Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction

Chengxu Li Shiyan Xiao Haojun Liang

Chengxu Li, Shiyan Xiao, Haojun Liang. Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction[J]. Chinese Journal of Chemical Physics . doi: 10.1063/1674-0068/cjcp2302015
Citation: Chengxu Li, Shiyan Xiao, Haojun Liang. Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction[J]. Chinese Journal of Chemical Physics . doi: 10.1063/1674-0068/cjcp2302015

doi: 10.1063/1674-0068/cjcp2302015

Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction

More Information
    • 关键词:
    •  / 
    •  / 
    •  / 
    •  
  • Figure  1.  Schematic diagram of two-step DNA circuit based on TMSDR. The 5' end of signal strand (Sig) and the 3' end of substrate strand (S) are labelled with different fluorophore dyes and quenchers, respectively. The invading toehold domain a* (marked in red) has 5 bases. The solid arrows represent steric hindrance brought by labels and the dotted arrow represents the tendency of these fluorophore dyes and quenchers to bind to each other.

    Figure  2.  Real-time fluorescent kinetic curves of the circuit in FIG. 1. (A) The 5' end of the signal strand (Sig) is labelled with fluorophore dye, while the 3' end of the substrate strand (S) is modified with the corresponding quencher. (B) The 3' end of the substrate strand (S) is labelled with fluorophore dye, while the 5' end of the signal strand (Sig) is modified with its corresponding quencher. The experimental conditions were T = 25 °C, [Invader] = 10 nmol/L, [S-Sig] = 10 nmol/L, [R-Q] = 20 nmol/L. Three parallel experiments were performed for each system.

    Figure  3.  (A) Melting temperatures of signal-substrate duplexes with fluorophore dyes labelled at the 5' end of signal strand, and quenchers labelled at the 3' end of substrate strand. (B) Melting temperatures of signal-substrate duplexes with quenchers labelled at the 5' end of signal strand, and fluorophore dyes labelled at the 3' end of substrate strand. Error bars show the standard deviation on the mean. The concentrations of signal-substrate duplexes were 1 μmol/L. Three parallel experiments were performed for each system.

    Figure  4.  (A) Free energy changes of dual-labelled signal-substrate duplexes with fluorophore dyes labelled at the 5' end of signal strand, and quenchers labelled at the 3' end of substrate strand. (B) Free energy changes of dual-labelled signal-substrate duplexes with quenchers labelled at the 5' end of signal strand, and fluorophore dyes labelled at the 3' end of substrate strand. The change of free energy caused by the fluorescent labels combination was calculated via $\Delta {\Delta }{G}_{T}^{0}=({{\Delta }{G}_{T}^{0})}_{\rm{labelled\ duplex}}-{\left({\Delta }{G}_{T}^{0}\right)}_{\rm{no\ label}}$. In all calculations, the temperature was chosen as T = 25 °C in line with the experimental temperature.

  • [1] Y. J. Chen, N. Dalchau, N. Srinivas, A. Phillips, L. Cardelli, D. Soloveichik, and G. Seelig, Nat. Nanotechnol. 8, 755 (2013). doi: 10.1038/nnano.2013.189
    [2] A. Phillips and L. Cardelli, J. R. Soc. Interface 6, S419 (2009). doi: 10.1098/rsif.2009.0072.focus
    [3] L. Qian, E. Winfree, and J. Bruck, Nature 475, 368 (2011). doi: 10.1038/nature10262
    [4] L. Qian and E. Winfree, Science 332, 1196 (2011). doi: 10.1126/science.1200520
    [5] A. J. Thubagere, W. Li, R. F. Johnson, Z. Chen, S. Doroudi, Y. L. Lee, G. Izatt, S. Wittman, N. Srinivas, D. Woods, E. Winfree, and L. Qian, Science 357, eaan6558 (2017). doi: 10.1126/science.aan6558
    [6] P. Wu, Y. Tu, Y. Qian, H. Zhang, and C. Cai, Chem. Commun. 50, 1012 (2014). doi: 10.1039/C3CC46773B
    [7] A. Ono, S. Cao, H. Togashi, M. Tashiro, T. Fujimoto, T. Machinami, S. Oda, Y. Miyake, I. Okamoto, and Y. Tanaka, Chem. Commun. 39, 4825 (2008). doi: 10.1039/b808686a
    [8] H. Yamaguchi, J. Šebera, J. Kondo, S. Oda, T. Komuro, T. Kawamura, T. Dairaku, Y. Kondo, I. Okamoto, A. Ono, J. V. Burda, C. Kojima, V. Sychrovský, and Y. Tanaka, Nucleic Acids Res. 42, 4094 (2014). doi: 10.1093/nar/gkt1344
    [9] L. Tang, Y. Liu, M. M. Ali, D. K. Kang, W. Zhao, and J. Li, Anal. Chem. 84, 4711 (2012). doi: 10.1021/ac203274k
    [10] D. Han, C. Wu, M. You, T. Zhang, S. Wan, T. Chen, L. Qiu, Z. Zheng, H. Liang, and W. Tan, Nat. Chem. 7, 835 (2015). doi: 10.1038/nchem.2325
    [11] P. Q. Ma, Q. Huang, H. D. Li, B. C. Yin, and B. C. Ye, J. Am. Chem. Soc. 142, 3851 (2020). doi: 10.1021/jacs.9b11545
    [12] B. Yurke, A. J. Turberfield, A. P. Mills, F. C. Simmel, and J. L. Neumann, Nature 406, 605 (2000). doi: 10.1038/35020524
    [13] D. Y. Zhang and E. Winfree, J. Am. Chem. Soc. 131, 17303 (2009). doi: 10.1021/ja906987s
    [14] D. Y. Zhang and G. Seelig, Nat. Chem. 3, 103 (2011). doi: 10.1038/nchem.957
    [15] D. Scalise and R. Schulman, Annu. Rev. Biomed. Eng. 21, 469 (2019). doi: 10.1146/annurev-bioeng-060418-052357
    [16] N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, and E. Winfree, Nucleic Acids Res. 41, 10641 (2013). doi: 10.1093/nar/gkt801
    [17] R. R. F. Machinek, T. E. Ouldridge, N. E. C. Haley, J. Bath, and A. J. Turberfield, Nat. Commun. 5, 5324 (2014). doi: 10.1038/ncomms6324
    [18] P. Irmisch, T. E. Ouldridge, and R. Seidel, J. Am. Chem. Soc. 142, 11451 (2020). doi: 10.1021/jacs.0c03105
    [19] N. E. C. Haley, T. E. Ouldridge, I. Mullor Ruiz, A. Geraldini, A. A. Louis, J. Bath, and A. J. Turberfield, Nat. Commun. 11, 2562 (2020). doi: 10.1038/s41467-020-16353-y
    [20] A. J. Genot, D. Y. Zhang, J. Bath, and A. J. Turberfield, J. Am. Chem. Soc. 133, 2177 (2011). doi: 10.1021/ja1073239
    [21] Q. Li, G. Luan, Q. Guo, and J. Liang, Nucleic Acids Res. 30, e5 (2002). doi: 10.1093/nar/30.2.e5
    [22] S. Tyagi, D. P. Bratu, and F. R. Kramer, Nat. Biotechnol. 16, 49 (1998). doi: 10.1038/nbt0198-49
    [23] X. Sun, B. Wei, Y. Guo, S. Xiao, X. Li, D. Yao, X. Yin, S. Liu, and H. Liang, J. Am. Chem. Soc. 140, 9979 (2018). doi: 10.1021/jacs.8b05203
    [24] R. A. Cardullo, S. Agrawal, C. Flores, P. C. Zamecnik, and D. E. Wolf, Proc. Natl. Acad. Sci. USA 85, 8790 (1988). doi: 10.1073/pnas.85.23.8790
    [25] L. E. Morrison and L. M. Stols, Biochem. 32, 3095 (1993). doi: 10.1021/bi00063a022
    [26] B. G. Moreira, Y. You, M. A. Behlke, and R. Owczarzy, Biochem. Biophys. Res. Commun. 327, 473 (2005). doi: 10.1016/j.bbrc.2004.12.035
    [27] S. A. E. Marras, F. R. Kramer, and S. Tyagi, Nucleic Acids Res. 30, e122 (2002). doi: 10.1093/nar/gnf121
    [28] C. Li, Z. Li, W. Han, X. Yin, X. Liu, S. Xiao, and H. Liang, Chem. Commun. 58, 5849 (2022). doi: 10.1039/D2CC01072K
    [29] J. N. Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, and N. A. Pierce, J. Comput. Chem. 32, 170 (2011). doi: 10.1002/jcc.21596
    [30] J. D. Puglisi and I. Tinoco Jr., Method Enzymol. 180, 304 (1989). doi: 10.1016/0076-6879(89)80108-9
    [31] L. A. Marky and K. J. Breslauer, Biopolymers 26, 1601 (1987). doi: 10.1002/bip.360260911
  • suppl_data.zip
  • 加载中
图(4)
计量
  • 文章访问数:  317
  • HTML全文浏览量:  228
  • PDF下载量:  26
  • 被引次数: 0
出版历程
  • 收稿日期:  2023-02-15
  • 录用日期:  2023-03-14
  • 网络出版日期:  2023-03-16

目录

    /

    返回文章
    返回