Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity

Abstract

Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (Kd: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.

Statistical mechanics of dimerizations and its consequences for small systems

“…Yet with recent advancements of technology experimental studies, able to conduct and monitor associations of the type shown in Eq. 1 in systems with small numbers of reactants, reported that bound products are observed at higher concentrations than predicted by the expression of K mentioned above [4][5][6][7][8][9][10][11] . Different explanations were put forward that include conformational changes of the unbound molecule(s), non-fluorescent bindings, and missed events due to transient interactions 12 .…”

“…We note the validity of the 'classical' translation approximation diminishes with decreasing temperature, mass, and volume. In Section SI-2 of the ESI † we analyze and check the equality of eqn (12). Although for the vast majority of molecular systems this equality seems to hold to an acceptable degree of accuracy, there are special cases of low molecular weight gases (such as hydrogen and helium) at low temperatures and confined to small volumes for which the 'classical' approximation yields large discrepancies.…”

“…Yet with recent advancements of technology, experimental studies, able to conduct and monitor associations of the type shown in eqn (1) in systems with small numbers of reactants, reported that bound products are observed at higher concentrations than predicted by the expression of K mentioned above. [4][5][6][7][8][9][10][11][12] Different explanations were put forward that include conformational changes of the unbound molecule(s), non-fluorescent bindings, and missed events due to transient interactions. 13,14 Several theoretical studies proposed that small systems, attributed to be stochastic in nature, are characterized by equilibrium constants different than that observed for a macroscopic system, which attributed to be deterministic.…”

Mechanosensing view of SARS-CoV-2 infection by a DNA nano-assembly

“…In addition, the developed strategy can be used to evaluate the efficacy of neutralizing antibodies and other neutralizing agents. Moreover, leveraging delicate DNA nanostructures and superior aptamers, 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 multifaceted efforts are expected to unravel the infection mechanisms of more disease-causing pathogens.…”

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

“…We surmise that the zeptoreactor used here may serve as a spatial restriction to enforce the direct destabilizing interaction between ethylene glycol and a G-quadruplex. We anticipate that the DNA origami zeptoreactor described here can reveal detailed interactions between ligands and nanoconfined biomolecules, 30 which occur frequently in nanocavities of enzymes and other protein machineries in cells.…”