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.
The dense medium modulates the molecular structure and bioreactions in living cells via both noncovalent interactions and macromolecular crowding and confinement effects. However, the interplay between the volume effect and noncovalent interactions remains unclear. In this work, we studied in detail on how electrostatic interactions influence the crowding and confinement effect by comparing the formation and elongation of DNA nanotubes in branched dextran and charged hyaluronic acid (HA) solution of a broad concentration range, with and without 150 mM NaCl. In all the studied cases, three concentration regimes are identified: a crowding regime, a double-effect regime, and a confinement regime. In the crowding and double-effect regimes, the addition of 150 mM NaCl enhances the assembly of DNA tiles by screening the electrostatic repulsion, and a higher dextran solution is required to confine the DNA assembly into nanotubes. However, the screening effect on the HA network is more than that on the DNA assembly, so DNA tubes formed in HA solution at much lower concentrations. In the confinement regime, the electrostatic interaction exhibits a negligible effect on the DNA assembly in both dextran medium and HA medium. Our study demonstrates that the volume effect and noncovalent interactions are system specific and concentration dependent. Their interplay governs the living processes in crowded cells.
With the application of surface acoustic wave (SAW) of 39.5 MHz to a model polymer liquid film, polyisobutylene, deposited on the solid substrates, the liquid film is densified, proved by the decrease of film thickness and the increase of refractive index, measured by ellipsometry. Rotational motion of fluorescent probes doped inside the liquid film, measured by polarization-resolved single molecule fluorescence microscopy, is retarded and the dynamical heterogeneity is reduced. It is demonstrated that the application of SAW of high frequency makes the thin polymeric liquid film densified and more dynamically homogeneous.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.