Citation: Li-Jia Yu, Wei Gai, Qian-Fan Yang, Jun-Feng Xiang, Hong-Xia Sun, Qian Li, Li-Xia Wang, Ai-Jiao Guan, Ya-Lin Tang. Recognizing parallel-stranded G-quadruplex by cyanine dye dimer based on dual-site binding mode[J]. Chinese Chemical Letters, ;2015, 26(6): 705-708. doi: 10.1016/j.cclet.2015.02.002 shu

Recognizing parallel-stranded G-quadruplex by cyanine dye dimer based on dual-site binding mode

Li-Jia Yu ^a,b ,
Wei Gai ^a,b ,
Qian-Fan Yang ^a,, ,
Jun-Feng Xiang ^a ,
Hong-Xia Sun ^a ,
Qian Li ^a ,
Li-Xia Wang ^a ,
Ai-Jiao Guan ^a ,
Ya-Lin Tang ^a,,

1.
a Beijing National Laboratory for Molecular Science, Center for Molecular Science, State Key Laboratory for Structural Chemistry for Unstable and State Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
2.
b University of Chinese Academy of Sciences, Beijing 100049, China

Corresponding author: Qian-Fan Yang, Ya-Lin Tang,
Received Date: 23 October 2014
Available Online: 9 February 2015
Fund Project: This present study was supported by Major National Basic Research Projects (973, No. 2013CB733701) (973, No. 2013CB733701)

G-quadruplexes (G4s) play important roles in biological systems, such as telomere maintenance, replication, and transcription. Based on the DNA sequence, loop geometry, and the local environments, G4s can be classified into different conformations. It is important to detect different types of G4s to monitor the diseases related with G4s. Most ligands bind to G4s based on end-stacking modes, while rare ligands bind to G4s through groove binding modes. We have found that a cyanine dye DMSB interacts with parallel G4 by end-stacking and groove simultaneous binding mode. In this article, we found that DMSB could simply discriminate parallel G4s from other DNA motifs by using UV-vis spectrum. These results give some clues to develop high specificity G4 probes.
- Parallel-stranded G-quadruplex,
- Cyanine dye,
- Dual-site binding mode,
- c-myc
1. [1]
  [1] A. Siddiqui-Jain, C.L. Grand, D.J. Bearss, L.H. Hurley, Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription, Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 11593-11598.
2. [2]
  [2] J.T. Davis, G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry, Angew. Chem. Int. Ed. 43 (2004) 668-698.
3. [3]
  [3] S. Burge, G.N. Parkinson, P. Hazel, A.K. Todd, S. Neidle, Quadruplex DNA: sequence, topology and structure, Nucleic Acids Res. 34 (2006) 5402-5415.
4. [4]
  [4] J.R. Williamson, G-quartet structures in telomeric DNA, Annu. Rev. Biophys. Biomol. Struct. 23 (1994) 703-730.
5. [5]
  [5] J.R. Williamson, M.K. Raghuraman, T.R. Cech, Monovalent cation-induced structure of telomeric DNA: the G-quartet model, Cell 59 (1989) 871-880.
6. [6]
  [6] J.L. Huppert, S. Balasubramanian, G-quadruplexes in promoters throughout the human genome, Nucleic Acids Res. 35 (2007) 406-413.
7. [7]
  [7] G.W. Collie, G.N. Parkinson, The application of DNA and RNA G-quadruplexes to therapeutic medicines, Chem. Soc. Rev. 40 (2011) 5867-5892.
8. [8]
  [8] Q.F. Yang, J.F. Xiang, S. Yang, et al., Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: I. Recognizing mixed G-quadruplex in human telomeres, Chem. Commun. (2009) 1103-1105.
9. [9]
  [9] Q.F. Yang, J.F. Xiang, S. Yang, et al., Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism, Nucleic Acids Res. 38 (2010) 1022-1033.
10. [10]
  [10] L.J. Yu, Q.F. Yang, J.F. Xiang, et al. Analyst (2015), http://dx.doi.org/10.1039/c4an01912a.
11. [11]
  [11] Q.F. Yang, J.F. Xiang, S. Yang, et al., Verification of intramolecular hybrid/parallel G-quadruplex structure under physiological conditions using novel cyanine dye H-aggregates: both in solution and on Au film, Anal. Chem. 82 (2010) 9135-9137.
12. [12]
  [12] B. Pagano, A. Virno, C.A.Mattia, et al., Targeting DNA quadruplexeswith distamycin A and its derivatives: an ITC and NMR study, Biochimie 90 (2008) 1224-1232.
13. [13]
  [13] C. Rajput, R. Rutkaite, L. Swanson, I. Haq, J.A. Thomas, Dinuclear monointercalating RuII complexes that display high affinity binding to duplex and quadruplex DNA, Chemistry 12 (2006) 4611-4619.
14. [14]
  [14] T. Wilson, M.P. Williamson, J.A. Thomas, Differentiating quadruplexes: binding preferences of a luminescent dinuclear ruthenium(II) complex with four-stranded DNA structures, Org. Biomol. Chem. 8 (2010) 2617-2621.
15. [15]
  [15] Z. Li, J.H. Tan, J.H. He, et al., Disubstituted quinazoline derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA, Eur. J. Med. Chem. 47 (2012) 299-311.
16. [16]
  [16] P.Z. Zhang, H.L. Yang, C.C. Li, et al., Synthesis of novel, azasugar-modified anthraquinone derivatives and their cytotoxicity, Chin. Chem. Lett. 25 (2014) 1057-1059.
17. [17]
  [17] E.W. White, F. Tanious, M.A. Ismail, et al., Structure-specific recognition of quadruplex DNA by organic cations: influence of shape, substituents and charge, Biophys. Chem. 126 (2007) 140-153.
18. [18]
  [18] S. Cosconati, L. Marinelli, R. Trotta, et al., Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle, J. Am. Chem. Soc. 132 (2010) 6425-6433.
19. [19]
  [19] W. Gai, Q.F. Yang, J.F. Xiang, et al., A dual-site simultaneous binding mode in the interaction between parallel-stranded G-quadruplex [d(TGGGGT)]4 and cyanine dye 2,2'-diethyl-9-methyl-selenacarbocyanine bromide, Nucleic Acids Res. 41 (2013) 2709-2722.
20. [20]
  [20] F.M. Hamer, The Chemistry of Heterocyclic Compounds, Interscience, New York, 1964.
21. [21]
  [21] L.G.S. Brooker, F.L. White, Studies in the cyanine dye series: I. A new method of preparing certain carbocyanines, J. Am. Chem. Soc. 57 (1935) 547-551.
22. [22]
  [22] A.H. Herz, Aggregation of sensitizing dyes in solution and their adsorption onto silver halides, Adv. Colloid Interface Sci. 8 (1977) 237-298.
23. [23]
  [23] A.H. Herz, Dye-dye interactions of cyanines in solution and at AgBr surfaces, Photogr. Sci. Eng. 18 (1974) 323-335.
24. [24]
  [24] W. West, S. Pearce, Dimeric state of cyanine dyes, J. Phys. Chem. 69 (1965) 1894-1903.
25. [25]
  [25] E.G. Mcrae, M. Kasha, Enhancement of phosphorescence ability upon aggregation of dye molecules, J. Chem. Phys. 28 (1958) 721-722.
26. [26]
  [26] A.K. Chibisov, H. Görner, Photophysics of aggregated 9-methylthiacarbocyanine bound to polyanions, Chem. Phys. Lett. 357 (2002) 434-439.
27. [27]
  [27] J.T. McPhee, E. Scott, N.E. Levinger, A. Van Orden, Cy3 in AOT reverse micelles: I. Dimer formation revealed through steady-state and time-resolved spectroscopy, J. Phys. Chem. B 115 (2011) 9576-9584.
28. [28]
  [28] G. Laughlan, A.I. Murchie, D.G. Norman, et al., The high-resolution crystal structure of a parallel-stranded guanine tetraplex, Science 265 (1994) 520-524.
29. [29]
  [29] G.N. Parkinson, M.P.H. Lee, S. Neidle, Crystal structure of parallel quadruplexes from human telomeric DNA, Nature 417 (2002) 876-880.
30. [30]
  [30] S. Neidle, S. Burge, G.N. Parkinson, P. Hazel, A.K. Todd, Quadruplex DNA: sequence, topology and structure, Nucleic Acids Res. 34 (2006) 5402-5415.
31. [31]
  [31] J.W. Yan, W.J. Ye, S.B. Chen, et al., Development of a universal colorimetric indicator for G-quadruplex structures by the fusion of thiazole orange and isaindigotone skeleton, Anal. Chem. 84 (2012) 6288-6292.
1. [1]
  Yuwan Lu , Xiaodan Zhang , Yuming Huang . Dual-site Se/NC specific peroxidase-like nanozyme for highly sensitive methimazole detection. Chinese Chemical Letters, 2025, 36(4): 110129-. doi: 10.1016/j.cclet.2024.110129
2. [2]
  Tianze Wang , Junyi Ren , Dongxiang Zhang , Huan Wang , Jianjun Du , Xin-Dong Jiang , Guiling Wang . Development of functional dye with redshifted absorption based on Knoevenagel condensation at 1-site in phenyl[b]-fused BODIPY. Chinese Chemical Letters, 2024, 35(6): 108862-. doi: 10.1016/j.cclet.2023.108862
3. [3]
  Guangchang Yang , Shenglong Yang , Jinlian Yu , Yishun Xie , Chunlei Tan , Feiyan Lai , Qianqian Jin , Hongqiang Wang , Xiaohui Zhang . Regulating local chemical environment in O3-type layered sodium oxides by dual-site Mg²⁺/B³⁺ substitution achieves durable and high-rate cathode. Chinese Chemical Letters, 2024, 35(9): 109722-. doi: 10.1016/j.cclet.2024.109722
4. [4]
  Wenkai Liu , Yanxian Hou , Weijian Liu , Ran Wang , Shan He , Xiang Xia , Chengyuan Lv , Hua Gu , Qichao Yao , Qingze Pan , Zehou Su , Danhong Zhou , Wen Sun , Jiangli Fan , Xiaojun Peng . Se-substituted pentamethine cyanine for anticancer photodynamic therapy mediated using the hot band absorption process. Chinese Chemical Letters, 2024, 35(12): 109631-. doi: 10.1016/j.cclet.2024.109631
5. [5]
  Hejie Zheng , Zhili Wang , Guizhen Luo , Cuicui Du , Xiaohua Zhang , Jinhua Chen . A novel PEC-EC dual-mode biosensing platform for dual target detection of miRNA-133a and cTnI. Chinese Chemical Letters, 2025, 36(4): 110131-. doi: 10.1016/j.cclet.2024.110131
6. [6]
  Xuying Yu , Jiarong Mi , Yulan Han , Cai Sun , Mingsheng Wang , Guocong Guo . A stable radiochromic semiconductive viologen-based metal–organic framework for dual-mode direct X-ray detection. Chinese Chemical Letters, 2024, 35(9): 109233-. doi: 10.1016/j.cclet.2023.109233
7. [7]
  Qiuye Wang , Yabing Sun , Liangxue Lai , Haijing Cui , Yonglong Ye , Ming Yang , Weihao Zhu , Bo Yuan , Quanliang Mao , Wenzhi Ren , Aiguo Wu . MMP-9-responsive probe for fluorescence-magnetic resonance dual-mode imaging of hepatocellular carcinoma models with different metastatic capacities. Chinese Chemical Letters, 2025, 36(4): 110212-. doi: 10.1016/j.cclet.2024.110212
8. [8]
  Jiajun Wang , Guolin Yi , Shengling Guo , Jianing Wang , Shujuan Li , Ke Xu , Weiyi Wang , Shulai Lei . Computational design of bimetallic TM₂@g-C₉N₄ electrocatalysts for enhanced CO reduction toward C₂ products. Chinese Chemical Letters, 2024, 35(7): 109050-. doi: 10.1016/j.cclet.2023.109050
9. [9]
  Kai Han , Guohui Dong , Ishaaq Saeed , Tingting Dong , Chenyang Xiao . Morphology and photocatalytic tetracycline degradation of g-C3N4 optimized by the coal gangue. Chinese Journal of Structural Chemistry, 2024, 43(2): 100208-100208. doi: 10.1016/j.cjsc.2023.100208
10. [10]
  Xuejiao Wang , Suiying Dong , Kezhen Qi , Vadim Popkov , Xianglin Xiang . Photocatalytic CO₂ Reduction by Modified g-C₃N₄. Acta Physico-Chimica Sinica, 2024, 40(12): 2408005-. doi: 10.3866/PKU.WHXB202408005
11. [11]
  Liang Ma , Zhou Li , Zhiqiang Jiang , Xiaofeng Wu , Shixin Chang , Sónia A. C. Carabineiro , Kangle Lv . Effect of precursors on the structure and photocatalytic performance of g-C3N4 for NO oxidation and CO2 reduction. Chinese Journal of Structural Chemistry, 2024, 43(11): 100416-100416. doi: 10.1016/j.cjsc.2024.100416
12. [12]
  Yanghanbin Zhang , Dongxiao Wen , Wei Sun , Jiahe Peng , Dezhong Yu , Xin Li , Yang Qu , Jizhou Jiang . State-of-the-art evolution of g-C3N4-based photocatalytic applications: A critical review. Chinese Journal of Structural Chemistry, 2024, 43(12): 100469-100469. doi: 10.1016/j.cjsc.2024.100469
13. [13]
  Tao Ban , Xi-Yang Yu , Hai-Kuo Tian , Zheng-Qing Huang , Chun-Ran Chang . One-step conversion of methane and formaldehyde to ethanol over SA-FLP dual-active-site catalysts: A DFT study. Chinese Chemical Letters, 2024, 35(4): 108549-. doi: 10.1016/j.cclet.2023.108549
14. [14]
  Gengchen Guo , Tianyu Zhao , Ruichang Sun , Mingzhe Song , Hongyu Liu , Sen Wang , Jingwen Li , Jingbin Zeng . Au-Fe₃O₄ dumbbell-like nanoparticles based lateral flow immunoassay for colorimetric and photothermal dual-mode detection of SARS-CoV-2 spike protein. Chinese Chemical Letters, 2024, 35(6): 109198-. doi: 10.1016/j.cclet.2023.109198
15. [15]
  Wenhao Wang , Guangpu Zhang , Qiufeng Wang , Fancang Meng , Hongbin Jia , Wei Jiang , Qingmin Ji . Hybrid nanoarchitectonics of TiO₂/aramid nanofiber membranes with softness and durability for photocatalytic dye degradation. Chinese Chemical Letters, 2024, 35(7): 109193-. doi: 10.1016/j.cclet.2023.109193
16. [16]
  Xiao-Fang Lv , Xiao-Yun Ran , Yu Zhao , Rui-Rui Zhang , Li-Na Zhang , Jing Shi , Ji-Xuan Xu , Qing-Quan Kong , Xiao-Qi Yu , Kun Li . Combing NIR-Ⅱ molecular dye with magnetic nanoparticles for enhanced photothermal theranostics with a 95.6% photothermal conversion efficiency. Chinese Chemical Letters, 2025, 36(4): 110027-. doi: 10.1016/j.cclet.2024.110027
17. [17]
  Min WANG , Dehua XIN , Yaning SHI , Wenyao ZHU , Yuanqun ZHANG , Wei ZHANG . Construction and full-spectrum catalytic performance of multilevel Ag/Bi/nitrogen vacancy g-C₃N₄/Ti₃C₂T_x Schottky junction. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1123-1134. doi: 10.11862/CJIC.20230477
18. [18]
  Yan-Bo Li , Yi Li , Liang Yin . Copper(Ⅰ)-catalyzed diastereodivergent construction of vicinal P-chiral and C-chiral centers facilitated by dual "soft-soft" interaction. Chinese Chemical Letters, 2024, 35(7): 109294-. doi: 10.1016/j.cclet.2023.109294
19. [19]
  Hong-Tao Ji , Yu-Han Lu , Yan-Ting Liu , Yu-Lin Huang , Jiang-Feng Tian , Feng Liu , Yan-Yan Zeng , Hai-Yan Yang , Yong-Hong Zhang , Wei-Min He . Nd@C₃N₄-photoredox/chlorine dual catalyzed synthesis and evaluation of antitumor activities of 4-alkylated sulfonyl ketimines. Chinese Chemical Letters, 2025, 36(2): 110568-. doi: 10.1016/j.cclet.2024.110568
20. [20]
  Zhi Zhu , Xiaohan Xing , Qi Qi , Wenjing Shen , Hongyue Wu , Dongyi Li , Binrong Li , Jialin Liang , Xu Tang , Jun Zhao , Hongping Li , Pengwei Huo . Fabrication of graphene modified CeO2/g-C3N4 heterostructures for photocatalytic degradation of organic pollutants. Chinese Journal of Structural Chemistry, 2023, 42(12): 100194-100194. doi: 10.1016/j.cjsc.2023.100194

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(689)
HTML views(3)

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