Crowding-induced polymer trapping in a channel

JL Chen and L Sun and SM Wang and FJ Tian and HQ Zhu and RQ Zhang and L Dai, PHYSICAL REVIEW E, 104, 054502 (2021).

DOI: 10.1103/PhysRevE.104.054502

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, 0*, which scales as 0* - (ac/Lp)1/3 for ac > am and 0* - (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, 0* is estimated to be around 0.25 for crowders with ac = 2 nm. We find that 0* also strongly depends on the shape of the channel cross section, and 0* 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.

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