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, Φ*, which scales as Φ* ∼ (a_c/L_p)^1/3 for a_c ≫ a_m and Φ* ∼ (a_c/L_p)^1/3(a_c/a_m)^1/2 for a_c ≪ a_m, where a_c is the crowder diameter, a_m is the monomer diameter, and L_p is the polymer persistence length. For DNA, Φ* is estimated to be around 0.25 for crowders with a_c = 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.