Natural Computing

, Volume 13, Issue 4, pp 559–572

Enforcing logical delays in DNA computing systems

  • Nathanaël Aubert
  • Yannick Rondelez
  • Teruo Fujii
  • Masami Hagiya
Article

Abstract

DNA computing has the potential to create powerful devices, but, in the context of well-mixed systems, sequentiality of operations is hard to achieve. To enforce such sequentiality, we propose a generic delay gate that can be interfaced with virtually any DNA system. Since it is system-independent, our delay gate can be used as an off-the-shelf library to accelerate the design of increasingly complex systems. Additionally, we checked the feasibility of our design by testing various in vitro implementations. We also present a theoretical proof of concept of its applicability by using it to complement an existing DNA module library, the DNA toolbox, to design new systems.

Keywords

DNA computing Delay mechanism Sequentiality Concurrency DNA toolbox 

References

  1. Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429(6990):423–429CrossRefGoogle Scholar
  2. Condon A, Hu AJ, Maňuch J, Thachuk C (2012) Less haste, less waste: on recycling and its limits in strand displacement systems. Interface Focus 2(4):512–521CrossRefGoogle Scholar
  3. Fujii T, Rondelez Y (2012) Predator–prey molecular ecosystems. ACS Nano 7(1):27–34CrossRefGoogle Scholar
  4. Genot AJ, Zhang DY, Bath J, Turberfield AJ (2011) Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. J Am Chem Soc 133(7):2177–2182CrossRefGoogle Scholar
  5. Genot AJ, Fujii T, Rondelez Y (2012) Computing with competition in biochemical networks. Phys Rev Lett 109(20):208102CrossRefGoogle Scholar
  6. Genot AJ, Fujii T, Rondelez Y (2013) Scaling down DNA circuits with competitive neural networks. J R Soc Interface 10(85):20130212CrossRefGoogle Scholar
  7. Hagiya M, Arita M, Kiga D, Sakamoto K, Yokoyama S (1999) Towards parallel evaluation and learning of boolean-formulas with molecules, vol. 48. DNA based computers III, DIMACS series in discrete mathematics and theoretical computer science. pp 57–72Google Scholar
  8. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Wengel J (1998) LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54(14):3607–3630CrossRefGoogle Scholar
  9. Lamport L (1977a) Concurrent reading and writing. Commun ACM 20(11):806–811CrossRefMATHMathSciNetGoogle Scholar
  10. Lamport L (1977b) Proving the correctness of multiprocess programs. IEEE Trans Softw Eng 3(2):125–143CrossRefMATHMathSciNetGoogle Scholar
  11. Montagne K, Plasson R, Sakai Y, Fujii T, Rondelez Y (2011a) Programming an in vitro DNA oscillator using a molecular networking strategy. Mol Syst Biol 7(1):466CrossRefGoogle Scholar
  12. Montagne K, Plasson R, Padirac A, Fujii F, Rondelez Y (2011b) A toolbox to build time-responsive in vitro DNA networks. In: Oral presentation, 17th international conference of DNA computing and molecular programmingGoogle Scholar
  13. Padirac A, Fujii T, Rondelez Y (2012a) Quencher-free multiplexed monitoring of DNA reaction circuits. Nucleic Acids Res 40(15):e118CrossRefGoogle Scholar
  14. Padirac A, Fujii T, Rondelez Y (2012b) Bottom-up construction of in vitro switchable memories. Proc Natl Acad Sci 109(47):E3212–E3220CrossRefGoogle Scholar
  15. Pei R, Matamoros E, Liu M, Stefanovic D, Stojanovic MN (2010) Training a molecular automaton to play a game. Nat Nanotechnol 5(11):773–777CrossRefGoogle Scholar
  16. Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034):1196–1201CrossRefGoogle Scholar
  17. Soloveichik D, Seelig G, Winfree E (2010) DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci 107(12):5393–5398CrossRefGoogle Scholar
  18. Thachuk C, Condon A (2012) Space and energy efficient computation with DNA strand displacement systems, vol. 7433. In: DNA computing and molecular programming. Lecture notes in computer science. pp 135–149Google Scholar
  19. Whitcombe D, Theaker J, Guy SP, Brown T, Little S (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 17:804–807CrossRefGoogle Scholar
  20. Zhang DY, Winfree E (2009) Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc 131(47):17303–17314CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Nathanaël Aubert
    • 1
  • Yannick Rondelez
    • 2
  • Teruo Fujii
    • 2
  • Masami Hagiya
    • 1
  1. 1.Graduate School of Information Science and TechnologyUniversity of TokyoTokyoJapan
  2. 2.LIMMS/CNRS-IIS, Institute of Industrial ScienceUniversity of TokyoTokyoJapan

Personalised recommendations