Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts

Authors Antti Lankinen, Ismael Mullor Ruiz, Thomas E. Ouldridge



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Antti Lankinen
  • Department of Bioengineering, Imperial College London, UK
Ismael Mullor Ruiz
  • Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, UK
Thomas E. Ouldridge
  • Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, UK

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Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge. Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 7:1-7:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
https://doi.org/10.4230/LIPIcs.DNA.2020.7

Abstract

DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct "catalyst" strand from the one that triggered the reaction. These facts make emulation of the out-of-equilibrium catalytic circuitry of living cells more difficult. Here, we propose a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC). ACDC components are all double-stranded complexes, with reactions occurring through 4-way strand exchange. Catalysts directly bind to their substrates, and the "identity" strand of the catalyst recovered at the end of a reaction is the same molecule as the one that initiated it. We analyse the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells. We also propose two methods of systematically introducing mismatches within DNA strands to avoid leak reactions and introduce driving through net base pair formation. We then combine these results into a compiler to automate the process of designing DNA strands that realise any catalytic network allowed by our framework.

Subject Classification

ACM Subject Classification
  • Hardware → Biology-related information processing
Keywords
  • DNA strand displacement
  • Catalysis
  • Information-processing networks

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References

  1. Leonard Adleman. Molecular computation of solutions to combinatorial problems. Science, 266(5187):1021-1024, November 1994. URL: https://doi.org/10.1126/science.7973651.
  2. Uri Alon. An introduction to systems biology: design principles of biological circuits, Second Edition. CRC Press LLC, Boca Raton, UNITED STATES, 2019. Google Scholar
  3. Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, and Erik Winfree. A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities. In DNA computing and molecular programming, Lecture notes in computer science, pages 232-248. Springer, Cham, September 2017. URL: https://doi.org/10.1007/978-3-319-66799-7_15.
  4. David Barford, Amit K. Das, and Marie-Pierre Egloff. The structure and mechanism of protein phosphatases: insights into catalysis and regulation. Annual Review of Biophysics and Biomolecular Structure, 27(1):133-164, June 1998. Publisher: Annual Reviews. URL: https://doi.org/10.1146/annurev.biophys.27.1.133.
  5. John P. Barton and Eduardo D. Sontag. The energy costs of insulators in biochemical networks. Biophysical Journal, 104(6):1380-1390, March 2013. URL: https://doi.org/10.1016/j.bpj.2013.01.056.
  6. Hieu Bui, Shalin Shah, Reem Mokhtar, Tianqi Song, Sudhanshu Garg, and John Reif. Localized DNA hybridization chain reactions on DNA origami. ACS Nano, 12(2):1146-1155, February 2018. Publisher: American Chemical Society. URL: https://doi.org/10.1021/acsnano.7b06699.
  7. Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, and Georg Seelig. A spatially localized architecture for fast and modular DNA computing. Nature Nanotechnology, 12(9):920-927, September 2017. Number: 9 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/nnano.2017.127.
  8. Yuan-Jyue Chen, Neil Dalchau, Niranjan Srinivas, Andrew Phillips, Luca Cardelli, David Soloveichik, and Georg Seelig. Programmable chemical controllers made from DNA. Nature Nanotechnology, 8(10):755-762, October 2013. URL: https://doi.org/10.1038/nnano.2013.189.
  9. Kevin M. Cherry and Lulu Qian. Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks. Nature, 559(7714):370-376, July 2018. URL: https://doi.org/10.1038/s41586-018-0289-6.
  10. Nadine L. Dabby. Synthetic molecular machines for active self-assembly: prototype algorithms, designs, and experimental study. PhD thesis, California Institute of Technology, Pasadena, California, 2013. URL: https://pdfs.semanticscholar.org/e668/440cdb786ea7c2d0d6ae306c5aefef1208f6.pdf.
  11. Wiet de Ronde and Pieter Rein ten Wolde. Multiplexing oscillatory biochemical signals. Physical Biology, 11(2):026004, April 2014. URL: https://doi.org/10.1088/1478-3975/11/2/026004.
  12. Abhishek Deshpande and Thomas E. Ouldridge. High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits. Engineering Biology, 1(2):86-99, December 2017. Publisher: IET Digital Library. URL: https://doi.org/10.1049/enb.2017.0017.
  13. Robert M. Dirks, Justin S. Bois, Joseph M. Schaeffer, Erik Winfree, and Niles A. Pierce. Thermodynamic analysis of interacting nucleic acid strands. SIAM Review, 49(1):65-88, January 2007. Publisher: Society for Industrial and Applied Mathematics. URL: https://doi.org/10.1137/060651100.
  14. Elaine A. Elion. Ste5: a meeting place for MAP kinases and their associates. Trends in Cell Biology, 5(8):322-327, August 1995. URL: https://doi.org/10.1016/S0962-8924(00)89055-8.
  15. Michael B. Elowitz and Stanislas Leibler. A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767):335-338, January 2000. Number: 6767 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/35002125.
  16. Timothy S. Gardner, Charles R. Cantor, and James J. Collins. Construction of a genetic toggle switch in Escherichia coli. Nature, 403(6767):339-342, January 2000. Number: 6767 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/35002131.
  17. Anthony J. Genot, Teruo Fujii, and Yannick Rondelez. Scaling down DNA circuits with competitive neural networks. Journal of The Royal Society Interface, 10(85):20130212, August 2013. Publisher: Royal Society. URL: https://doi.org/10.1098/rsif.2013.0212.
  18. Christopher C. Govern and Pieter Rein ten Wolde. Energy dissipation and noise correlations in biochemical sensing. Physical Review Letters, 113(25):258102, December 2014. Publisher: American Physical Society. URL: https://doi.org/10.1103/PhysRevLett.113.258102.
  19. Natalie E. C. Haley, Thomas E. Ouldridge, Ismael Mullor Ruiz, Alessandro Geraldini, Ard A. Louis, Jonathan Bath, and Andrew J. Turberfield. Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement. Nature Communications, 11(1):2562, May 2020. Number: 1 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/s41467-020-16353-y.
  20. Ira Herskowitz. MAP kinase pathways in yeast: for mating and more. Cell, 80(2):187-197, January 1995. URL: https://doi.org/10.1016/0092-8674(95)90402-6.
  21. Robert F. Johnson. Impossibility of sufficiently simple chemical reaction network implementations in DNA strand displacement. In Ian McQuillan and Shinnosuke Seki, editors, Unconventional computation and natural computation, Lecture notes in computer science, pages 136-149. Springer International Publishing, 2019. URL: https://doi.org/10.1007/978-3-030-19311-9_12.
  22. Shohei Kotani and William L. Hughes. Multi-arm junctions for dynamic DNA nanotechnology. Journal of the American Chemical Society, 139(18):6363-6368, May 2017. URL: https://doi.org/10.1021/jacs.7b00530.
  23. Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, and Andrew Phillips. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics, 27(22):3211-3213, November 2011. URL: https://doi.org/10.1093/bioinformatics/btr543.
  24. Antti Lankinen. ACDC compiler, July 2020. URL: https://zenodo.org/record/3948343.
  25. Tong Lin, Jun Yan, Luvena L. Ong, Joanna Robaszewski, Hoang D. Lu, Yongli Mi, Peng Yin, and Bryan Wei. Hierarchical assembly of DNA nanostructures based on four-way toehold-mediated strand displacement. Nano Letters, 18(8):4791-4795, August 2018. Publisher: American Chemical Society. URL: https://doi.org/10.1021/acs.nanolett.8b01355.
  26. Robert R. F. Machinek, Thomas E. Ouldridge, Natalie E. C. Haley, Jonathan Bath, and Andrew J. Turberfield. Programmable energy landscapes for kinetic control of DNA strand displacement. Nature Communications, 5(1):1-9, November 2014. Number: 1 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/ncomms6324.
  27. Marcelo O. Magnasco. Chemical kinetics is Turing universal. Physical Review Letters, 78(6):1190-1193, February 1997. URL: https://doi.org/10.1103/PhysRevLett.78.1190.
  28. G. Manning, D. B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam. The protein kinase complement of the human genome. Science, 298(5600):1912-1934, December 2002. Publisher: American Association for the Advancement of Science Section: Review. URL: https://doi.org/10.1126/science.1075762.
  29. Christopher J. Marshall. MAP kinase kinase kinase, MAP kinase kinase and MAP kinase. Current Opinion in Genetics & Development, 4(1):82-89, February 1994. URL: https://doi.org/10.1016/0959-437X(94)90095-7.
  30. Pankaj Mehta, Alex H. Lang, and David J. Schwab. Landauer in the agea of synthetic biology: energy consumption and information processing in biochemical networks. Journal of Statistical Physics, 162(5):1153-1166, March 2016. URL: https://doi.org/10.1007/s10955-015-1431-6.
  31. Thomas E. Ouldridge, Christopher C. Govern, and Pieter Rein ten Wolde. Thermodynamics of computational copying in biochemical systems. Physical Review X, 7(2):021004, April 2017. Publisher: American Physical Society. URL: https://doi.org/10.1103/PhysRevX.7.021004.
  32. Thomas E. Ouldridge, Ard A. Louis, and Jonathan P. K. Doye. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. The Journal of Chemical Physics, 134(8):085101, February 2011. Publisher: American Institute of Physics. URL: https://doi.org/10.1063/1.3552946.
  33. Tomislav Plesa. Stochastic approximation of high-molecular by bi-molecular reactions. arXiv:1811.02766 [math, q-bio], November 2018. arXiv: 1811.02766. URL: http://arxiv.org/abs/1811.02766.
  34. Lulu Qian, David Soloveichik, and Erik Winfree. Efficient Turing-universal computation with DNA polymers. In Yasubumi Sakakibara and Yongli Mi, editors, DNA computing and molecular programming, Lecture notes in computer science, pages 123-140, Berlin, Heidelberg, 2011. Springer. URL: https://doi.org/10.1007/978-3-642-18305-8_12.
  35. Lulu Qian and Erik Winfree. Scaling up digital circuit computation with DNA strand displacement cascades. Science, 332(6034):1196-1201, June 2011. URL: https://doi.org/10.1126/science.1200520.
  36. Lulu Qian and Erik Winfree. A simple DNA gate motif for synthesizing large-scale circuits. Journal of the Royal Society Interface, 8(62):1281-1297, September 2011. URL: https://doi.org/10.1098/rsif.2010.0729.
  37. Lulu Qian and Erik Winfree. Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface. In Satoshi Murata and Satoshi Kobayashi, editors, DNA computing and molecular programming, Lecture notes in computer science, pages 114-131, Cham, 2014. Springer International Publishing. URL: https://doi.org/10.1007/978-3-319-11295-4_8.
  38. Lulu Qian, Erik Winfree, and Jehoshua Bruck. Neural network computation with DNA strand displacement cascades. Nature, 475(7356):368-372, July 2011. URL: https://doi.org/10.1038/nature10262.
  39. Ismael Mullor Ruiz, Jean-Michel Arbona, Amitkumar Lad, Oscar Mendoza, Jean-Pierre Aimé, and Juan Elezgaray. Connecting localized DNA strand displacement reactions. Nanoscale, 7(30):12970-12978, July 2015. Publisher: The Royal Society of Chemistry. URL: https://doi.org/10.1039/C5NR02434J.
  40. John SantaLucia and Donald Hicks. The thermodynamics of DNA structural motifs. Annual Review of Biophysics and Biomolecular Structure, 33(1):415-440, 2004. _eprint: URL: https://doi.org/10.1146/annurev.biophys.32.110601.141800.
  41. Hans J. Schaeffer, Andrew D. Catling, Scott T. Eblen, Lara S. Collier, Anke Krauss, and Michael J. Weber. MP1: a MEK binding partner that enhances enzymatic activation of the MAP kinase cascade. Science, 281(5383):1668-1671, September 1998. Publisher: American Association for the Advancement of Science Section: Report. URL: https://doi.org/10.1126/science.281.5383.1668.
  42. Georg Seelig, David Soloveichik, David Yu Zhang, and Erik Winfree. Enzyme-free nucleic acid logic circuits. Science, 314(5805):1585-1588, December 2006. Publisher: American Association for the Advancement of Science Section: Report. URL: https://doi.org/10.1126/science.1132493.
  43. Nadrian C. Seeman and Hanadi F. Sleiman. DNA nanotechnology. Nature Reviews Materials, 3(1):1-23, November 2017. URL: https://doi.org/10.1038/natrevmats.2017.68.
  44. David Soloveichik, Georg Seelig, and Erik Winfree. DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences, 107(12):5393-5398, March 2010. URL: https://doi.org/10.1073/pnas.0909380107.
  45. Carlo Spaccasassi, Matthew R. Lakin, and Andrew Phillips. A logic programming language for computational nucleic acid devices. ACS synthetic biology, 8(7):1530-1547, July 2019. URL: https://doi.org/10.1021/acssynbio.8b00229.
  46. Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, and David Soloveichik. Enzyme-free nucleic acid dynamical systems. Science, 358(6369), December 2017. URL: https://doi.org/10.1126/science.aal2052.
  47. J. David Sweatt. The neuronal MAP kinase cascade: a biochemical signal integration system subserving synaptic plasticity and memory. Journal of Neurochemistry, 76(1):1-10, 2001. URL: https://doi.org/10.1046/j.1471-4159.2001.00054.x.
  48. Mario Teichmann, Enzo Kopperger, and Friedrich C. Simmel. Robustness of localized DNA strand displacement cascades. ACS Nano, 8(8):8487-8496, August 2014. Publisher: American Chemical Society. URL: https://doi.org/10.1021/nn503073p.
  49. Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, and Niles A. Pierce. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnology, 2(8):490-494, August 2007. Number: 8 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/nnano.2007.225.
  50. Alan J. Whitmarsh, Julie Cavanagh, Cathy Tournier, Jun Yasuda, and Roger J. Davis. A mammalian scaffold complex that selectively mediates MAP kinase activation. Science, 281(5383):1671-1674, September 1998. Publisher: American Association for the Advancement of Science Section: Report. URL: https://doi.org/10.1126/science.281.5383.1671.
  51. Christian Widmann, Spencer Gibson, Matthew B. Jarpe, and Gary L. Johnson. Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human. Physiological Reviews, 79(1):143-180, January 1999. Publisher: American Physiological Society. URL: https://doi.org/10.1152/physrev.1999.79.1.143.
  52. Wataru Yahiro and Masami Hagiya. Implementation of Turing machine using DNA strand displacement. In Carlos Martín-Vide, Takaaki Mizuki, and Miguel A. Vega-Rodríguez, editors, Theory and Practice of Natural Computing, Lecture notes in computer science, pages 161-172, Cham, 2016. Springer International Publishing. URL: https://doi.org/10.1007/978-3-319-49001-4_13.
  53. Peng Yin, Harry M. T. Choi, Colby R. Calvert, and Niles A. Pierce. Programming biomolecular self-assembly pathways. Nature, 451(7176):318-322, January 2008. Number: 7176 Publisher: Nature Publishing Group. URL: https://doi.org/10.1038/nature06451.
  54. Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, and Niles A. Pierce. NUPACK: Analysis and design of nucleic acid systems. Journal of Computational Chemistry, 32(1):170-173, 2011. URL: https://doi.org/10.1002/jcc.21596.
  55. David Yu Zhang and Georg Seelig. Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chemistry, 3(2):103-113, February 2011. URL: https://doi.org/10.1038/nchem.957.
  56. David Yu Zhang, Andrew J. Turberfield, Bernard Yurke, and Erik Winfree. Engineering entropy-driven reactions and networks catalyzed by DNA. Science, 318(5853):1121-1125, November 2007. Publisher: American Association for the Advancement of Science Section: Report. URL: https://doi.org/10.1126/science.1148532.
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