Control of DNA Strand Displacement Kinetics Using Toehold Exchange

TLDR

DNA is increasingly used as an engineering material for nanoscale circuits, where enzyme‑free constructions rely on strand displacement reactions whose kinetics can be tuned by toeholds, and the recently introduced toehold exchange enables fast, reversible displacement. The study characterizes DNA toehold exchange kinetics and models it as a three‑step process. The authors model toehold exchange as a three‑step process and demonstrate its use by building a simple catalytic reaction. The model accurately predicts the kinetics of 85 strand displacement reactions and enhances understanding of nucleic acid reaction kinetics, aiding rational design of dynamic DNA and RNA circuits and nanodevices.

Abstract

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.