Zeptoliter DNA Origami Reactor to Reveal Cosolute Effects on Nanoconfined G-Quadruplexes

Abstract

Cellular environments such as nanoconfinement and molecular crowding can change biomolecular properties. However, in nanoconfinement, it is extremely challenging to investigate effects of crowding cosolutes on macromolecules. By using optical tweezers, here, we elucidated the effects of hexaethylene glycol (HEG) on the mechanical stability of a telomeric G-quadruplex (GQ) in a zeptoliter DNA origami reactor (zepto-reactor). When HEG molecules were introduced in the GQ-containing zepto-reactor at different positions, we found that the GQ species split into two equilibrated populations, reflecting diverse effects of the oligoethylene glycol on the GQ via either a long-range dehydration effect or direct interactions. When the number of HEG molecules was increased, the stability of the GQ unexpectedly decreased, suggesting that the direct destabilizing interaction between the GQ and HEG is dominating over the long-range stabilizing dehydration effects of the HEG in hydrophilic nanocavities. These findings indicate that a nanoconfined environment can alter regular effects of cosolutes on biomacromolecules.

Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers

“…We note that DNA nanostructure 74 , 75 , DNA micelle 76 , protein organelle 77 , protein nanopore 78 , viral 79 , vesicle 80 , MOFs 81 , and polymersome 82 nanoreactors or zeptoreactors 83 have been explored before, but none with the specific advantages provided by DOL. Viral capsids have encapsulated single enzymes 79 and hollow DNA origami have encapsulated exact numbers of enzymes within a cascade 84 , 85 but neither has yet enabled the exact number of reactants to be defined.…”

Digital nanoreactors for control over absolute stoichiometry and spatiotemporal behavior of receptors within lipid bilayers

“…Thus, while DOL could be examined with a single molecule technique, the DOL platform also enables a type of experiment whose window on the molecular world lies somewhere between that of a single molecule experiment and classical bulk technique ('single molecule in bulk assay'). We note that DNA nanostructure, 73,74 DNA micelle, 75 protein organelle, 76 protein nanopore, 77 viral, 78 vesicle, 79 MOFs 80 and polymersome 81 nanoreactors or zeptoreactors 82 have been explored before, but none with the specific advantages provided by DOL. Viral capsids have encapsulated single enzymes 78 and hollow DNA origami have encapsulated exact numbers of enzymes within a cascade 83,84 but neither has yet enabled the exact number of reactants to be defined.…”

“…We note that DNA nanostructure, 73,74 DNA micelle, 75 protein organelle, 76 protein nanopore, 77 viral, 78 vesicle, 79 MOFs 80 and polymersome 81 nanoreactors or zeptoreactors 82 have been explored before, but none with the specific advantages provided by DOL. Viral capsids have encapsulated single enzymes 78 and hollow DNA origami have encapsulated exact numbers of enzymes within a cascade 83,84 but neither has yet enabled the exact number of reactants to be defined.…”