Robustness of Localized DNA Strand Displacement Cascades

Abstract

Colocalization can strongly alter the kinetics and efficiency of chemical processes. For instance, in DNA-templated synthesis unfavorable reactions are sped up by placing reactants into close proximity onto a DNA scaffold. In biochemistry, clustering of enzymes has been demonstrated to enhance the reaction flux through some enzymatic cascades. Here we investigate the effect of colocalization on the performance of DNA strand displacement (DSD) reactions, an important class of reactions utilized in dynamic DNA nanotechnology. We study colocalization by immobilizing a two-stage DSD reaction cascade comprised of a “sender” and a “receiver” gate onto a DNA origami platform. The addition of a DNA (or RNA) input strand displaces a signal strand from the sender gate, which can then transfer to the receiver gate. The performance of the cascade is found to vary strongly with the distance between the gates. A cascade with an intermediate gate distance of ≈20 nm exhibits faster kinetics than those with larger distances, whereas a cascade with smaller distance is corrupted by excessive intraorigami leak reactions. The 20 nm cascade is found to be considerably more robust with respect to a competing reaction, and implementation of multiple receiver gates further increases this robustness. Our results indicate that for the 20 nm distance a fraction of signal strands is transferred locally to a receiver gate on the same platform, probably involving direct physical contact between the gates. The performance of the cascade is consistent with a simple model that takes “local” and “global” transfer processes into account.

Microscopic agents programmed by DNA circuits

“…The competition between global and local effects has already been pointed out for other tethered DNA systems 33 and imposes constraints on the miniaturization of molecular programming approaches.…”

Modular verification of chemical reaction network encodings via serializability analysis

“…Designs such as this that do not meet our criteria may be investigated further, to see if they are indeed flawed or if there may be a weaker version of our conditions that they do satisfy. Analyses such as ours are particularly important for low copy-number systems, such as surface-tethered strand displacement networks that have recently been proposed [40, 41] and implemented in the laboratory [42]. …”

DNA nanotechnology: understanding and optimisation through simulation

“…For example, displacement reactions have recently been reported in the context of unconventional left-handed super-helices formed by conventional B-DNA domains in a complex pseudoknotted structure 181 -such a system would an ideal candidate for study with oxDNA. Other possibilities include studying the influence of single-stranded hairpins, which are frequently present both by accident and design, on hybridisation and displacement kinetics, and considering general properties of displacement cascades on surfaces 94 . oxDNA's strengths are its efficiency and good overall representation of the structural, mechanical and thermodynamic changes associated with short duplex formation.…”