Crowding and Confinement Effects in Different Polymer Concentration Regimes and Their Roles in Regulating the Growth of Nanotubes

Among numerous research studies focusing on macromolecular crowding and confinement, few are concerned with the medium at a broad range of concentrations, let alone the interplay between the crowding effect and confinement effect. In this work, we systematically studied the assembly of DNA tiles into nanotubes in polyethylene oxide (PEO) and polyacrylamide (PAM) media covering the concentration range of dilute, semidilute, and concentrated regimes. In light of the structure and kinetics of DNA assembly, both the PEO and PAM media can be divided into three regimes with increasing polymer concentration: the crowding regime, double-effect regime, and confinement regime. In the crowding regime, DNA tiles only form clusters because the assembly into a tube structure is hindered. In the double-effect regime, polymer chains form a transient network whose pore size is close to the diameter of DNA nanotubes. The confinement effect, together with the crowding effect, facilitates the assembly of DNA tiles into a tube structure. In the confinement regime, the length of DNA tubes decreases with polymer concentration, which can be quantitatively described by a scaling relationship. The borderlines of the three regimes are polymer-specific. The PEO medium enters the double-effect regime and confinement regime at concentrations much lower than the PAM medium, suggesting that the PEO medium exhibits stronger macromolecular crowding and confinement effects. We attribute it to the special hydrophilicity of PEO, which has the capability to couple with the lattice structure of a water network, leading to a decrease in thermal motion and hence a mutual stabilization.