Modelling DNA-strand displacement reactions from single base-pair steps to reaction networks

Abstract

DNA strand displacement reactions are the most abundantly used method to achieve dynamic switching in DNA-based nanotechnology. A single-stranded ‘invader' strand binds to the ‘toehold' overhang of a target strand and replaces a target-bound 'incumbent' strand. Hereby, complementarity of the invader to the single-stranded toehold provides the energetic bias of the reaction. Precise knowledge and easy tunability of the kinetics of the strand displacement process is highly important when establishing dynamic devices and complex chemical reaction networks.