Citation: Hu Zhengli, Du Jihui, Ying Yilun, Peng Yueyi, Cao Chan, Long Yi-Tao. Single-Molecule Analysis of Colorectal Cancer-associated MicroRNAs via a Biological Nanopore[J]. Acta Chimica Sinica, ;2017, 75(11): 1087-1090. doi: 10.6023/A17090433 shu

Single-Molecule Analysis of Colorectal Cancer-associated MicroRNAs via a Biological Nanopore

Hu Zhengli ^a ,
Du Jihui ^b ,
Ying Yilun ^a ,
Peng Yueyi ^a ,
Cao Chan ^a ,
Long Yi-Tao ^a,,

a.
Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
b.
Central Laboratory, Affiliated Nanshan Hospital, Shenzhen University, Shenzhen 518052, China

Corresponding author: Long Yi-Tao, ytlong@ecust.edu.cn
Received Date: 22 September 2017
Available Online: 7 November 2017
Fund Project: Project supported by the National Key R & D Program of China (No. 2017YFC0906500), the National Natural Science Foundation of China (No. 21505043), Innovation Program of Shanghai Municipal Education Commission (No. 2017-01-07-00-02-E00023) and the Fundamental Research Funds for the Central Universities (Nos. 222201714012, 222201718001, 222201717003)the Fundamental Research Funds for the Central Universities 222201714012Innovation Program of Shanghai Municipal Education Commission 2017-01-07-00-02-E00023the Fundamental Research Funds for the Central Universities 222201718001the National Key R & D Program of China 2017YFC0906500the National Natural Science Foundation of China 21505043the Fundamental Research Funds for the Central Universities 222201717003

Figures(3)

MicroRNAs (miRNAs), 18~22 nucleotides in length, are a class of single-strand noncoding short RNAs and have been used as biomarkers for diagnosis and prognosis of cancers. Herein, an α-hemolysin (α-HL) nanopore was adapted for the colorectal cancer-associated miRNAs analysis, with the merits of high-throughput, ultra-sensitivity and no requirements of amplification/labelling. DNA probes, consisting of a signal tag in each end and a response element in the middle section, were designed. The response element could be well-matched with miRNA and utilized for specific recognition of the target miRNA, while the signal tag increased the capture rate of the miRNA·probe complex. Due to the poor stacking of thymine residues, poly(dT)_n need to overcome a high entropic barrier when traversing through the α-HL nanopore confined space, resulting in distinct double-level blocked events, which contributes to the visualized differences in signal shape and prolonged duration. Thus, poly(dT)_n was selected as the signal tag of probe. Added in the cis side of α-HL, miRNA·probe was forced to traverse across the nanopore confined space under the potential of 140 mV through a pair of Ag/AgCl electrodes (cis grounded). Typical three-stage blocked event was observed, reflecting the translocation process:capture and dissociation of miRNA·probe, translocation of probe, temporarily residence and translocation of miRNA. Stage 1 (S1) represented the process from capture of miRNA·probe complex to translocation of the entire probe. The typical blocked events of miRNA 92·probe 92 showed a two-level S1, where Level 1 (L1) with a current blockage of 0.57±0.01 was generated mainly by translocation of the poly(dT)₄₀ signal tag. As the duration is associated with DNA length, probe 21 with smaller poly(dT)₂₀ signal tag was designed to detect miRNA 21, resulting in a shorter L1 of miRNA 21·probe 21 whose duration (t_D-L1) was 1/3 of that for miRNA 92·probe 92. As the signal shapes vary with DNA sequences, probe 16 with signal tag of poly(dC)₄₀ was used to sense miRNA 16, with miRNA 16·probe 16 producing a different single-level S1 with miRNA 92·probe 92 and miRNA 21·probe 21. The statistical results demonstrated that the three kinds of miRNA·probe produced different durations for S1 (t_D-S1), possibly indicating the differences in probe-α-HL interaction. Therefore, miRNA 92, miRNA 21 and miRNA 16 could be well identified by t_D-L1 (signal shape) and t_D-S1 (duration). Moreover, the serum sample have been tested. Hence, α-HL nanopore can be applied to build ultrasensitive single molecule biosensor for miRNA.
- microRNA,
- α-hemolysin,
- nanopore confined space,
- single molecule biosensor
1. [1]
  Lu, J.; Getz, G.; Miska, E. A.; Alvarez-saavedra, E.; Lamb, J.; Peck, D.; Sweet-cordero, A.; Ebert, B. L.; Mak, R. H.; Ferrando, A. A.; Downing, J. R.; Jacks, T.; Horvitz, H. R.; Golub, T. R. Nature 2005, 435, 834. doi: 10.1038/nature03702
2. [2]
  Várallyay, E.; Burgyán, J.; Havelda, Z. Nature Protocols 2008, 3, 190. doi: 10.1038/nprot.2007.528
3. [3]
  Park, J. L.; Park, S. M.; Kwon, O. H.; Lee, H. C.; Kim, J. Y.; Seok, H. H.; Lee, W. S.; Lee, S. H.; Kim, Y. S.; Woo, K. M.; Kim, S. Y. Electrophoresis 2014, 35, 3062. doi: 10.1002/elps.v35.21-22
4. [4]
  Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Proc. Natl. Acad. Sci. 1996, 93, 13770. doi: 10.1073/pnas.93.24.13770
5. [5]
  Cao, C.; Liao, D.-F.; Ying, Y.-L.; Long, Y.-T. Acta Chim. Sinica 2016, 74, 734(in Chinese).
6. [6]
  Wang, H.-Y.; Li, Y.; Qin, L.-X.; Heyman, A.; Shoseyov, O.; Willner, I.; Long, Y.-T.; Tian, H. Chem. Commun. 2013, 49, 1741. doi: 10.1039/c3cc38939a
7. [7]
  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
8. [8]
  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
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]
  Stefureac, R.; Long, Y.-T.; Kraatz, H.-B.; Howard, P.; Lee, J. S. Biochemistry 2006, 45, 9172. doi: 10.1021/bi0604835
11. [11]
  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
12. [12]
  Wang, H.-Y.; Ying, Y.-L.; Li, Y.; Kraatz, H.-B.; Long, Y.-T. Anal. Chem. 2011, 83, 1746. doi: 10.1021/ac1029874
13. [13]
  Ying, Y.-L.; Zhang, X.; Liu, Y.; Xue, M.-Z.; Li, H.-L.; Long, Y.-T. Acta Chim. Sinica 2013, 71, 44(in Chinese).
14. [14]
  Ying, Y.-L.; Wang, H.-Y.; Sutherland, T. C.; Long, Y.-T. Small 2011, 7, 87. doi: 10.1002/smll.v7.1
15. [15]
  Meng, F.-N.; Yao, X.-Y.; Zhang, J.-J.; Ying, Y.-L.; Tian, H. ACS Sens. 2016, 1, 1398. doi: 10.1021/acssensors.6b00575
16. [16]
  Rauf, S.; Zhang, L.; Ali, A.; Liu, Y.; Li, J.-H. ACS Sens. 2017, 2, 227. doi: 10.1021/acssensors.6b00627
17. [17]
  Ying, Y.-L.; Long, Y.-T. Sci. China:Chem. 2017, 60, 1187. doi: 10.1007/s11426-017-9082-5
18. [18]
  Long, Y.-T.; Zhang, M. N. Sci. China Ser. B-Chem. 2009, 52, 731. doi: 10.1007/s11426-009-0078-z
19. [19]
  Wang, Y.; Zheng, D.-L.; Tan, Q.-L.; Wang, M. X.; Gu, L.-Q. Nat. Nanotechnol. 2011, 6, 668. doi: 10.1038/nnano.2011.147
20. [20]
  Song, L.-Z.; Hobaugh, M. R.; Shustak, C.; Cheley, S.; Bayley, H.; Gouauxt, J. E. Science 1996, 274, 1859. doi: 10.1126/science.274.5294.1859
21. [21]
  Ying, Y.-L.; Li, D.-W.; Li, Y.; Lee, J. S.; Long, Y.-T. Chem. Commun. 2011, 47, 5690. doi: 10.1039/c0cc05787h
22. [22]
  Xi, D.-M.; Shang, J.-Z.; Fan, E.-G.; You, J.-M.; Zhang, S.-S.; Wang, H. Anal. Chem. 2016, 88, 10540. doi: 10.1021/acs.analchem.6b02620
23. [23]
  Meller, A.; Branton, D. Electrophoresis 2002, 23, 2583. doi: 10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H
24. [24]
  Gu, Z.; Ying, Y.-L.; Cao, C.; He, P.-G.; Long, Y.-T. Anal. Chem. 2015, 87, 907. doi: 10.1021/ac5028758
1. [1]
  Yang Meiqing , 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): 100018-0. doi: 10.3866/PKU.WHXB202310046
2. [2]
  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
3. [3]
  Qiaoqiao BAI , Anqi ZHOU , Xiaowei LI , Tang LIU , Song LIU . Construction of pressure-temperature dual-functional flexible sensors and applications in biomedicine. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2259-2274. doi: 10.11862/CJIC.20240128
4. [4]
  Min Huang , Ru Cheng , Shuai Wen , Liangtong Li , Jie Gao , Xiaohui Zhao , Chunmei Li , Hongyan Zou , Jian Wang . Ultrasensitive detection of microRNA-21 in human serum based on the confinement effect enhanced chemical etching of gold nanorods. Chinese Chemical Letters, 2024, 35(9): 109379-. doi: 10.1016/j.cclet.2023.109379
5. [5]
  Fanghua Zhang , Yuyan Li , Hongyan Zhang , Wendong Liu , Zhe Hao , Mingzheng Shao , Ruizhong Zhang , Xiyan Li , Libing Zhang . Logically integrating exo/endogenous gated DNA trackers for precise microRNA imaging via synergistic manipulation. Chinese Chemical Letters, 2025, 36(1): 109848-. doi: 10.1016/j.cclet.2024.109848
6. [6]
  Chenshi Lin , Chao Teng , Bingbing Li , Wei He . Anti-inflammatory drug-assisted microRNA gene therapy for effectively improving pulmonary hemodynamics. Chinese Chemical Letters, 2025, 36(7): 110450-. doi: 10.1016/j.cclet.2024.110450
7. [7]
  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
8. [8]
  Leyu DING , Ying HE , Zhihe WEI , Yang PENG , Zhao DENG . Conductive polypyrrole-confined Co-MOF-74 for high-performance lithium metal anodes. Chinese Journal of Inorganic Chemistry, 2025, 41(12): 2491-2502. doi: 10.11862/CJIC.20250176
9. [9]
  Ke Zhao , Zhen Liu , Luyao Liu , Changyuan Yu , Jingshun Pan , Xuguang Huang . Functionalized Reflective Structure Fiber-Optic Interferometric Sensor for Trace Detection of Lead Ions. Acta Physico-Chimica Sinica, 2024, 40(4): 2304029-0. doi: 10.3866/PKU.WHXB202304029
10. [10]
  Lin′an CAO , Dengyue MA , Gang XU . Research advances in electrically conductive metal-organic frameworks-based electrochemical sensors. Chinese Journal of Inorganic Chemistry, 2025, 41(10): 1953-1972. doi: 10.11862/CJIC.20250160
11. [11]
  Wei Zheng , Yanyu Chen , Rizhong Gao , Chao Lu . Development and Application of Primary Battery-based Humidity Sensors: Advancing a New Paradigm for Integrated Experimental Teaching through Science-Education Synergy. University Chemistry, 2026, 41(4): 393-399. doi: 10.12461/PKU.DXHX202503009
12. [12]
  Xingchao Zhao , Xiaoming Li , Ming Liu , Zijin Zhao , Kaixuan Yang , Pengtian Liu , Haolan Zhang , Jintai Li , Xiaoling Ma , Qi Yao , Yanming Sun , Fujun Zhang . Photomultiplication-Type All-Polymer Photodetectors and Their Applications in Photoplethysmography Sensor. Acta Physico-Chimica Sinica, 2025, 41(1): 100007-0. doi: 10.3866/PKU.WHXB202311021
13. [13]
  Junlin Ma , Enze Wang , Haixia Wu . 柔性电化学传感器的制备及其在重金属离子现场便携检测中的应用. University Chemistry, 2026, 41(5): 455-468. doi: 10.12461/PKU.DXHX202509102
14. [14]
  Jianfang QIN , Yuying ZHANG , Lijuan JIA , Jiaqi LIANG , Yuxing YANG , Haiying YANG , Xu LIU . Accurate determination of profenofos by Au_25-xAg_x(PET)₁₈ (PET=2-phenylethanethiol) nanocluster-based electrochemical sensors. Chinese Journal of Inorganic Chemistry, 2026, 42(6): 1164-1174. doi: 10.11862/CJIC.20250378
15. [15]
  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
16. [16]
  Mengfan Gong , Dongju Zhang . Estimating Delocalization Energies of 1,3-Butadiene and Benzene with Isodesmic Reactions: A Relatively Precise Approach. University Chemistry, 2026, 41(4): 457-463. doi: 10.12461/PKU.DXHX202505036
17. [17]
  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
18. [18]
  Jinghan ZHANG , Guanying CHEN . Progress in the application of rare-earth-doped upconversion nanoprobes in biological detection. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2335-2355. doi: 10.11862/CJIC.20240249
19. [19]
  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
20. [20]
  Yuhao SUN , Qingzhe DONG , Lei ZHAO , Xiaodan JIANG , Hailing GUO , Xianglong MENG , Yongmei GUO . Synthesis and antibacterial properties of silver-loaded sod-based zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 761-770. doi: 10.11862/CJIC.20230169

Get Citation

PDF

XML

Metrics

PDF Downloads(38)
Abstract views(4722)
HTML views(604)

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