Citation: Wei Zhou, Yunchao Li, Louzhen Fan, Xiaohong Li. Thioflavin T Specifically Binding with G-Quadruplex Flanked by DoubleStranded DNA[J]. Acta Physico-Chimica Sinica, ;2022, 38(4): 200401. doi: 10.3866/PKU.WHXB202004017 shu

Thioflavin T Specifically Binding with G-Quadruplex Flanked by DoubleStranded DNA

College of Chemistry, Beijing Normal University, Beijing 100875, China

Corresponding author: Xiaohong Li, lxhxiao@bnu.edu.cn
Received Date: 4 April 2020
Revised Date: 20 May 2020
Accepted Date: 21 May 2020
Available Online: 27 May 2020
Fund Project: the National Natural Science Foundation of China 21673022

G-rich DNA sequences can transform into G-quadruplexes (G4s) in the presence of metal ions. Based on the structural switches, G4 has been recognized as an attractive signal-transducing element for constructing colorimetric, electrochemical, and fluorescent sensing platforms capable of recognizing ions, small biological molecules, proteins, and even cells. For fluorescent sensing platforms, fluorescent small molecules (FSMs) specifically binding with G4s, such as crystal violet (CV), protoporphyrin IX (PPIX), zinc protoporphyrin IX (ZnPPIX), and Thioflavin T (ThT), are usually applied as fluorescent signal readout probes. It was noticed that the binding affinity of FSM with G4 is highly dependent on G4 morphologies because G-rich DNA sequences can fold into multiple G4 conformations, such as parallel, antiparallel, or hybrid. For example, CV only binds with antiparallel G4, PPIX or ZnPPIX preferentially interacts with parallel G4, and ThT displays high affinity for hybrid G4. Furthermore, the binding affinity of FSMs with G4 is also dependent on co-existing ions and ion concentrations, especially elevated Na⁺ level (140 mmol·L^-1). It is the reason why the performance of G4-based sensors in biological and environmental samples is decreased with different extents. Therefore, how to design G-rich DNA sequences to generally achieve FSMs specifically binding with G4, which is independent of G4 morphologies and co-existing Na⁺ and Na⁺ concentrations remains a challenge. In this study, a simple G-rich DNA sequence (thrombin binding aptamer, TBA) flanked by 10-mer single-stranded DNA at the 3' and 5' termini (TBA-10 bp) is designed. In the presence of K⁺, TBA transforms into antiparallel G4 (K⁺-TBA) and TBA-10 bp transforms into antiparallel K⁺-TBA flanked by fully hybridized double-stranded DNA (ds-DNA) (K⁺-TBA-10 bp). Actually, ThT cannot effectively bind with antiparallel K⁺-TBA. Compared with K⁺-TBA, upon K⁺-TBA-10 bp binding with ThT, ThT emission fluorescence increased by 100-fold. Importantly, the binding affinity improved by 1000-fold, which is independent of co-existing Na⁺ and Na⁺ concentrations (5-140 mmol·L^-1). Integrated with UV-Vis spectroscopy, fluorescent spectroscopy, and circular dichroism spectroscopy, it is believed that ThT can specifically and efficiently imbed in the junction between K⁺-TBA and ds-DNA. To corroborate the binding mode, TBA in TBA-10 bp is substituted by other G-rich DNA sequences transforming into parallel and antiparallel G4 in the presence of K⁺, respectively. The resulting improved ThT emission fluorescence indicated that such a specific binding mode generally improved the binding affinity of FSMs with G4. Our findings provide new insights into the improvement of the binding affinity of FSMs and G4, and reveal potential biochemical and bioanalytical applications of G4.
- Thioflavin T,
- G-quadruplex,
- Potassium ion,
- Sodium ion,
- Double-stranded DNA
1. [1]
  Davis, J. T. Angew. Chem. Int. Ed. 2004, 43, 668. doi: 10.1002/anie.200300589 doi: 10.1002/anie.200300589
2. [2]
  Maizels, N. Nat. Struct. Mol. Biol. 2006, 13, 1055. doi: 10.1038/nsmb1171 doi: 10.1038/nsmb1171
3. [3]
  Sun, H.; Li, X.; Li, Y.; Fan, L.; Kraatz, H. B. Analyst 2013, 138, 856. doi: 10.1039/c2an36564b doi: 10.1039/c2an36564b
4. [4]
  Xu, L.; Shen, X.; Hong, S.; Wang, J.; Zhang, Y.; Wang, H.; Zhang, J.; Pei, R. Chem. Commun. 2015, 51, 8165. doi: 10.1039/c5cc01590a doi: 10.1039/c5cc01590a
5. [5]
  Liu, J.; Lu, Y. J. Am. Chem. Soc. 2003, 125, 6642. doi: 10.1021/ja034775u doi: 10.1021/ja034775u
6. [6]
  Li, C. L.; Liu, K. T.; Lin, Y. W.; Chang, H. T. Anal. Chem. 2011, 83, 225. doi: 10.1021/ac1028787 doi: 10.1021/ac1028787
7. [7]
  Kim, H. N.; Ren, W. X.; Kim, J. S.; Yoon, J. Chem. Soc. Rev. 2012, 41, 3210. doi: 10.1039/c1cs15245a doi: 10.1039/c1cs15245a
8. [8]
  Hwang, K.; Wu, P.; Kim, T.; Lei, L.; Tian, S.; Wang, Y.; Lu, Y. Angew. Chem. Int. Ed. 2014, 53, 13798. doi: 10.1002/anie.201408333 doi: 10.1002/anie.201408333
9. [9]
  Yang, L.; Qing, Z.; Liu, C.; Tang, Q.; Li, J.; Yang, S.; Zheng, J.; Yang, R.; Tan, W. Anal. Chem. 2016, 88, 9285. doi: 10.1021/acs.analchem.6b02667 doi: 10.1021/acs.analchem.6b02667
10. [10]
  Yang, J.; Dou, B.; Yuan, R.; Xiang, Y. Anal. Chem. 2016, 88, 8218. doi: 10.1021/acs.analchem.6b02035 doi: 10.1021/acs.analchem.6b02035
11. [11]
  Liu, Z.; Luo, X.; Li, Z.; Huang, Y.; Nie, Z.; Wang, H. H.; Yao, S. Anal. Chem. 2017, 89, 1892. doi: 10.1021/acs.analchem.6b04360 doi: 10.1021/acs.analchem.6b04360
12. [12]
  Li, X. M.; Zheng, K. W.; Hao, Y. H.; Tan, Z. Angew. Chem. Int. Ed. 2016, 55, 13759. doi: 10.1002/anie.201607195 doi: 10.1002/anie.201607195
13. [13]
  Hansel-Hertsch, R.; Antonio, M. D.; Balasubramanian, S. Nat. Rev. Mol. Cell Biol. 2017, 18, 279. doi: 10.1038/nrm.2017.3 doi: 10.1038/nrm.2017.3
14. [14]
  Ge, L.; Wang, W.; Sun, X.; Hou, T.; Li, F. Anal. Chem. 2016, 88, 9691. doi: 10.1021/acs.analchem.6b02584 doi: 10.1021/acs.analchem.6b02584
15. [15]
  Li, X. H.; Yu, Z.; Li, Y. C.; Ye, M. F. Acta Phys. -Chim. Sin. 2018, 34, 1293. doi: 10.3866/PKU.WHXB201804111
16. [16]
  Ou, Z. Z.; Gao, Y. Y.; Cai, W. J.; Ma, T. T.; Yi, N.; Li, Z. Y. Acta Phys. -Chim. Sin. 2019, 35, 230. doi: 10.3866/PKU.WHXB201711281
17. [17]
  Wang, M.; Wang, W.; Kang, T. S.; Leung, C. H.; Ma, D. L. Anal. Chem. 2016, 88, 981. doi: 10.1021/acs.analchem.5b04064 doi: 10.1021/acs.analchem.5b04064
18. [18]
  Liu, Z.; Luo, X.; Li, Z.; Huang, Y.; Nie, Z.; Wang, H. H.; Yao, S. Anal. Chem. 2017, 89, 1892. doi: 10.1021/acs.analchem.6b04360 doi: 10.1021/acs.analchem.6b04360
19. [19]
  Ge, B.; Huang, Y. C.; Sen, D.; Yu, H. Z., Angew. Chem. Int. Ed. 2010, 49, 9965. doi: 10.1002/anie.201004946 doi: 10.1002/anie.201004946
20. [20]
  Leung, K. H.; He, B.; Yang, C.; Leung, C. H.; Wang, H. M.; Ma, D. L. ACS Appl. Mater. Interfaces 2015, 7, 24046. doi: 10.1021/acsami.5b08314 doi: 10.1021/acsami.5b08314
21. [21]
  Zhang, L.; Zhu, J.; Li, T.; Wang, E. Anal. Chem. 2011, 83, 8871. doi: 10.1021/ac2006763 doi: 10.1021/ac2006763
22. [22]
  Hud, N. V. Nucleic Acid-Metal Ion Interactions; Royal Society of Chemistry: Cambridge, UK, 2009.
23. [23]
  Neidle, S.; Balasubramanian, S. Quadruplex Nucleic Acids; Royal Society of Chemistry: Cambridge, UK, 2006; Vol. 7.
24. [24]
  Kong, D. M.; Ma, Y. E.; Guo, J. H.; Yang, W.; Shen, H. X. Anal. Chem. 2009, 81, 2678. doi: 10.1021/ac802558f doi: 10.1021/ac802558f
25. [25]
  Li, T.; Wang, E.; Dong, S. Anal. Chem. 2010, 82, 7576. doi: 10.1021/ac1019446 doi: 10.1021/ac1019446
26. [26]
  Liu, L.; Shao, Y.; Peng, J.; Huang, C.; Liu, H.; Zhang, L. Anal. Chem. 2014, 86, 1622. doi: 10.1021/ac403326m doi: 10.1021/ac403326m
27. [27]
  Hu, M. H.; Zhou, J.; Luo, W. H.; Chen, S. B.; Huang, Z. S.; Wu, R.; Tan, J. H. Anal. Chem. 2019, 91, 2480. doi: 10.1021/acs.analchem.8b05298 doi: 10.1021/acs.analchem.8b05298
28. [28]
  Wang, M.; Wang, W.; Kang, T. S.; Leung, C. H.; Ma, D. L. Anal. Chem. 2016, 88, 981. doi: 10.1021/acs.analchem.5b04064 doi: 10.1021/acs.analchem.5b04064
29. [29]
  Wu, S.; Wang, L.; Zhang, N.; Liu, Y.; Zheng, W.; Chang, A.; Wang, F.; Li, S.; Shangguan, D. Chem. -Eur. J. 2016, 22, 6037. doi: 10.1002/chem.201505170 doi: 10.1002/chem.201505170
30. [30]
  Zhao, D.; Dong, X.; Jiang, N.; Zhang, D.; Liu, C. Nucleic Acids Res. 2014, 42, 11612. doi: 10.1093/nar/gku833 doi: 10.1093/nar/gku833
31. [31]
  Renaud de la Faverie, A.; Guedin, A.; Bedrat, A.; Yatsunyk, L. A.; Mergny, J. L. Nucleic Acids Res. 2014, 42, e65. doi: 10.1093/nar/gku111 doi: 10.1093/nar/gku111
32. [32]
  Mohanty, J.; Barooah, N.; Dhamodharan, V.; Harikrishna, S.; Pradeepkumar, P. I.; Bhasikuttan, A. C. J. Am. Chem. Soc. 2013, 135, 367. doi: 10.1021/ja309588h doi: 10.1021/ja309588h
33. [33]
  Zhou, W.; Yu, Z.; Ma, G.; Jin, T.; Li, Y.; Fan, L.; Li, X. Analyst 2019, 144, 2284. doi: 10.1039/C8AN02430H doi: 10.1039/C8AN02430H
34. [34]
  De Rache, A.; Kejnovska, I.; Vorlickova, M.; Buess-Herman, C. Chem. -Eur. J. 2012, 18, 4392. doi: 10.1002/chem.201103381 doi: 10.1002/chem.201103381
35. [35]
  Vorlíčková, M.; Kejnovská, I.; Bednářová, K.; Renčiuk, D.; Kypr, J. Chirality 2012, 24, 691. doi: 10.1002/chir.22064 doi: 10.1002/chir.22064
36. [36]
  Dutta, K.; Fujimoto, T.; Inoue, M.; Miyoshi, D.; Sugimoto, N. Chem. Commun. 2010, 46, 7772. doi: 10.1039/c0cc00710b doi: 10.1039/c0cc00710b
37. [37]
  Zhang, D.; Han, J.; Li, Y.; Fan, L.; Li, X. J. Phys. Chem. B 2016, 120, 6606. doi: 10.1021/acs.jpcb.6b05002 doi: 10.1021/acs.jpcb.6b05002
38. [38]
  Kong, D. M.; Ma, Y. E.; Guo, J. H.; Yang, W.; Shen, H. X. Anal. Chem. 2009, 81, 2678. doi: 10.1021/ac802558f doi: 10.1021/ac802558f
39. [39]
  Waller, Z. A. E.; Sewitz, S. A.; Hsu, S. T. D.; Balasubramanian, S. J. Am. Chem. Soc. 2009, 131, 12628. doi: 10.1021/ja901892u doi: 10.1021/ja901892u
40. [40]
  Zhang, R.; Cheng, M.; Zhang, L. M.; Zhu, L. N.; Kong, D. M. ACS Appl. Mater. Interfaces 2018, 10, 13350. doi: 10.1021/acsami.8b01901 doi: 10.1021/acsami.8b01901
41. [41]
  Liu, L.; Shao, Y.; Peng, J.; Huang, C.; Liu, H.; Zhang, L. Anal. Chem. 2014, 86, 1622. doi: 10.1021/ac403326m doi: 10.1021/ac403326m
1. [1]
  Wendian XIE , Yuehua LONG , Jianyang XIE , Liqun XING , Shixiong SHE , Yan YANG , Zhihao HUANG . Preparation and ion separation performance of oligoether chains enriched covalent organic framework membrane. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1528-1536. doi: 10.11862/CJIC.20240050
2. [2]
  Yuyao Wang , Zhitao Cao , Zeyu Du , Xinxin Cao , Shuquan Liang . Research Progress of Iron-based Polyanionic Cathode Materials for Sodium-Ion Batteries. Acta Physico-Chimica Sinica, 2025, 41(4): 100035-. doi: 10.3866/PKU.WHXB202406014
3. [3]
  Yu Guo , Zhiwei Huang , Yuqing Hu , Junzhe Li , Jie Xu . 钠离子电池中铁基异质结构负极材料的最新研究进展. Acta Physico-Chimica Sinica, 2025, 41(3): 2311015-. doi: 10.3866/PKU.WHXB202311015
4. [4]
  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
5. [5]
  Zhuo Wang , Xue Bai , Kexin Zhang , Hongzhi Wang , Jiabao Dong , Yuan Gao , Bin Zhao . MOF模板法合成氮掺杂碳材料用于增强电化学钠离子储存和去除. Acta Physico-Chimica Sinica, 2025, 41(3): 2405002-. doi: 10.3866/PKU.WHXB202405002
6. [6]
  Xiaotian ZHU , Fangding HUANG , Wenchang ZHU , Jianqing ZHAO . Layered oxide cathode for sodium-ion batteries: Surface and interface modification and suppressed gas generation effect. Chinese Journal of Inorganic Chemistry, 2025, 41(2): 254-266. doi: 10.11862/CJIC.20240260
7. [7]
  Jianbao Mei , Bei Li , Shu Zhang , Dongdong Xiao , Pu Hu , Geng Zhang . Enhanced Performance of Ternary NASICON-Type Na_3.5-xMn_0.5V_1.5-xZr_x(PO₄)₃/C Cathodes for Sodium-Ion Batteries. Acta Physico-Chimica Sinica, 2024, 40(12): 2407023-. doi: 10.3866/PKU.WHXB202407023
8. [8]
  Kexin Dong , Chuqi Shen , Ruyu Yan , Yanping Liu , Chunqiang Zhuang , Shijie Li . Integration of Plasmonic Effect and S-Scheme Heterojunction into Ag/Ag₃PO₄/C₃N₅ Photocatalyst for Boosted Photocatalytic Levofloxacin Degradation. Acta Physico-Chimica Sinica, 2024, 40(10): 2310013-. doi: 10.3866/PKU.WHXB202310013
9. [9]
  Pengyang FAN , Shan FAN , Qinjin DAI , Xiaoying ZHENG , Wei DONG , Mengxue WANG , Xiaoxiao HUANG , Yong ZHANG . Preparation and performance of rich 1T-MoS₂ nanosheets for high-performance aqueous zinc ion battery cathode materials. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 675-682. doi: 10.11862/CJIC.20240339
10. [10]
  Jiaxuan Zuo , Kun Zhang , Jing Wang , Xifei Li . 锂离子电池Ni-Co-Mn基正极材料前驱体的形核调控及机制. Acta Physico-Chimica Sinica, 2025, 41(1): 2404042-. doi: 10.3866/PKU.WHXB202404042
11. [11]
  Wenjun Zheng . Application in Inorganic Synthesis of Ionic Liquids. University Chemistry, 2024, 39(8): 163-168. doi: 10.3866/PKU.DXHX202401020
12. [12]
  Guoze Yan , Bin Zuo , Shaoqing Liu , Tao Wang , Ruoyu Wang , Jinyang Bao , Zhongzhou Zhao , Feifei Chu , Zhengtong Li , Yusuke Yamauchi , Saad Melhi , Xingtao Xu . Opportunities and Challenges of Capacitive Deionization for Uranium Extraction from Seawater. Acta Physico-Chimica Sinica, 2025, 41(4): 100032-. doi: 10.3866/PKU.WHXB202404006
13. [13]
  Hong LI , Xiaoying DING , Cihang LIU , Jinghan ZHANG , Yanying RAO . Detection of iron and copper ions based on gold nanorod etching colorimetry. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 953-962. doi: 10.11862/CJIC.20230370
14. [14]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
15. [15]
  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
16. [16]
  Doudou Qin , Junyang Ding , Chu Liang , Qian Liu , Ligang Feng , Yang Luo , Guangzhi Hu , Jun Luo , Xijun Liu . Addressing Challenges and Enhancing Performance of Manganese-based Cathode Materials in Aqueous Zinc-Ion Batteries. Acta Physico-Chimica Sinica, 2024, 40(10): 2310034-. doi: 10.3866/PKU.WHXB202310034
17. [17]
  Feiya Cao , Qixin Wang , Pu Li , Zhirong Xing , Ziyu Song , Heng Zhang , Zhibin Zhou , Wenfang Feng . Magnesium-Ion Conducting Electrolyte Based on Grignard Reaction: Synthesis and Properties. University Chemistry, 2024, 39(3): 359-368. doi: 10.3866/PKU.DXHX202308094
18. [18]
  Xuyang Wang , Jiapei Zhang , Lirui Zhao , Xiaowen Xu , Guizheng Zou , Bin Zhang . Theoretical Study on the Structure and Stability of Copper-Ammonia Coordination Ions. University Chemistry, 2024, 39(3): 384-389. doi: 10.3866/PKU.DXHX202309065
19. [19]
  Dongqi Cai , Fuping Tian , Zerui Zhao , Yanjuan Zhang , Yue Dai , Feifei Huang , Yu Wang . Exploration of Factors Influencing the Determination of Ion Migration Number by Hittorf Method. University Chemistry, 2024, 39(4): 94-99. doi: 10.3866/PKU.DXHX202310031
20. [20]
  Jiayu Tang , Jichuan Pang , Shaohua Xiao , Xinhua Xu , Meifen Wu . Improvement for Measuring Transference Numbers of Ions by Moving-Boundary Method. University Chemistry, 2024, 39(5): 193-200. doi: 10.3866/PKU.DXHX202311021

Get Citation

PDF

XML

Metrics

PDF Downloads(18)
Abstract views(448)
HTML views(59)

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