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

Abstract

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.

Catalytic confinement effects in nanochannels: from biological synthesis to chemical engineering

“…36 Meantime, the high concentration causes the synergy of the crowding effects and confinement effects, which influence the reaction production together. 37 And also, the nanochannels limit the volume or size of the molecular and make the reactants to be arranged in a certain order. Liu et al proposed a concept of ordered-assembly reaction (OAR) based on frontier molecular orbital theory (FMO).…”

Macromolecular Crowding and Confinement Effect on the Growth of DNA Nanotubes in Dextran and Hyaluronic Acid Media

“…The procedures on surface modification and TIRFM detection can be found in our previous paper. 45 Viscosity of Dextran and HA. The viscosities of polymer solutions, i.e., HA and dextran dissolved in 1× TAE buffer and 1× TAE + 150 mM NaCl buffer, are measured at 25 °C on an Anton Paar Physica MCR301 rheometer (Anton Paar GmbH, Austria).…”

“…Even though such branched structures are also formed by end-toend or end-to-side connections (Figures S1 and S2), they are not observed in media of linear polymers, such as polyacrylamide. 44,45 As the dextran concentration reaches a certain value, only linear DNA tubes are formed (Figure 2E,F′). With further increasing dextran concentration, the length of the DNA tubes became shorter (Figure 2F,G,G′).…”

“…The three regimes with increasing polymer concentration can be attributed to crowding regime, double-effect regime, and confinement regime, on the basis of the effective pore size of the network formed by polymers compared with the diameter of DNA nanotubes. 45 If the polymer chains do not form a network or the effective pore size of the formed network is much larger than the diameter of DNA tubes, the assembly of DNA tiles is controlled mainly by the crowding effect. With increasing polymer concentration, the pore size becomes comparable or smaller than the tube diameter, and the growth of the DNA tube is hindered.…”

“…Our previous study on PAM and PEO indicates that the critical pore size is about 2∼3 times the diameter of the DNA tube. 45 Therefore, the second regime is a transition stage and has a narrow concentration range. The borderlines of the regimes are dependent on the effective pore size of the network, which is not directly related to the c* and c e values (the dotted vertical lines in Figures 3 and 5) that divide polymer solution into dilute, semidilute, and concentrated regions.…”