provided numerous and striking examples of how chain-uncrossability defines an impressive range of polymer properties. Topological constraints can endow linear and circular chains with peculiar relaxation kinetics, − and metric scaling behavior − and can affect very distinctively the response of chains to elongational flows, − mechanical stretching, − and pore translocation. − …”