Design and Analysis of Localized DNA Hybridization Chain Reactions

Theoretical models of localized DNA hybridization reactions on nanoscale substrates indicate potential benefits over conventional DNA hybridization reactions. Recently, a few approaches have been proposed to speed‐up DNA hybridization reactions; however, experimental confirmation and quantification of the acceleration factor have been lacking. Here, a system to investigate localized DNA hybridization reactions on a nanoscale substrate is presented. The system consists of six metastable DNA hairpins that are tethered to a long DNA track. The localized DNA hybridization reaction of the proposed system is triggered by a DNA strand which initiates the subsequent self‐assembly. Fluorescence kinetics indicates that the half‐time completion of a localized DNA hybridization chain reaction is six times faster than the same reaction in the absence of the substrate. The proposed system provides one of the first known quantification of the speed‐up of DNA hybridization reactions due to the locality effect. Localized DNA hybridization chain reactions are experimentally demonstrated to have six times speed‐up over nonlocalized DNA reactions. With the goal of increasing the reaction rates, a surface‐bound method by tethering metastable DNA hairpins to a long DNA track is shown to influence the reaction rate via thermal equilibrium gel data and real‐time fluorescence kinetic studies.