Citation: Li Mengyin, Ying Yilun, Long Yi-Tao. Unveiling the Synergistic Effect from Key Sensing Regions in Aerolysin-Based Single Oligonucleotide Detection[J]. Acta Chimica Sinica, ;2019, 77(10): 984-988. doi: 10.6023/A19060202 shu

Unveiling the Synergistic Effect from Key Sensing Regions in Aerolysin-Based Single Oligonucleotide Detection

Li Mengyin ^a ,
Ying Yilun ^a,b ,
Long Yi-Tao ^a,b,,

a.
School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237
b.
State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023

Corresponding author: Long Yi-Tao, yitaolong@nju.edu.cn
Received Date: 8 June 2019
Available Online: 11 October 2019
Fund Project: the National Natural Science Foundation of China 61871183Project supported by the National Natural Science Foundation of China (Nos. 21834001, 61871183)the National Natural Science Foundation of China 21834001

Figures(5)

Nanopore technology are being developed for large areas in life science, not only in DNA sequencing and protein sequencing, but also in biomolecule detection, bio-interaction measurement and drug screening. Aerolysin is regarded as new powerful tool for oligonucleotide sensing and peptide sensing due to its high charged pore lumen. Applied a transmembrane potential with a pair of Ag/AgCl electrodes, the negatively charged oligonucleotides are driven into the aerolysin nanopore, inducing a series of ionic current blockages, which could distinguish the oligonucleotides with different length or single base variation. However, due to the lack of high-resolution structure of aerolysin nanopore, the mechanism of its high sensing capability is not clear, limiting the further applications of aerolysin. Recently, we presented two sensing regions inside aerolysin, R1 (near R220) and R2 (near K238), having huge influences on oligonucleotide sensing. Especially, the R1 is responsible for distinguished all 4 bases and 2 modified based in the mixture. However, the detailed mechanism of synergistic effect for these two regions in detection of single nucleotides is still unclear. Here, we use dA₁₄-4-X, dA₁₄-11-X, dA₁₄-4-X-11-X (X=C, T, G) as probes to investigate the effects of base types on the sensing ability of R1 and R2. The results show that the A, C or T in R2 region did not change the sensing ability of R1 region, while G in R2 would hinder the base discrimination in R1 region. This may be caused by the large volume of G that would nearly fully occupy the R2 region and the stronger non-covalent interaction between G and R2 region, resulting in determining the residual current of the whole nanopore. Moreover, we evaluated the interaction between different bases with the sensing region. The results show that the interaction is independent with the volume of the bases, which is ordered by A > G > C > T, suggesting the interaction inside the aerolysin lumen is a considerable factor for its sensing capability. These results would guide us to directly design the mutant Aerolysin nanopore that aims for DNA sequencing and peptide sequencing.
- nanopore,
- single-molecule interface,
- electro confinement,
- aerolysin,
- oligonucleotide
1. [1]
  Kasianowicz, J.; Brandin, E.; Branton, D.; Deamer, D. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 13770. doi: 10.1073/pnas.93.24.13770
2. [2]
  Bayley, H.; Cremer, P. Nature 2001, 413, 226. doi: 10.1038/35093038
3. [3]
  Cao, C.; Long, Y.-T. Acc. Chem. Res. 2018, 5, 331.
4. [4]
  Ying, Y.; Zhang, X.; Liu, Y.; Xue, M.; Li, H.; Long, Y.-T. Acta Chim. Sinica 2013, 71, 44.
5. [5]
  Gao, P.; Ma, Q.; Ding, D.; Wang, D.; Lou, X.; Zhai, T.; Xia, F. Nat. Commun. 2018, 9, 4557. doi: 10.1038/s41467-018-06873-z
6. [6]
  Cao, C.; Liao, D.-F.; Ying, Y.-L.; Long, Y.-T. Acta Chim. Sinica 2016, 74, 734.
7. [7]
  Deamer, D.; Branton, D. Acc. Chem. Res. 2002, 35, 817. doi: 10.1021/ar000138m
8. [8]
  Li, Q.; Lin, Y.; Ying, Y.-L.; Liu, S.-C.; Long, Y.-T. Sci. Sin. Chim. 2017, 47, 1445.
9. [9]
  Clarke, J.; Wu, H.-C.; Jayasinghe, L.; Patel, A.; Reid, S.; Bayley, H. Nat. Nanotechnol. 2009, 4, 265. doi: 10.1038/nnano.2009.12
10. [10]
  Manrao, E. A.; Derrington, I. M.; Laszlo, A. H.; Langford, K. W.; Hopper, M. K.; Gillgren, N.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H. Nat. Biotechnol. 2012, 30, 349. doi: 10.1038/nbt.2171
11. [11]
  Garalde, D. R.; Snell, E. A.; Jachimowicz, D.; Sipos, B.; Lloyd, J. H.; Bruce, M.; Pantic, N.; Admassu, T.; James, P.; Warland, A.; Jordan, M.; Ciccone, J.; Serra, S.; Keenan, J.; Martin, S.; McNeill, L.; Wallace, E. J.; Jayasinghe, L.; Wright, C.; Blasco, J.; Young, S.; Brocklebank, D.; Juul, S.; Clarke, J.; Heron, A. J.; Turner, D. J. Nat. Methods 2018, 15, 201. doi: 10.1038/nmeth.4577
12. [12]
  Sutherland, T. C.; Long, Y.-T.; Stefureac, R.-I.; Bediako-Amoa, I.; Kraatz, H.-B.; Lee, J. S. Nano Lett. 2004, 4, 1273. doi: 10.1021/nl049413e
13. [13]
  Yang, J.; Li, S.; Wu, X.-Y.; Long, Y.-T. Chin. J. Anal. Chem. 2017, 45, 1766. doi: 10.11895/j.issn.0253-3820.171201
14. [14]
  Pigue, F.; Ouldali, H.; Pastoriza-Gallego, M.; Manivet, P.; Pelta, J.; Oukhaled, A. Nat. Commun. 2018, 9, 966. doi: 10.1038/s41467-018-03418-2
15. [15]
  Li, S.; Cao, C.; Yang, J.; Long, Y.-T. ChemElectroChem 2018, 6, 126.
16. [16]
  Si, W.; Aksimentiev, A. ACS Nano 2017, 11, 7091. doi: 10.1021/acsnano.7b02718
17. [17]
  Hu, Z.; Du, J.; Ying, Y.; Peng, Y.; Cao, C.; Long, Y.-T. Acta Chim. Sinica 2017, 75, 1087.
18. [18]
  Wanunu, M.; Dadosh, T.; Ray, V.; Jin, J.; McReynolds, L.; Drndić, M. Nat. Nanotechnol. 2010, 5, 807. doi: 10.1038/nnano.2010.202
19. [19]
  Xi, D.; Shang, J.; Fan, E.; You, J.; Zhang, S.; Wang, H. Anal. Chem. 2016, 88, 10540. doi: 10.1021/acs.analchem.6b02620
20. [20]
  Uram, J.; Ke, K.; Hunt, A.; Mayer, M. Angew. Chem. 2006, 118, 2339. doi: 10.1002/ange.200502862
21. [21]
  Jiang, Y.; Feng, Y.; Su, J.; Nie, J.; Cao, L.; Mao, L.; Jiang, L.; Guo, W. J. Am. Chem. Soc. 2017, 139, 18739. doi: 10.1021/jacs.7b11732
22. [22]
  Stoddart, D.; Heron, A. J.; Mikhailova, E.; Maglia, G.; Bayley, H. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 7702. doi: 10.1073/pnas.0901054106
23. [23]
  Cao, C.; Li, M.-Y.; Cirauqui, N.; Wang, Y.-Q.; Peraro, M.; Tian, H.; Long, Y.-T. Nat. Commun. 2018, 9, 2823. doi: 10.1038/s41467-018-05108-5
24. [24]
  Maglia, G.; Restrepo, M.; Mikhailova, E.; Bayley, H. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 19720. doi: 10.1073/pnas.0808296105
25. [25]
  Derrington, I.; Butler, T.; Collins, M.; Manrao, E.; Pavlenok, M.; Niederweis, M.; Gundlach, J. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16060. doi: 10.1073/pnas.1001831107
26. [26]
  Duan, J.; Zhuo, S.; Yao, F.-J.; Zhang, Y.-N.; Kang, X.-F. Chin. J. Anal. Chem. 2016, 44, 1801.
27. [27]
  Gao, R.; Ying, Y.-L.; Yan, B.-Y.; Long, Y.-T. Chin. Sci. Bull. 2014, 59, 4968. doi: 10.1007/s11434-014-0656-0
28. [28]
  Zhang, Z.; Li, T.; Sheng, Y.; Liu, L.; Wu, H.-C. Small 2019, 15, 1804078. doi: 10.1002/smll.201804078
29. [29]
  Ying, Y.-L.; Chao, C.; Hu, Y.-X.; Long, Y.-T. Natl. Sci. Rev. 2018, 5, 450. doi: 10.1093/nsr/nwy029
30. [30]
  Iacovache, I.; Carlo, S.; Cirauqui, N.; Peraro, M.; van der Goot, G.; Zuber, B. Nat. Commun. 2016, 7, 12062. doi: 10.1038/ncomms12062
31. [31]
  Stefureac, R.; Long, Y.-T.; Kraatz, H. B.; Howard, P.; Lee, J. S. Biochemistry 2006, 60, 9172.
32. [32]
  Cressiot, B.; Braselmann, E.; Oukhaled, A.; Elcock, A. H.; Pelta, J.; Clark, P. L. ACS Nano 2015, 9, 9050. doi: 10.1021/acsnano.5b03053
33. [33]
  Fennouri, A.; Daniel, R.; Pastoriza-Gallego, M.; Auvray, L.; Pelta, J.; Bacri, L. Anal. Chem. 2013, 85, 8488. doi: 10.1021/ac4020929
34. [34]
  Baaken, G.; Halimeh, I.; Bacri, L.; Pelta, J.; Oukhaled, A.; Behrends, J. ACS Nano 2015, 9, 6443. doi: 10.1021/acsnano.5b02096
35. [35]
  Cao, C.; Ying, Y.-L.; Hu, Z.-L.; Liao, D.-F.; Tian, H.; Long, Y.-T. Nat. Nanotechnol. 2016, 11, 713. doi: 10.1038/nnano.2016.66
36. [36]
  Wang, Y.-Q.; Li, M.-Y.; Qiu, H.; Cao, C.; Wang, M.-B.; Wu, X.-Y.; Huang, J.; Ying, Y.-L.; Long, Y.-T. Anal. Chem. 2018, 90, 7790. doi: 10.1021/acs.analchem.8b01473
37. [37]
  Hu, Z.-L.; Li, Z.-Y.; Ying, Y.-L.; Zhang, J.; Cao, C.; Long, Y.-T.; Tian, H. Anal. Chem. 2018, 90, 4268. doi: 10.1021/acs.analchem.8b00096
1. [1]
  Jingwen Wang , Minghao Wu , Xing Zuo , Yaofeng Yuan , Yahao Wang , Xiaoshun Zhou , Jianfeng Yan . Advances in the Application of Electrochemical Regulation in Investigating the Electron Transport Properties of Single-Molecule Junctions. University Chemistry, 2025, 40(3): 291-301. doi: 10.12461/PKU.DXHX202406023
2. [2]
  Meijin Li , Xirong Fu , Xue Zheng , Yuhan Liu , Bao Li . The Marvel of NAD⁺: Nicotinamide Adenine Dinucleotide. University Chemistry, 2024, 39(9): 35-39. doi: 10.12461/PKU.DXHX202401027
3. [3]
  Meifeng Zhu , Jin Cheng , Kai Huang , Cheng Lian , Shouhong Xu , Honglai Liu . Classical Density Functional Theory for Understanding Electrochemical Interface. University Chemistry, 2025, 40(3): 148-152. doi: 10.12461/PKU.DXHX202405166
4. [4]
  Zhengli Hu , Jia Wang , Yi-Lun Ying , Shaochuang Liu , Hui Ma , Wenwei Zhang , Jianrong Zhang , Yi-Tao Long . Exploration of Ideological and Political Elements in the Development History of Nanopore Electrochemistry. University Chemistry, 2024, 39(8): 344-350. doi: 10.3866/PKU.DXHX202401072
5. [5]
  Cen Zhou , Biqiong Hong , Yiting Chen . Application of Electrochemical Techniques in Supramolecular Chemistry. University Chemistry, 2025, 40(3): 308-317. doi: 10.12461/PKU.DXHX202406086
6. [6]
  Lu XU , Chengyu ZHANG , Wenjuan JI , Haiying YANG , Yunlong FU . Zinc metal-organic framework with high-density free carboxyl oxygen functionalized pore walls for targeted electrochemical sensing of paracetamol. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 907-918. doi: 10.11862/CJIC.20230431
7. [7]
  Jing SU , Bingrong LI , Yiyan BAI , Wenjuan JI , Haiying YANG , Zhefeng Fan . Highly sensitive electrochemical dopamine sensor based on a highly stable In-based metal-organic framework with amino-enriched pores. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1337-1346. doi: 10.11862/CJIC.20230414
8. [8]
  Chunmei GUO , Weihan YIN , Jingyi SHI , Jianhang ZHAO , Ying CHEN , Quli FAN . Facile construction and peroxidase-like activity of single-atom platinum nanozyme. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1633-1639. doi: 10.11862/CJIC.20240162
9. [9]
  Yang WANG , Xiaoqin ZHENG , Yang LIU , Kai ZHANG , Jiahui KOU , Linbing SUN . Mn single-atom catalysts based on confined space: Fabrication and the electrocatalytic oxygen evolution reaction performance. Chinese Journal of Inorganic Chemistry, 2024, 40(11): 2175-2185. doi: 10.11862/CJIC.20240165
10. [10]
  Qingtang ZHANG , Xiaoyu WU , Zheng WANG , Xiaomei WANG . Performance of nano Li₂FeSiO₄/C cathode material co-doped by potassium and chlorine ions. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1689-1696. doi: 10.11862/CJIC.20240115
11. [11]
  Jiahong ZHENG , Jingyun YANG . Preparation and electrochemical properties of hollow dodecahedral CoNi₂S₄ supported by MnO₂ nanowires. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1881-1891. doi: 10.11862/CJIC.20240170
12. [12]
  Meiqing Yang , Lu Wang , Haozi Lu , Yaocheng Yang , Song Liu . Recent Advances of Functional Nanomaterials for Screen-Printed Photoelectrochemical Biosensors. Acta Physico-Chimica Sinica, 2025, 41(2): 100018-. doi: 10.3866/PKU.WHXB202310046
13. [13]
  Jiarong Feng , Yejie Duan , Chu Chu , Dezhen Xie , Qiu'e Cao , Peng Liu . Preparation and Application of a Streptomycin Molecularly Imprinted Electrochemical Sensor: A Suggested Comprehensive Analytical Chemical Experiment. University Chemistry, 2024, 39(8): 295-305. doi: 10.3866/PKU.DXHX202401016
14. [14]
  Yuting ZHANG , Zunyi LIU , Ning LI , Dongqiang ZHANG , Shiling ZHAO , Yu ZHAO . Nickel vanadate anode material with high specific surface area through improved co-precipitation method: Preparation and electrochemical properties. Chinese Journal of Inorganic Chemistry, 2024, 40(11): 2163-2174. doi: 10.11862/CJIC.20240204
15. [15]
  Pingwei Wu . Application of Diamond Software in Simplex Teaching. University Chemistry, 2024, 39(3): 118-121. doi: 10.3866/PKU.DXHX202311043
16. [16]
  Yuanpei ZHANG , Jiahong WANG , Jinming HUANG , Zhi HU . Preparation of magnetic mesoporous carbon loaded nano zero-valent iron for removal of Cr(Ⅲ) organic complexes from high-salt wastewater. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1731-1742. doi: 10.11862/CJIC.20240077
17. [17]
  Rui Li , Huan Liu , Yinan Jiao , Shengjian Qin , Jie Meng , Jiayu Song , Rongrong Yan , Hang Su , Hengbin Chen , Zixuan Shang , Jinjin Zhao . 卤化物钙钛矿的单双向离子迁移. Acta Physico-Chimica Sinica, 2024, 40(11): 2311011-. doi: 10.3866/PKU.WHXB202311011
18. [18]
  Linbao Zhang , Weisi Guo , Shuwen Wang , Ran Song , Ming Li . Electrochemical Oxidation of Sulfides to Sulfoxides. University Chemistry, 2024, 39(11): 204-209. doi: 10.3866/PKU.DXHX202401009
19. [19]
  Shuhui Li , Xucen Wang , Yingming Pan . Exploring the Role of Electrochemical Technologies in Everyday Life. University Chemistry, 2025, 40(3): 302-307. doi: 10.12461/PKU.DXHX202406059
20. [20]
  Zihan Lin , Wanzhen Lin , Fa-Jie Chen . Electrochemical Modifications of Native Peptides. University Chemistry, 2025, 40(3): 318-327. doi: 10.12461/PKU.DXHX202406089

Get Citation

PDF

XML

Metrics

PDF Downloads(9)
Abstract views(1470)
HTML views(177)

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