DNA dynamics and computation based on toehold-free strand displacement

Hong Kang; Tong Lin; Xiaojin Xu; Qing-Shan Jia; Richard Lakerveld; Bryan Wei

doi:10.1038/s41467-021-25270-7

DNA dynamics and computation based on toehold-free strand displacement

Nat Commun. 2021 Aug 17;12(1):4994. doi: 10.1038/s41467-021-25270-7.

Authors

Hong Kang¹, Tong Lin^{1

2}, Xiaojin Xu², Qing-Shan Jia³, Richard Lakerveld⁴, Bryan Wei⁵

Affiliations

¹ School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.
² Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
³ Center for Intelligent and Networked Systems, Department of Automation, Beijing National Research Center for Information Science and Technology (BNRist), Tsinghua University, Beijing, China. jiaqs@tsinghua.edu.cn.
⁴ Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China. r.lakerveld@ust.hk.
⁵ School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China. bw@tsinghua.edu.cn.

Abstract

We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA / chemistry*
Electrophoresis
Molecular Dynamics Simulation
Nanostructures*
Recombination, Genetic

Substances

DNA