Citation: Huan Liu, Zhihao Ming, Yuanpeng Zhang, Qidong Xia, Hao Hu, Ruijie Liu, Yuheng Liao, Yizhou Liu, Xiao Liu, Xiaoping Zhang, Longjie Li, Shaogang Wang, Xianjin Xiao. Triplex-structure based DNA circuits with ultra-low leakage and high signal-to-noise ratio[J]. Chinese Chemical Letters, ;2024, 35(1): 108555. doi: 10.1016/j.cclet.2023.108555 shu

Triplex-structure based DNA circuits with ultra-low leakage and high signal-to-noise ratio

Huan Liu ^{a, 1} ,
Zhihao Ming ^{b, 1} ,
Yuanpeng Zhang ^{a, c, 1} ,
Qidong Xia ^b ,
Hao Hu ^a ,
Ruijie Liu ^a ,
Yuheng Liao ^a ,
Yizhou Liu ^a ,
Xiao Liu ^a ,
Xiaoping Zhang ^c ,
Longjie Li ^{a, d, *,} ,
Shaogang Wang ^{b, *,} ,
Xianjin Xiao ^{a, e, *,}

a.
Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
b.
Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
c.
Department and Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
d.
School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430030, China
e.
Department of Laboratory Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China

lilongjie@whpu.edu.cn

sgwangtjm@163.com

xiaoxianjin@hust.edu.cn

Received Date: 29 November 2022
Revised Date: 8 April 2023
Accepted Date: 9 May 2023
Available Online: 19 May 2023

Figures(5)

DNA circuits are powerful tools in various applications such as logical computation, molecular diagnosis and synthetic biology. Leakage is a major problem in constructing complex DNA circuits. It directly affects the output signal and harms the circuit's performance significantly. In the traditional DNA circuits, the gate complex is a duplex structure. There are insufficient energy barriers to prevent spontaneous detachment of strands, resulting in a leak prone. Herein, we have developed triplex-structure based DNA circuit with ultra-low leakage and high signal-to-noise ratio (SNR). The triplex structure improves the stability in the absence of input. At the same time, the driving force of the strand displacement cascades reduces the influence of the triplex structure on the desired reaction. The SNR of the DNA circuit was increased to 695, while the desired reaction rate remained 90% of the conventional translator circuit. The triplex-structure mediated leakage prevention strategy was further tested at different temperatures and in DNA translator and seesaw circuits. We also constructed modular basic logic gates with a high efficiency and low leakage. On this basis, we further constructed triplex-structure based tertiary DNA logic circuits, and the SNR reached 295, which, to the best of our knowledge, was among the highest of the field. We believe that our scheme provides a novel, valid, and general tool for reducing leakages, and we anticipate that it will be widely adopted in DNA nanotechnology.
- Leakage,
- DNA strand displacement cascades,
- Triplex,
- DNA circuits,
- Molecular programming
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