Citation: Yang Qin, Jiangtian Li, Xuehao Zhang, Kaixuan Wan, Heao Zhang, Feiyang Huang, Limei Wang, Hongxun Wang, Longjie Li, Xianjin Xiao. Toeless and reversible DNA strand displacement based on Hoogsteen-bond triplex[J]. Chinese Chemical Letters, ;2024, 35(5): 108826. doi: 10.1016/j.cclet.2023.108826 shu

Toeless and reversible DNA strand displacement based on Hoogsteen-bond triplex

Yang Qin ^{a, b, 1} ,
Jiangtian Li ^{a, 1} ,
Xuehao Zhang ^c ,
Kaixuan Wan ^c ,
Heao Zhang ^a ,
Feiyang Huang ^a ,
Limei Wang ^c ,
Hongxun Wang ^c ,
Longjie Li ^{a, c, *,} ,
Xianjin Xiao ^{a, *,}

a.
Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
b.
Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
c.
Wuhan Polytechnic University, Wuhan 430023, China

lilongjie@whpu.edu.cn

xiaoxianjin@hust.edu.cn

Received Date: 1 June 2023
Revised Date: 17 July 2023
Accepted Date: 19 July 2023
Available Online: 20 July 2023

Figures(5)

Strand displacement reaction is a crucial component in the assembly of diverse DNA-based nanodevices, with the toehold-mediated strand displacement reaction representing the prevailing strategy. However, the single-stranded Watson-Crick sticky region that serves as the trigger for strand displacement can also cause leakage reactions by introducing crosstalk in complex DNA circuits. Here, we proposed the toeless and reversible DNA strand displacement reaction based on the Hoogsteen-bond triplex, which is compatible with most of the existing DNA circuits. We demonstrated that our proposed reaction can occur at pH 5 and can be reversed at pH 9. We also observed an approximately linear relationship between the degree of reaction and pH within the range of pH 5–6, providing the potential for precise regulation of the reaction. Meanwhile, by altering the sequence orientation, we have demonstrated that our proposed reaction can be initiated or regulated through the same toeless mechanism without the requirement for protonation in low pH conditions. Based on the proposed reaction principle, we further constructed a variety of DNA nanodevices, including two types of DNA logic gates that rely on pH 5/pH 9 changes for initiating and reversing: the AND gate and the OR gate. We also successfully constructed a DNA Walker based on our proposed reaction modes, which can move along a given track after the introduction of a programmable DNA sequence and complete a cycle after 4 steps. Our findings suggest that this innovative approach will have broad utility in the development of DNA circuits, molecular sensors, and other complex biological systems.
- DNA strand displacement,
- Toeless,
- Triplex DNA strands,
- Reversible,
- DNA circuit,
- DNA walker
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