Sprecher
Beschreibung
Metabolic compartmentalization enables the separation of pathways and components in the cell and is a key feature found throughout biology [1]. Compartments offer two primary advantages: isolation and condensation [2]. While the former shields the reaction from the environment, the latter typically increases the local concentration of reactants. In this study, we use a DNA origami compartment to model spatial confinement. The programmability of DNA opens unique opportunities to explore the effect of stoichiometry, segregation and spatial distribution on the internalized reaction [3]. Our compartment contains two DNA species, a sender and a receiver. Addition of a trigger strand initiates a DNA strand displacement (DSD) reaction that releases a transmitter from the sender complex. The transmitter then binds to the receiver complex, terminating the cascade. Since the DSD species are modified with fluorophores, the entire cascade is monitored by fluorescence spectroscopy. We hypothesize that the kinetics of the reaction and diffusion of the transmitter within the compartment or across its boundaries will be affected by the degree of permeability of the DNA walls and by the effective concentration of the species, which is determined by the spatial constraints. These aspects essentially represent the isolation and condensation features typically observed in natural compartments. To systematically examine these phenomena, we aim to modulate the permeability and internal dimensions of the DNA compartments through various strategies, including the addition of an miniscaffold-based inner layer of DNA helices [4], and to complement ensemble measurements with single-molecule FRET to investigate the process in detail.
- Bar-Peled, L., Kory, N. Nat Metab 4, 1232-1244 (2022).
- Ichihashi, N., Yomo, T. Curr Opin Chem Biol 22, 12-17 (2014).
- Huang, J., Gambietz, S., Sacca, B. Small 19, e2202253 (2023).
- Ke, Y. et al. Chem Sci 3, 2587-2597 (2012).
