Citation: Kuangdi Luo, Yang Qin, Xuehao Zhang, Hanxu Ji, Heao Zhang, Jiangtian Li, Xianjin Xiao, Xinyu Wang. Regulable toehold lock for the effective control of strand displacement reaction sequence and circuit leakage[J]. Chinese Chemical Letters, ;2024, 35(7): 109104. doi: 10.1016/j.cclet.2023.109104 shu

Regulable toehold lock for the effective control of strand displacement reaction sequence and circuit leakage

Kuangdi Luo ^{a, b, 1} ,
Yang Qin ^{b, d, 1} ,
Xuehao Zhang ^{b, e} ,
Hanxu Ji ^{b, e} ,
Heao Zhang ^b ,
Jiangtian Li ^b ,
Xianjin Xiao ^{a, b, c, *,} ,
Xinyu Wang ^{a, *,}

a.
Department of Breast Surgery, Second Hospital of Jilin University, Changchun 130041, China
b.
Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
c.
Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
d.
Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
e.
School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China

xiaoxianjin@hust.edu.cn

410802898@qq.com

Received Date: 17 June 2023
Revised Date: 12 September 2023
Accepted Date: 14 September 2023
Available Online: 16 September 2023

Figures(4)

Strand displacement reaction enables the construction of enzyme-free DNA reaction networks, thus has been widely applied to DNA circuit and nanotechnology. It has the characteristics of high efficiency, universality and regulatability. However, the existing regulation tools cannot enable effective control of the reaction sequence, which undoubtedly limits the construction of complex nucleic acid circuits. Herein, we developed a regulation tool, toehold lock, and achieved strict control of reaction sequence without loss of the main reaction signal output. Furthermore, we applied the tool to scenarios such as seesaw circuits, AND/OR logic gates, and entropy-driven circuits, and respectively demonstrated its significant superiority compared to the original method. We believe that the proposed toehold lock has greatly optimized the efficiency of DNA strand displacement-based networks, and we anticipate that the tool will be widely used in multiple fields.
- DNA circuit,
- Toehold lock,
- DNA strand displacement,
- Reaction sequence,
- Seesaw circuit
1. [1]
  J. Zhang, M. Hou, G. Chen, J. Chen, et al., Chin. Chem. Lett. 32 (2021) 3474–3478. doi: 10.1016/j.cclet.2021.04.056
2. [2]
  L. Li, S. Li, J. Wang, et al., Chin. Chem. Lett. 34 (2023) 108399. doi: 10.1016/j.cclet.2023.108399
3. [3]
  Z. Lv, M. Huang, P. Li, et al., Chin. Chem. Lett. 35 (2024) 108601. doi: 10.1016/j.cclet.2023.108601
4. [4]
  X. Zheng, J. Yang, C. Zhou, et al., Nucleic Acids Res. 47 (2019) 1097–1109. doi: 10.1093/nar/gky1245
5. [5]
  H. Wang, H. Wang, Q. Wu, et al., Chem. Sci. 10 (2019) 9597–9604. doi: 10.1039/c9sc03552d
6. [6]
  J. Pan, D. Bao, E. Bao, J. Chen, Analyst 146 (2021) 3673–3678. doi: 10.1039/d1an00028d
7. [7]
  E. Del Grosso, A.M. Dallaire, Nano Lett. 15 (2015) 8407–8411. doi: 10.1021/acs.nanolett.5b04566
8. [8]
  A. Baccouche, K. Montagne, A. Padirac, T. Fujii, Y. Rondelez, Methods 67 (2014) 234–249. doi: 10.1016/j.ymeth.2014.01.015
9. [9]
  T. Song, A. Eshra, S. Shah, J. Reif, et al., Nat. Nanotechnol. 14 (2019) 1075–1081. doi: 10.1038/s41565-019-0544-5
10. [10]
  D.Y. Zhang, E. Winfree, J. Am. Chem. Soc. 131 (2009) 17303–17314. doi: 10.1021/ja906987s
11. [11]
  T. Luo, S. Fan, Y. Liu, J. Song, Nanoscale 13 (2021) 2100–2112. doi: 10.1039/d0nr07865d
12. [12]
  E. Del Grosso, P. Irmisch, S. Gentile, et al., Angew. Chem. Int. Ed. 61 (2022) e202201929. doi: 10.1002/anie.202201929
13. [13]
  F.C. Simmel, B. Yurke, H.R. Singh, Chem. Rev. 119 (2019) 6326–6369. doi: 10.1021/acs.chemrev.8b00580
14. [14]
  D.Y. Zhang, R.F. Hariadi, H.M. Choi, E. Winfree, Nat. Commun. 4 (2013) 1965. doi: 10.1038/ncomms2965
15. [15]
  X. Gong, S. He, R. Li, et al., Chem. Sci. 13 (2022) 10428–10436. doi: 10.1039/d2sc03757b
16. [16]
  Q. Wu, L. Yang, L. Xie, F. Wang, et al., Small 18 (2022) e2200983. doi: 10.1002/smll.202200983
17. [17]
  Y. Wang, Y. Chen, Y. Wan, et al., ACS Appl. Mater. Interfaces 14 (2022) 31727–31736. doi: 10.1021/acsami.2c08523
18. [18]
  M. Oishi, K. Nakatani, Small 15 (2019) e1900490. doi: 10.1002/smll.201900490
19. [19]
  Y.X. Liu, T.J. Xie, C.H. Li, et al., Anal. Chim. Acta 1154 (2021) 338319. doi: 10.1016/j.aca.2021.338319
20. [20]
  Y. Sun, S. Qi, X. Dong, et al., J. Hazard. Mater. 443 (2023) 130252. doi: 10.1016/j.jhazmat.2022.130252
21. [21]
  J. Fern, R. Schulman, Nat. Commun. 9 (2018) 3766. doi: 10.1038/s41467-018-06218-w
22. [22]
  H. Yang, L. Wen, X. Wang, et al., Mikrochim. Acta 189 (2022) 50. doi: 10.1007/s00604-021-05150-z
23. [23]
  W.E. Arter, Y. Yusim, Q. Peter, et al., ACS Nano 14 (2020) 5763–5771. doi: 10.1021/acsnano.0c00628
24. [24]
  Z. Dong, X. Xu, J. Ni, et al., J. Mater. Chem. B 11 (2022) 204–210.
25. [25]
  Y. Xie, G. Xie, J. Yuan, et al., Anal. Chim. Acta 1232 (2022) 340449. doi: 10.1016/j.aca.2022.340449
26. [26]
  F. Li, Y. Chen, J. Shang, et al., Anal. Chem. 94 (2022) 4495–4503. doi: 10.1021/acs.analchem.2c00037
27. [27]
  Y. Zhang, Y. Feng, Y. Liang, J. Yang, C. Zhang, Nanomaterials 11 (2021) 2955. doi: 10.3390/nano11112955
28. [28]
  Y.S. Ang, J.J. Li, P.J. Chua, et al., Anal. Chem. 90 (2018) 6193–6198. doi: 10.1021/acs.analchem.8b00722
29. [29]
  A. Lopiccolo, B. Shirt-Ediss, E. Torelli, et al., Nat. Commun. 12 (2021) 4861. doi: 10.1038/s41467-021-25023-6
30. [30]
  M.C. Inniss, P.A. Silver, Curr. Biol. 23 (2013) R812–R816. doi: 10.1016/j.cub.2013.06.047
31. [31]
  R.U. Sheth, H.H. Wang, Nat. Rev. Genet. 19 (2018) 718–732. doi: 10.1038/s41576-018-0052-8
32. [32]
  P. Siuti, J. Yazbek, T.K. Lu, Nat. Biotechnol. 31 (2013) 448–452. doi: 10.1038/nbt.2510
33. [33]
  A. Padirac, T. Fujii, Y. Rondelez, Proc. Natl. Acad. Sci. U. S. A. 109 (2012) E3212–E3220. doi: 10.1073/pnas.121206910
34. [34]
  A.R. Chandrasekaran, O. Levchenko, D.S. Patel, M. MacIsaac, K. Halvorsen, Nucleic Acids Res. 45 (2017) 11459–11465. doi: 10.1093/nar/gkx777
35. [35]
  L. Ceze, J. Nivala, K. Strauss, Nat. Rev. Genet. 20 (2019) 456–466. doi: 10.1038/s41576-019-0125-3
36. [36]
  L. Qian, E. Winfree, Science 332 (2011) 1196–1201. doi: 10.1126/science.1200520
37. [37]
  H. Hu, L. Liu, L. Zhang, et al., Nano Res. 16 (2023) 865–872. doi: 10.1007/s12274-022-4761-0
38. [38]
  C. Zhang, Z. Wang, Y. Liu, et al., J. Am. Chem. Soc. 141 (2019) 17189–17197. doi: 10.1021/jacs.9b07521
39. [39]
  D.Y. Zhang, A.J. Turberfield, B. Yurke, E. Winfree, Science 318 (2007) 1121–1125. doi: 10.1126/science.1148532
40. [40]
  F. Deng, J. Pan, Z. Liu, L. Zeng, J. Chen, Biosens. Bioelectron. 223 (2023) 115025. doi: 10.1016/j.bios.2022.115025
41. [41]
  K.M. Cherry, L. Qian, Nature 559 (2018) 370–376. doi: 10.1038/s41586-018-0289-6
42. [42]
  C. Zou, Q. Zhang, C. Zhou, W. Cao, Nanoscale 14 (2022) 6585–6599. doi: 10.1039/d1nr06861j
43. [43]
  X. Liu, K.K. Parhi, IEEE Trans. Biomed. Circuits Syst. 14 (2020) 490–503. doi: 10.1109/tbcas.2020.2979485
44. [44]
  S. Liu, C. Xin, X. Yu, Z. Ding, S. Liu, Analyst 144 (2019) 5923–5927. doi: 10.1039/c9an01568j
45. [45]
  A. Amodio, E. Del Grosso, A. Troina, E. Placidi, F. Ricci, Nano Lett. 18 (2018) 2918–2923. doi: 10.1021/acs.nanolett.8b00179
1. [1]
  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. Chinese Chemical Letters, 2024, 35(5): 108826-. doi: 10.1016/j.cclet.2023.108826
2. [2]
  Minghao Hu , Tianci Xie , Yuqiang Hu , Longjie Li , Ting Wang , Tongbo Wu . Allosteric DNAzyme-based encoder for molecular information transfer. Chinese Chemical Letters, 2024, 35(7): 109232-. doi: 10.1016/j.cclet.2023.109232
3. [3]
  Chang Liu , Tao Wu , Lijiao Deng , Xuzi Li , Xin Fu , Shuzhen Liao , Wenjie Ma , Guoqiang Zou , Hai Yang . Programmed DNA walkers for biosensors. Chinese Chemical Letters, 2024, 35(9): 109307-. doi: 10.1016/j.cclet.2023.109307
4. [4]
  Jia-Li Xie , Tian-Jin Xie , Yu-Jie Luo , Kai Mao , Cheng-Zhi Huang , Yuan-Fang Li , Shu-Jun Zhen . Octopus-like DNA nanostructure coupled with graphene oxide enhanced fluorescence anisotropy for hepatitis B virus DNA detection. Chinese Chemical Letters, 2024, 35(6): 109137-. doi: 10.1016/j.cclet.2023.109137
5. [5]
  Xiaohong Wen , Mei Yang , Lie Li , Mingmin Huang , Wei Cui , Suping Li , Haiyan Chen , Chen Li , Qiuping Guo . Enzymatically controlled DNA tetrahedron nanoprobes for specific imaging of ATP in tumor. Chinese Chemical Letters, 2024, 35(8): 109291-. doi: 10.1016/j.cclet.2023.109291
6. [6]
  Jingwen Zhao , Jianpu Tang , Zhen Cui , Limin Liu , Dayong Yang , Chi Yao . A DNA micro-complex containing polyaptamer for exosome separation and wound healing. Chinese Chemical Letters, 2024, 35(9): 109303-. doi: 10.1016/j.cclet.2023.109303
7. [7]
  Tian Feng , Yun-Ling Gao , Di Hu , Ke-Yu Yuan , Shu-Yi Gu , Yao-Hua Gu , Si-Yu Yu , Jun Xiong , Yu-Qi Feng , Jie Wang , Bi-Feng Yuan . Chronic sleep deprivation induces alterations in DNA and RNA modifications by liquid chromatography-mass spectrometry analysis. Chinese Chemical Letters, 2024, 35(8): 109259-. doi: 10.1016/j.cclet.2023.109259
8. [8]
  Zhe-Han Yang , Jie Yin , Lei Xin , Yuanfang Li , Yijie Huang , Ruo Yuan , Ying Zhuo . Research advancement of DNA-based intelligent hydrogels: Manufacture, characteristics, application of disease diagnosis and treatment. Chinese Chemical Letters, 2024, 35(10): 109558-. doi: 10.1016/j.cclet.2024.109558
9. [9]
  Zhenjie Yang , Chenyang Hu , Xuan Pang , Xuesi Chen . Sequence design in terpolymerization of ε-caprolactone, CO₂ and cyclohexane oxide: Random ester-carbonate distributions lead to large-span tunability. Chinese Chemical Letters, 2024, 35(5): 109340-. doi: 10.1016/j.cclet.2023.109340
10. [10]
  Na Wang , Wang Luo , Huaiyi Shen , Huakai Li , Zejiang Xu , Zhiyuan Yue , Chao Shi , Hengyun Ye , Leping Miao . Crystal engineering regulation achieving inverse temperature symmetry breaking ferroelasticity in a cationic displacement type hybrid perovskite system. Chinese Chemical Letters, 2024, 35(5): 108696-. doi: 10.1016/j.cclet.2023.108696
11. [11]
  Rui Wang , Yang Liang , Julius Rebek Jr. , Yang Yu . Stabilization and detection of labile reaction intermediates in supramolecular containers. Chinese Chemical Letters, 2024, 35(6): 109228-. doi: 10.1016/j.cclet.2023.109228
12. [12]
  Yi Zhang , Biao Wang , Chao Hu , Muhammad Humayun , Yaping Huang , Yulin Cao , Mosaad Negem , Yigang Ding , Chundong Wang . Fe–Ni–F electrocatalyst for enhancing reaction kinetics of water oxidation. Chinese Journal of Structural Chemistry, 2024, 43(2): 100243-100243. doi: 10.1016/j.cjsc.2024.100243
13. [13]
  Xianxu Chu , Lu Wang , Junru Li , Hui Xu . Surface chemical microenvironment engineering of catalysts by organic molecules for boosting electrocatalytic reaction. Chinese Chemical Letters, 2024, 35(8): 109105-. doi: 10.1016/j.cclet.2023.109105
14. [14]
  Kebo Xie , Qian Zhang , Fei Ye , Jungui Dai . A multi-enzymatic cascade reaction for the synthesis of bioactive C-oligosaccharides. Chinese Chemical Letters, 2024, 35(6): 109028-. doi: 10.1016/j.cclet.2023.109028
15. [15]
  Zhao Li , Huimin Yang , Wenjing Cheng , Lin Tian . Recent progress of in situ/operando characterization techniques for electrocatalytic energy conversion reaction. Chinese Chemical Letters, 2024, 35(9): 109237-. doi: 10.1016/j.cclet.2023.109237
16. [16]
  Kunsong Hu , Yulong Zhang , Jiayi Zhu , Jinhua Mai , Gang Liu , Manoj Krishna Sugumar , Xinhua Liu , Feng Zhan , Rui Tan . Nano-engineered catalysts for high-performance oxygen reduction reaction. Chinese Chemical Letters, 2024, 35(10): 109423-. doi: 10.1016/j.cclet.2023.109423
17. [17]
  Xiao Li , Wanqiang Yu , Yujie Wang , Ruiying Liu , Qingquan Yu , Riming Hu , Xuchuan Jiang , Qingsheng Gao , Hong Liu , Jiayuan Yu , Weijia Zhou . Metal-encapsulated nitrogen-doped carbon nanotube arrays electrode for enhancing sulfion oxidation reaction and hydrogen evolution reaction by regulating of intermediate adsorption. Chinese Chemical Letters, 2024, 35(8): 109166-. doi: 10.1016/j.cclet.2023.109166
18. [18]
  Jing Cao , Dezheng Zhang , Bianqing Ren , Ping Song , Weilin Xu . Mn incorporated RuO₂ nanocrystals as an efficient and stable bifunctional electrocatalyst for oxygen evolution reaction and hydrogen evolution reaction in acid and alkaline. Chinese Chemical Letters, 2024, 35(10): 109863-. doi: 10.1016/j.cclet.2024.109863
19. [19]
  Zizhuo Liang , Fuming Du , Ning Zhao , Xiangxin Guo . Revealing the reason for the unsuccessful fabrication of Li3Zr2Si2PO12 by solid state reaction. Chinese Journal of Structural Chemistry, 2023, 42(11): 100108-100108. doi: 10.1016/j.cjsc.2023.100108
20. [20]
  Guan-Nan Xing , Di-Ye Wei , Hua Zhang , Zhong-Qun Tian , Jian-Feng Li . Pd-based nanocatalysts for oxygen reduction reaction: Preparation, performance, and in-situ characterization. Chinese Journal of Structural Chemistry, 2023, 42(11): 100021-100021. doi: 10.1016/j.cjsc.2023.100021

Get Citation

PDF

XML

Metrics

PDF Downloads(1)
Abstract views(85)
HTML views(2)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142