Crowding-induced polymer trapping in a channel

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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Detail(s)

Original languageEnglish
Article number054502
Journal / PublicationPhysical Review E
Volume104
Issue number5
Online published8 Nov 2021
Publication statusPublished - Nov 2021

Abstract

In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, Φ*, which scales as Φ* ∼ (ac/Lp)1/3 for ac ≫ am and Φ* ∼ (ac/Lp)1/3(ac/am)1/2 for ac ≪ am, where ac is the crowder diameter, am is the monomer diameter, and Lp is the polymer persistence length. For DNA, Φ* is estimated to be around 0.25 for crowders with ac = 2 nm. We find that Φ* also strongly depends on the shape of the channel cross section, and Φ* is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.

Research Area(s)

  • FREE-ENERGY, GENE-EXPRESSION, DNA-MOLECULES, NANOCHANNEL, CHAIN, CONFINEMENT, STATE, CONFORMATION, COMPACTION, EXTENSION