Advertisement

A Triode-like Enzyme-free Catalytic Circuit with Junction Fuel

  • Tao Luo
  • Xiaojing Wang
  • Sisi Fan
  • Yan Liu
  • Jin Cheng
  • Linlin Tang
  • Jie SongEmail author
Article
  • 16 Downloads

Abstract

Target detection circuits have been previously designed, which are propelled by conventional PCR, isothermal amplification and strand-displacement reaction. These detection circuits obtain the target signal via the replication of the target strand, the aggregation of the signal particles or the branch migration. Here we constructed a triode-like enzyme-free catalyst strand-displacement circuit for target DNA detection. The target strand triggered the reaction and released the fluorescence signal strand circularly through branch migration. However, the main challenge of strand-displacement reaction is the signal leakage. Therefore, we designed a double strand structure “junction fuel”, which was used to increase the binding energy across the displacement process. Ultimately, the leakage of the system obtained stable inhabitation due to the junction fuel strand. The limit of detection of the system was as low as 0.11 nmol/L and the gain of the system was as high as 28-fold(the concentration of target was 50 nmol/L). Furthermore, the process of the system was visualized vividly in the reaction curve through the kinetic simulation implemented, which suggests that the combination of the kinetic simulation and the experiment exhibits a promising prospect towards the use of strand-displacement circuit in analytical, diagnostic application and synthetic biology.

Keywords

Catalysis Strand-displacement Junction fuel Triode-like Kinetic simulation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

40242_2019_25_MOESM1_ESM.pdf (17.4 mb)
A Triode-like Enzyme-free Catalytic Circuit with Junction Fuel

References

  1. [1]
    Yurke B., Andrew J. T., Allen P. M. J., Nature, 2000, 406(2000), 605PubMedCrossRefPubMedCentralGoogle Scholar
  2. [2]
    Simmel F. C., Yurke B., Singh H. R., Chem. Rev., 2019, 119(10), 6326PubMedPubMedCentralGoogle Scholar
  3. [3]
    Song J., Li Z., Wang P., Meyer T., Mao C., Ke Y., Science, 2017, 357(2017), 3377CrossRefGoogle Scholar
  4. [4]
    Wang D., Song J., Wang P., Pan V., Zhang Y., Cui D., Ke Y., Nat. Protoc., 2018, 13(10), 2312PubMedCrossRefPubMedCentralGoogle Scholar
  5. [5]
    Fan S., Chen J., Ji B., Gao C., Jiang K., Liu Y., Song J., Chinese Science Bulletin, 2018, 64(10), 1027CrossRefGoogle Scholar
  6. [6]
    Fan S., Wang D., Kenaan A., Cheng J., Cui D., Song J., Small, 2019, 15(26), 1805554CrossRefGoogle Scholar
  7. [7]
    Chen W., He B., Li C., Zhang X., Wu W., Yin X., Fan B., Fan X., Wang J., J. Med. Microbiol., 2007, 56(2007), 603PubMedCrossRefPubMedCentralGoogle Scholar
  8. [8]
    Zhao Y., Chen F., Li Q., Wang L., Fan C., Chem. Rev., 2015, 115(22), 12491PubMedCrossRefPubMedCentralGoogle Scholar
  9. [9]
    Wang X., Yan N., Song T., Wang B., Wei B., Lin L., Chen X., Tian H., Liang H., Advanced Biosystems, 2017, 1(6), 1700060CrossRefGoogle Scholar
  10. [10]
    Ho N. R. Y., Lim G. S., Sundah N. R., Lim D., Loh T. P., Shao H., Nat. Commun., 2018, 9(1), 3238PubMedPubMedCentralCrossRefGoogle Scholar
  11. [11]
    Sun X., Wei B., Guo Y., Xiao S., Li X., Yao D., Yin X., Liu S., Liang H., J. Am. Chem. Soc., 2018, 140(31), 9979PubMedCrossRefPubMedCentralGoogle Scholar
  12. [12]
    Fern J., Scalise D., Cangialosi A., Howie D., Potters L., Schulman R., ACS Synth Biol., 2017, 6(2), 190PubMedCrossRefPubMedCentralGoogle Scholar
  13. [13]
    Seelig G., Soloveichik. D., Zhang. D. Y., Winfree E., Science, 2006, 314(2006), 1585PubMedCrossRefPubMedCentralGoogle Scholar
  14. [14]
    Karunanayake M. A., Yu Q., Leon-Duque M. A., Zhao B., Wu R., You M., J. Am. Chem. Soc., 2018, 140(28), 8739CrossRefGoogle Scholar
  15. [15]
    Shi C., Liu Q., Ma C., Zhong W., Anal. Chem., 2014, 86(1), 336PubMedCrossRefPubMedCentralGoogle Scholar
  16. [16]
    Zhao Y., Zhou L., Tang Z., Nat. Commun., 2013, 4(2013), 1493PubMedCrossRefPubMedCentralGoogle Scholar
  17. [17]
    Song T., Eshra A., Shah S., Bui H., Fu D., Yang M., Mokhtar R., Reif J., Nat. Nanotechnol., 2019, 14(11), 1075PubMedCrossRefPubMedCentralGoogle Scholar
  18. [18]
    Rothemund P. W., Nature, 2006, 440(7082), 297PubMedCrossRefPubMedCentralGoogle Scholar
  19. [19]
    Ji B., Song J., Wang D., Kenaan A., Zhu Q., Wang J., Sonderskov S. M., Dong M., Langmuir, 2019, 35(11), 4140PubMedCrossRefPubMedCentralGoogle Scholar
  20. [20]
    Thubagere A. J., Li W., Johnson R. F., Chen Z., Doroudi S., Lee Y. L., Izatt G., Wittman S., Srinivas N., Woods D., Winfree E., Qian L., Science, 2017, 357(6356), No. eaan6558PubMedCrossRefPubMedCentralGoogle Scholar
  21. [21]
    Deng H., Liu Q., Wang X., Huang R., Liu H., Lin Q., Zhou X., Xing D., Biosens. Bioelectron., 2017, 87(2017), 931PubMedCrossRefPubMedCentralGoogle Scholar
  22. [22]
    Zhu W., Su X., Gao X., Dai Z., Zou X., Biosens. Bioelectron., 2014, 53(2014), 414PubMedCrossRefPubMedCentralGoogle Scholar
  23. [23]
    Wang J., Jiang X., Han H., Biosens. Bioelectron., 2016, 82(2016), 26PubMedCrossRefPubMedCentralGoogle Scholar
  24. [24]
    Ma Z. Y., Ruan Y. F., Xu F., Zhao W. W., Xu J. J., Chen H. Y., Anal. Chem., 2016, 88(7), 3864PubMedCrossRefPubMedCentralGoogle Scholar
  25. [25]
    Song T., Liang H., J. Am. Chem. Soc., 2012, 134(26), 10803PubMedCrossRefPubMedCentralGoogle Scholar
  26. [26]
    Song T., Xiao S., Yao D., Huang F., Hu M., Liang H., Adv. Mater., 2014, 26(35), 6181PubMedCrossRefPubMedCentralGoogle Scholar
  27. [27]
    Tavallaie R., McCarroll J., Le Grand M., Ariotti N., Schuhmann W., Bakker E., Tilley R. D., Hibbert D. B., Kavallaris M., Gooding J. J., Nat. Nanotechnol., 2018, 13(11), 1066PubMedCrossRefPubMedCentralGoogle Scholar
  28. [28]
    Wei X., Zhou W., Sanjay S. T., Zhang J., Jin Q., Xu F., Dominguez D. C., Li X., Anal. Chem., 2018, 90(16), 9888PubMedPubMedCentralCrossRefGoogle Scholar
  29. [29]
    Canoura J., Wang Z. W., Yu H. X., Alkhamis O., Fu F. F., Xiao Y., J. Am. Chem. Soc., 2018, 140(31), 9961PubMedPubMedCentralCrossRefGoogle Scholar
  30. [30]
    Ramlal S., Mondal B., Lavu P. S., N B., Kingston J., Int. J. Food Microbiol, 2018, 265(2018), 74PubMedCrossRefPubMedCentralGoogle Scholar
  31. [31]
    Song Y., Shi Y., Huang M., Wang W., Wang Y., Cheng J., Lei Z., Zhu Z., Yang C., Angew. Chem. Int. Ed. Engl., 2019, 58(8), 2236PubMedCrossRefPubMedCentralGoogle Scholar
  32. [32]
    Xiong X., Shi X., Liu Y., Lu L., You J., Analytical Methods, 2018, 10(3), 365CrossRefGoogle Scholar
  33. [33]
    Yang J., Jiang S. X., Liu X. R., Pan L. Q., Zhang C., ACS Applied Materials & Interfaces, 2016, 8(49), 34054CrossRefGoogle Scholar
  34. [34]
    Wang S. S., Ellington A. D., Chem. Rev., 2019, 119(10), 6370PubMedPubMedCentralGoogle Scholar
  35. [35]
    Frank-Kamenetskii M., Nature, 1987, 328(6125), 17PubMedCrossRefPubMedCentralGoogle Scholar
  36. [36]
    Qiao Y., Qian Y., Liu M., Liu N., Tang X., Chem. Res. Chinese Universities, 2019, 35(5), 837CrossRefGoogle Scholar
  37. [37]
    Li B., Ellington A. D., Chen X., Nucleic. Acids Res., 2011, 39(16), No. e100CrossRefGoogle Scholar
  38. [38]
    Shi K., Dou B., Yang C., Chai Y., Yuan R., Xiang Y., Anal. Chem., 2015, 87(16), 8578PubMedCrossRefPubMedCentralGoogle Scholar
  39. [39]
    Watson J. D., Crick J. D., Nature, 1953, 171(1953), 737CrossRefGoogle Scholar
  40. [40]
    Qian L., Winfree E., Bruck J., Nature, 2011, 475(7356), 368PubMedCrossRefPubMedCentralGoogle Scholar
  41. [41]
    Qian L., Winfree E., Science, 2011, 332(6034), 1196PubMedCrossRefPubMedCentralGoogle Scholar
  42. [42]
    Gao Z., Xia H., Zauberman J., Tomaiuolo M., Ping J., Zhang Q., Ducos P., Ye H., Wang S., Yang X., Lubna F., Luo Z., Ren L., Johnson A. T. C., Nano Lett., 2018, 18(6), 3509PubMedPubMedCentralCrossRefGoogle Scholar
  43. [43]
    Zhang C., Wang Z., Liu Y., Yang J., Zhang X., Li Y., Pan L., Ke Y., Yan H., J. Am. Chem. Soc., 2019, 141(43), 17189PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Jilin University, The Editorial Department of Chemical Research in Chinese Universities and Springer-Verlag GmbH 2019

Authors and Affiliations

  • Tao Luo
    • 1
  • Xiaojing Wang
    • 1
  • Sisi Fan
    • 1
  • Yan Liu
    • 1
  • Jin Cheng
    • 1
  • Linlin Tang
    • 1
  • Jie Song
    • 1
    Email author
  1. 1.Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical EngineeringShanghai Jiao Tong UniversityShanghaiP. R. China

Personalised recommendations