注册 English

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

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

downloadPDF
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

    • 通讯作者: Qian-Fan Yang,
    Ya-Lin Tang,
  • 基金项目:

    This present study was supported by Major National Basic Research Projects (973, No. 2013CB733701) (973, No. 2013CB733701)

    Chinese Academy of Sciences (No. KJCX2-EW-N06-01). (No. KJCX2-EW-N06-01)

摘要: 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.

English

  • 

    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.[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] 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.[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] 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.[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] J.R. Williamson, G-quartet structures in telomeric DNA, Annu. Rev. Biophys. Biomol. Struct. 23 (1994) 703-730.[4] J.R. Williamson, G-quartet structures in telomeric DNA, Annu. Rev. Biophys. Biomol. Struct. 23 (1994) 703-730.

    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.[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] J.L. Huppert, S. Balasubramanian, G-quadruplexes in promoters throughout the human genome, Nucleic Acids Res. 35 (2007) 406-413.[6] J.L. Huppert, S. Balasubramanian, G-quadruplexes in promoters throughout the human genome, Nucleic Acids Res. 35 (2007) 406-413.

    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.[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] 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.[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] 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.[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] L.J. Yu, Q.F. Yang, J.F. Xiang, et al. Analyst (2015), http://dx.doi.org/10.1039/c4an01912a.[10] L.J. Yu, Q.F. Yang, J.F. Xiang, et al. Analyst (2015), http://dx.doi.org/10.1039/c4an01912a.

    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.[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] 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.[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] 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.[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] 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.[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] 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.[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] 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.[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] 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.[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] 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.[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] 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.[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] F.M. Hamer, The Chemistry of Heterocyclic Compounds, Interscience, New York, 1964.[20] F.M. Hamer, The Chemistry of Heterocyclic Compounds, Interscience, New York, 1964.

    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.[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] A.H. Herz, Aggregation of sensitizing dyes in solution and their adsorption onto silver halides, Adv. Colloid Interface Sci. 8 (1977) 237-298.[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] A.H. Herz, Dye-dye interactions of cyanines in solution and at AgBr surfaces, Photogr. Sci. Eng. 18 (1974) 323-335.[23] A.H. Herz, Dye-dye interactions of cyanines in solution and at AgBr surfaces, Photogr. Sci. Eng. 18 (1974) 323-335.

    24. [24] W. West, S. Pearce, Dimeric state of cyanine dyes, J. Phys. Chem. 69 (1965) 1894-1903.[24] W. West, S. Pearce, Dimeric state of cyanine dyes, J. Phys. Chem. 69 (1965) 1894-1903.

    25. [25] E.G. Mcrae, M. Kasha, Enhancement of phosphorescence ability upon aggregation of dye molecules, J. Chem. Phys. 28 (1958) 721-722.[25] E.G. Mcrae, M. Kasha, Enhancement of phosphorescence ability upon aggregation of dye molecules, J. Chem. Phys. 28 (1958) 721-722.

    26. [26] A.K. Chibisov, H. Görner, Photophysics of aggregated 9-methylthiacarbocyanine bound to polyanions, Chem. Phys. Lett. 357 (2002) 434-439.[26] A.K. Chibisov, H. Görner, Photophysics of aggregated 9-methylthiacarbocyanine bound to polyanions, Chem. Phys. Lett. 357 (2002) 434-439.

    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.[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] 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.[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] G.N. Parkinson, M.P.H. Lee, S. Neidle, Crystal structure of parallel quadruplexes from human telomeric DNA, Nature 417 (2002) 876-880.[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] 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.[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] 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.[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.

  • 加载中
WeChat 扫一扫看文章
计量
  • PDF下载量:  0
  • 文章访问数:  1230
  • HTML全文浏览量:  20
文章相关
  • 发布日期:  2015-02-25
  • 收稿日期:  2014-10-23
  • 网络出版日期:  2015-02-09
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

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

/

返回文章

All Rights Reserved by the Chinese Chemical Society   中国化学会 版权所有 京ICP备05002797号

本系统由北京仁和汇智信息技术有限公司开发    技术支持: info@rhhz.net