Crowding-induced polymer trapping in a channel

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.

Automated summary

This work reports an intriguing phenomenon of crowding-induced polymer trapping in channels, where crowding particles push the polymer into channel corners through an effective polymer-corner attraction. The occurrence of polymer trapping depends on the minimum volume fraction of crowders, which scales with crowder and monomer diameters. The nearly fully stretched polymer conformation resulting from polymer trapping may have practical applications, such as in nanochannel-based genome mapping technologies.