New Generation Computing

, Volume 33, Issue 3, pp 213–229 | Cite as

Cascading DNA Generation Reaction for Controlling DNA Nanomachines at a Physiological Temperature

Article

Abstract

We developed a reaction system to generate multiple single-stranded DNA species at a physiological temperature for controlling the operation of DNA nanomachines. In this reaction system, cascading DNA generation is arbitrarily programmed by permutation and altering the combinations of template DNA sequences in a modular fashion. Because the dissociation of generated DNA strands from their templates is fully dependent on the strand displacement activity of DNA polymerase, generation and subsequent hybridization of DNA strands can be implemented in a one-pot reaction at the reaction temperature. We experimentally confirmed the generation and hybridization of DNA strands at a temperature remarkably lower than the melting temperature by monitoring the fluorescence change caused by the structural transition of molecular beacons as a simple DNA nanomachine operation. Then, we demonstrated the versatility and programmability of the cascading DNA generation up to three layers. By integrating the proposed DNA generation reaction with various types of DNA nanomachines, an intelligent molecular robotic system is expected to be achieved.

Keywords

DNA Nanomachine DNA Hybridization Melting Temperature DNA Polymerase Molecular Robotic System 

References

  1. 1.
    Seeman N.C.: “DNA in a material world,”. Nature 421, 427–431 (2003)MathSciNetCrossRefGoogle Scholar
  2. 2.
    Rothemund P.W.K.: “Folding DNA to create nanoscale shapes and patterns,”. Nature 440, 297–302 (2006)CrossRefGoogle Scholar
  3. 3.
    He Y., Ye T., Su M., Zhang C., Ribbe A.E., Jiang W., Mao C.: “Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra,”. Nature 452, 198–202 (2008)CrossRefGoogle Scholar
  4. 4.
    Wei B., Dai M., Yin P.: “Complex shapes self-assembled from single-stranded DNA tiles,”. Nature 485, 623–626 (2012)CrossRefGoogle Scholar
  5. 5.
    Bath J., Turberfield A.J.: “DNA nanomachines,”. Nature Nanotech. 2, 275–284 (2007)CrossRefGoogle Scholar
  6. 6.
    Yurke B., Turberfield A.J., Mills A.P. Jr, Simmel F.C., Neumann J.L.: “A DNA-fuelled molecular machine made of DNA,”. Nature 406, 605–608 (2000)CrossRefGoogle Scholar
  7. 7.
    Shin J.-S., Pierce N.A.: “A synthetic DNA walker for molecular transport,”. J. Am. Chem. Soc. 126, 10834–10835 (2004)CrossRefGoogle Scholar
  8. 8.
    Gu H., Chao J., Xiao S.-J, Seeman N.C.: “A proximity-based programmable DNA nanoscale assembly line,”. Nature 465, 202–205 (2010)CrossRefGoogle Scholar
  9. 9.
    Murata S., Konagaya A., Kobayashi S., Saito H., Hagiya M.: “Molecular robotics: a new paradigm for artifacts,”. New Gener. Comput. 31, 27–45 (2013)CrossRefGoogle Scholar
  10. 10.
    Hagiya M., Konagaya A., Kobayashi S., Saito H., Murata S.: “Molecular robots with sensors and intelligence,”. Acc. Chem. Res. 47, 1681–1690 (2014)CrossRefGoogle Scholar
  11. 11.
    Tyagi S., Kramer F.R.: “Molecular beacons: probes that fluoresce upon hybridization,”. Nature Biotechnol. 14, 303–308 (1996)CrossRefGoogle Scholar
  12. 12.
    Seelig G., Soloveichik D., Zhang D.Y., Winfree E.: “Enzyme-free nucleic acid logic circuits,”. Science 314, 1585–1588 (2006)CrossRefGoogle Scholar
  13. 13.
    Walker G.T., Little M.C., Nadeau J.G., Shank D.D.: “Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system,”. Proc. Natl. Acad. Sci. USA 89, 392–396 (1992)CrossRefGoogle Scholar
  14. 14.
    Matsuda D., Yamamura M.: “Cascading whiplash PCR with a nicking enzyme,”. Lect. Notes in Comp. Sci. 2568, 38–46 (2003)CrossRefGoogle Scholar
  15. 15.
    Van Ness J., Van Ness L.K., Galas D.J.: “Isothermal reactions for the amplification of oligonucleotides,”. Proc. Natl. Acad. Sci. USA 100, 4504–4509 (2003)CrossRefGoogle Scholar
  16. 16.
    Weizmann Y., Beissenhirtz M.K., Cheglakov Z., Nowarski R., Kotler M., Willner I.: “A virus spotlighted by an autonomous DNA machine,”. Angew. Chem., Int. Ed. 45, 7384–7388 (2006)CrossRefGoogle Scholar
  17. 17.
    Montagne, K., Plasson, R., Sakai, Y., Fujii, T. and Rondelez, Y., “Programming an in vitro DNA oscillator using a molecular networking strategy,” Mol. Sys. Biol., 7, Article Number 466, 2011Google Scholar
  18. 18.
    Markham N.R., Zuker M.: “DINAMelt web server for nucleic acid melting prediction,”. Nucleic Acids Res. 33, W577–W581 (2005)CrossRefGoogle Scholar
  19. 19.
    Tsourkas A., Behlke M.A., Rose S.D., Bao G.: “Hybridization kinetics and thermodynamics of molecular beacons,”. Nucleic Acids Res. 31, 1319–1330 (2003)CrossRefGoogle Scholar
  20. 20.
    Yurke B., Millis A.P. Jr.: “Using DNA to power nanostructures,”. Genetic Programming and Evolvable Machines 4, 111–122 (2003)CrossRefGoogle Scholar
  21. 21.
    Zhang D.Y., Winfree E.: “Control of DNA strand displacement kinetics using toehold exchange,”. J. Am. Chem. Soc. 131, 17303–17314 (2009)CrossRefGoogle Scholar
  22. 22.
    Komiya K., Yamamura M., Rose J.A.: “Experimental validation and optimization of signal dependent operation in whiplash PCR,”. Natural Computing 9, 207–218 (2010)MathSciNetCrossRefMATHGoogle Scholar

Copyright information

© Ohmsha and Springer Japan 2015

Authors and Affiliations

  1. 1.Interdisciplinary Graduate School of Science and EngineeringTokyo Institute of TechnologyYokohamaJapan

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