A study on reversibility and competition in DNA hybridization

Abstract

DNA origami is a promising assembly technique for nanofabrication that folds a single-stranded DNA template into a target structure by annealing it with many short ‘staple’ strands. Consequently, the design of a target structure can be programmed by design of the sequence of staple strands. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A key challenge is the possible occurrence of misfolded structures that are kinetically trapped. The problem can in principle be avoided if assembly pathway and kinetics are fully understood and then rationally optimized. The hybridization of staples to the scaffold is fundamental to the formation of DNA origami structures. In order to shed light on the DNA origami folding pathways, especially on the reversibility of hybridization, this study intentionally builds the process by simultaneously adding two sets of staples for two target one-helix origami structures, forcing competition. Stochastic simulation algorithm (SSA) is used for such discrete processes. By comparing the final equilibrium of the simulation, relative preference of structures were compared. The presented work demonstrates how a simplified DNA origami system is modelled and validated by applying the stochastic simulation algorithm and how the reversibility and competition of hybridization are explored by analyzing different parameters in kinetics and thermodynamics, which includes sequence of scaffold, strand displacement, relative position of two sets of staple and temperature.

Date of Award	2018
Original language	English
Awarding Institution	The Hong Kong University of Science and Technology