Citation: Zefeng Gu, Anchen Fu, Ru Qiu, Ru Sun, Zhijuan Cao. Facile and diverse logic circuits based on dumbbell DNA-templated fluorescent copper nanoclusters and S1 nuclease detection[J]. Chinese Chemical Letters, ;2022, 33(5): 2711-2714. doi: 10.1016/j.cclet.2021.09.020 shu

Facile and diverse logic circuits based on dumbbell DNA-templated fluorescent copper nanoclusters and S1 nuclease detection

Shanghai Key Laboratory of Bioactive Small Molecules & Department of Pharmaceutical Analysis, School of Pharmacy, Fudan University, Shanghai 201203, China

zjcao@fudan.edu.cn

Received Date: 14 June 2021
Revised Date: 16 August 2021
Accepted Date: 4 September 2021
Available Online: 10 September 2021

Figures(4)

DNA-based logic gates promote the development of molecular computing and show enormous potential in the fields of nanotechnology and biotechnology. Dumbbell oligonucleotides (DNA) with poly-thymine (poly-T) loops and a nicked random double strand have been demonstrated to be an efficient template for the formation of fluorescent copper nanoclusters (CuNCs) in our previous work. Herein, a new platform technology is presented with which to construct molecular logic gates by employing CuNCs probe as a basic output generator, coupling of functional nucleases as the inputs. Two dumbbell DNAs are used with the difference in stem length (8 bp and 16 bp, respectively). The degradation of DNA templates can be tuned by various nucleic acid enzymes, single-stranded nuclease (S1), double-stranded specific nuclease (DSN), E. coli DNA ligase, exonucleases Ⅰ and Ⅲ. Briefly, S1 can digest both DNA templates, while the cleavage ability of DSN will be resistant by the short stem of SS-DNA (short-stem DNA). Exonuclease Ⅰ and Ⅲ can degrade these two nicked DNA templates, which are inhibited due to the ligation of E. coli DNA ligase. With this novel strategy, a set of logic gates is successfully constructed at the molecular level, including "YES", "PASS 0", "OR", "INHIBIT", which take the advantages of no label, easy operation, fast speed, high efficiency and low cost. Furthermore, S1 nuclease, as the biomarker of numerous carcinogens, is selectively detected in the range of 0.05–50 U/mL with the detection limit of 0.005 U/mL (1 × 10⁻⁶ U) based on this platform.
- Logic gates,
- Dumbbell DNA templates,
- Poly-thymine loops,
- Copper nanoclusters,
- Nucleic acid enzymes
1. [1]
  D.L. Ma, H.Z. He, D.S.H. Chan, C.H. Leung, Chem. Sci. 4 (2013) 3366. doi: 10.1039/c3sc50924a
2. [2]
  U. Pischel, Angew. Chem. Int. Ed. 46 (2007) 4026–4040. doi: 10.1002/anie.200603990
3. [3]
  A.P. de Silva, Molecular Logic-based Computation, Royal Society of Chemistry, Cambridge, UK, 2013.
4. [4]
  A.P. de Silva, H.Q.N. Gunaratne, C.P. McCoy, Nature 364 (1993) 42–44. doi: 10.1038/364042a0
5. [5]
  L.M. Adleman, Science 266 (1994) 1021–1024. doi: 10.1126/science.7973651
6. [6]
  S. Erbas-Cakmak, S. Kolemen, A.C. Sedgwick, et al., Chem. Soc. Rev. 47 (2018) 2228. doi: 10.1039/C7CS00491E
7. [7]
  A.P. de Silva, N.D. McClenaghan, Chem. Eur. J. 10 (2004) 574–586. doi: 10.1002/chem.200305054
8. [8]
  P.L. Gentili, J. Phys. Chem. A 112 (2008) 11992–11997. doi: 10.1021/jp806772m
9. [9]
  M. Pita, S. Minko, E. Katz, J. Mater. Sci. Mater. Med. 2009, 20 (2) 457–462. doi: 10.1007/s10856-008-3579-y
10. [10]
  H. Komatsu, S. Matsumoto, S. Tamaru, et al., J. Am. Chem. Soc. 131 (2009) 5580–5585. doi: 10.1021/ja8098239
11. [11]
  H. Li, S. Guo, Q. Liu, et al., Adv. Sci. 2 (2015) 1500054. doi: 10.1002/advs.201500054
12. [12]
  R. Peng, X. Zheng, Y. Lyu, et al., J. Am. Chem. Soc. 140 (2018) 9793–9796. doi: 10.1021/jacs.8b04319
13. [13]
  D. Fan, E. Wang, S. Dong, Mater. Horiz. 6 (2019) 375. doi: 10.1039/c8mh01151f
14. [14]
  D. Fan, E. Wang, S. Dong, ACS Appl. Mater. Interfaces 9 (2017) 1322. doi: 10.1021/acsami.6b14317
15. [15]
  S. Mailloux, Y.V. Gerasimova, N. Guz, D.M. Kolpashchikov, E. Katz, Angew. Chem. Int. Ed. 54 (2015) 6562–6566. doi: 10.1002/anie.201411148
16. [16]
  H. Li, W. Hong, S. Dong, Y. Liu, E. Wang, ACS Nano 8 (2014) 2796–2803. doi: 10.1021/nn406523y
17. [17]
  X. Bu, Y. Fu, X. Jiang, H. Jin, R. Gui, Microchim. Acta 187 (2020) 154. doi: 10.1007/s00604-020-4146-6
18. [18]
  M. Zhang, B.C. Ye, Chem. Commun. 48 (2012) 3647–3649. doi: 10.1039/c2cc17906g
19. [19]
  A.A. Tregubov, I.P. Nikitin, M.P. Nikitin, Chem. Rev. 118 (2018) 10294. doi: 10.1021/acs.chemrev.8b00198
20. [20]
  S. Yang, C.R. Yang, D. Huang, et al., Chem. Eur. J. 25 (2019) 5389–5405. doi: 10.1002/chem.201804420
21. [21]
  C.R. Yang, L.B. Song, J.C. Chen, et al., NPG Asia Mater. 10 (2018) 497–508. doi: 10.1038/s41427-018-0051-4
22. [22]
  D. Huang, C.R. Yang, Y. Yao, et al., Chem. Eur. J. 25 (2019) 6996–7003. doi: 10.1002/chem.201900734
23. [23]
  M.M. Lv, W.J. Zhou, D.Q. Fan, et al., Adv. Mater. 32 (2020) 1908480. doi: 10.1002/adma.201908480
24. [24]
  B. Ani, T. Bürgi, Nanoscale 13 (2021) 6283–6340. doi: 10.1039/D0NR08489A
25. [25]
  C. Ma, M. Chen, H. Liu, et al., Chin. Chem. Lett. 29 (2018) 136–138. doi: 10.1016/j.cclet.2017.09.012
26. [26]
  C. Qiao, L. Jing, E.K. Wang, Biosens. Bioelectron. 132 (2019) 333–342. doi: 10.1016/j.bios.2019.01.046
27. [27]
  S. Kim, J.H. Kim, W.Y. Kwon, et al., Microchim. Acta 186 (2019) 479–479. doi: 10.1007/s00604-019-3620-5
28. [28]
  Y.N. Wang, H.Y. Cui, Z.J. Cao, C. Lau, J.Z. Lu, Talanta 154 (2016) 574–580. doi: 10.1016/j.talanta.2015.12.067
29. [29]
  P.C. Ray, A. Fortner, G.K. Darbha, J. Phys. Chem. B 110 (2006) 20745–20748. doi: 10.1021/jp065121l
30. [30]
  Z. Bartosova, L. Krejci, FEBS Lett. 588 (2014) 2446–2456. doi: 10.1016/j.febslet.2014.06.010
31. [31]
  Z. Gu, Z. Cao, Anal. Bioanal. Chem. 410 (2018) 4991–4999. doi: 10.1007/s00216-018-1149-9
32. [32]
  X. Qiu, H. Zhang, H. Yu, T. Jiang, Y. Luo, Trends Biotechnol. 33 (2015) 180–188. doi: 10.1016/j.tibtech.2014.12.008
33. [33]
  T. Nishino, K. Morikawa, Oncogene 21 (2002) 9022–9032. doi: 10.1038/sj.onc.1206135
34. [34]
  H. Zhang, C. Cheng, N.L. Dong, X.M. Ji, J.D. Hu, Biochem. Eng. J. 167 (2021) 107890. doi: 10.1016/j.bej.2020.107890
1. [1]
  Luyao Lu , Chen Zhu , Fei Li , Pu Wang , Xi Kang , Yong Pei , Manzhou Zhu . Ligand effects on geometric structures and catalytic activities of atomically precise copper nanoclusters. Chinese Journal of Structural Chemistry, 2024, 43(10): 100411-100411. doi: 10.1016/j.cjsc.2024.100411
2. [2]
  Zhihui Zhang , Ru Sun , Chong Bian , Hongbo Wang , Zhen Zhao , Panpan Lv , Jianzhong Lu , Haixin Zhang , Hulie Zeng , Yuanyuan Chen , Zhijuan Cao . A dual-protease-triggered chemiluminescent probe for precise tumor imaging. Chinese Chemical Letters, 2025, 36(2): 109784-. doi: 10.1016/j.cclet.2024.109784
3. [3]
  Xiaxue Chen , Yuxuan Yang , Ruolin Yang , Yizhu Wang , Hongyun Liu . Adjustable Polychromatic Fluorescence: Investigating the Photoluminescent Properties of Copper Nanoclusters. University Chemistry, 2024, 39(9): 328-337. doi: 10.3866/PKU.DXHX202308019
4. [4]
  Zhifeng CAI , Ying WU , Yanan LI , Guiyu MENG , Tianyu MIAO , Yihao ZHANG . Effective detection of malachite green by folic acid stabilized silver nanoclusters. Chinese Journal of Inorganic Chemistry, 2025, 41(5): 983-993. doi: 10.11862/CJIC.20240394
5. [5]
  Jing Guo , Zhi-Guo Lu , Rui-Chen Zhao , Bao-Ku Li , Xin Zhang . Nucleic acid therapy for metabolic-related diseases. Chinese Chemical Letters, 2025, 36(3): 109875-. doi: 10.1016/j.cclet.2024.109875
6. [6]
  Lihang Wang , Mary Li Javier , Chunshan Luo , Tingsheng Lu , Shudan Yao , Bing Qiu , Yun Wang , Yunfeng Lin . Research advances of tetrahedral framework nucleic acid-based systems in biomedicine. Chinese Chemical Letters, 2024, 35(11): 109591-. doi: 10.1016/j.cclet.2024.109591
7. [7]
  Yao HUANG , Yingshu WU , Zhichun BAO , Yue HUANG , Shangfeng TANG , Ruixue LIU , Yancheng LIU , Hong LIANG . Copper complexes of anthrahydrazone bearing pyridyl side chain: Synthesis, crystal structure, anticancer activity, and DNA binding. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 213-224. doi: 10.11862/CJIC.20240359
8. [8]
  Yiyue Ding , Qiuxiang Zhang , Lei Zhang , Qilu Yao , Gang Feng , Zhang-Hui Lu . Exceptional activity of amino-modified rGO-immobilized PdAu nanoclusters for visible light-promoted dehydrogenation of formic acid. Chinese Chemical Letters, 2024, 35(7): 109593-. doi: 10.1016/j.cclet.2024.109593
9. [9]
  Dexuan Xiao , Tianyu Chen , Tianxu Zhang , Sirong Shi , Mei Zhang , Xin Qin , Yunkun Liu , Longjiang Li , Yunfeng Lin . Transdermal treatment for malignant melanoma by aptamer-modified tetrahedral framework nucleic acid delivery of vemurafenib. Chinese Chemical Letters, 2024, 35(4): 108602-. doi: 10.1016/j.cclet.2023.108602
10. [10]
  Hanqing Zhang , Xiaoxia Wang , Chen Chen , Xianfeng Yang , Chungli Dong , Yucheng Huang , Xiaoliang Zhao , Dongjiang Yang . Selective CO2-to-formic acid electrochemical conversion by modulating electronic environment of copper phthalocyanine with defective graphene. Chinese Journal of Structural Chemistry, 2023, 42(10): 100089-100089. doi: 10.1016/j.cjsc.2023.100089
11. [11]
  Huimin Luan , Qinming Wu , Jianping Wu , Xiangju Meng , Feng-Shou Xiao . Templates for the synthesis of zeolites. Chinese Journal of Structural Chemistry, 2024, 43(4): 100252-100252. doi: 10.1016/j.cjsc.2024.100252
12. [12]
  Pei Cao , Yilan Wang , Lejian Yu , Miao Wang , Liming Zhao , Xu Hou . Dynamic asymmetric mechanical responsive carbon nanotube fiber for ionic logic gate. Chinese Chemical Letters, 2024, 35(6): 109421-. doi: 10.1016/j.cclet.2023.109421
13. [13]
  Kai Wang , Yun Wang , Lihang Wang , Zhuhai Li , Xi Yu , Xuanhe You , Diwei Wu , Yueming Song , Jiancheng Zeng , Zongke Zhou , Shishu Huang , Yunfeng Lin . Therapeutic siRNA targeting CC chemokine receptor 2 loaded with tetrahedral framework nucleic acid alleviates neuropathic pain by regulating microglial polarization. Chinese Chemical Letters, 2025, 36(3): 109868-. doi: 10.1016/j.cclet.2024.109868
14. [14]
  Yuxin Wang , Zhengxuan Song , Yutao Liu , Yang Chen , Jinping Li , Libo Li , Jia Yao . Methyl functionalization of trimesic acid in copper-based metal-organic framework for ammonia colorimetric sensing at high relative humidity. Chinese Chemical Letters, 2024, 35(6): 108779-. doi: 10.1016/j.cclet.2023.108779
15. [15]
  Weijian Zhang , Xianyu Deng , Liying Wang , Jian Wang , Xiuting Guo , Lianggui Huang , Xinyi Wang , Jun Wu , Linjia Jiang . Poly(ferulic acid) nanocarrier enhances chemotherapy sensitivity of acute myeloid leukemia by selectively targeting inflammatory macrophages. Chinese Chemical Letters, 2024, 35(9): 109422-. doi: 10.1016/j.cclet.2023.109422
16. [16]
  Wenya Jiang , Jianyu Wei , Kuan-Guan Liu . Atomically precise superatomic silver nanoclusters stabilized by O-donor ligands. Chinese Journal of Structural Chemistry, 2024, 43(9): 100371-100371. doi: 10.1016/j.cjsc.2024.100371
17. [17]
  Rakesh Kumar Gupta , Zhi Wang , Di Sun . Shining bright: Revolutionary near-unity NIR phosphorescent metal nanoclusters. Chinese Journal of Structural Chemistry, 2024, 43(11): 100417-100417. doi: 10.1016/j.cjsc.2024.100417
18. [18]
  Jun-Jie Fang , Yun-Peng Xie , Xing Lu . Organooxotin and cobalt/manganese heterometallic nanoclusters exhibiting single-molecule magnetism. Chinese Journal of Structural Chemistry, 2025, 44(4): 100515-100515. doi: 10.1016/j.cjsc.2025.100515
19. [19]
  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
20. [20]
  Cheng Cheng , Nasir Ali , Ji Liu , Juan Qiao , Ming Wang , Li Qi . Construction of degradable liposome-templated microporous metal-organic frameworks with commodious space for enzymes. Chinese Chemical Letters, 2024, 35(11): 109812-. doi: 10.1016/j.cclet.2024.109812

Get Citation

PDF

XML

Metrics

PDF Downloads(1)
Abstract views(1018)
HTML views(80)

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