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Two-domain DNA strand displacement


We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study fork and join signal processing gates based on these structures, and show that these systems are amenable to formalisation and mechanical verification.

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Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z. and Shapiro, E. (2001) Programmable and Autonomous Computing Machine made of Biomolecules. Nature 414 (22).
Berry, G. and Boudol, G. (1989) The Chemical Abstract Machine. Proceedings 17th POPL, ACM 8194.
Cardelli, L. (2011) Strand Algebras for DNA Computing. Natural Computing 10 (1)407428.
Fontana, W. (2006) Science 314 (8).
Green, S. J., Lubrich, D. and Turberfield, A. J. (2006) DNA Hairpins: Fuel for Autonomous DNA Devices. Biophysical Journal 91 29662975.
Hagiya, M. (2004) Towards Molecular Programming. In: Ciobanu, G. and Rozenberg, G. (eds.) Modelling in Molecular Biology, Springer-Verlag.
Hinton, A., Kwiatkowska, M., Norman, G. and Parker, D. (2006) PRISM: A tool for automatic verification of probabilistic systems. In: Hermanns, H. and Palsberg, J. (eds.) Proceedings 12th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS'06). Springer-Verlag Lecture Notes in Computer Science 3920 441444.
Milner, R. (1999) Communicating and Mobile Systems: The π-Calculus, Cambridge University Press.
Phillips, A. and Cardelli, L. (2009) A Programming Language for Composable DNA Circuits. Journal of the Royal Society Interface 6 S419–S436.
Qian, L. and Winfree, E. (2011) A simple DNA gate motif for synthesizing large-scale circuits. Journal of the Royal Society Interface doi: 10.1098/rsif.2010.0729.
Seelig, G., Soloveichik, D., Zhang, D. Y. and Winfree, E. (2006) Enzyme-Free Nucleic Acid Logic Circuits. Science 314 (8).
Soloveichik, D., Seelig, G. and Winfree, E. (2010) DNA as a Universal Substrate for Chemical Kinetics. PNAS 107 (12)53935398.
Yin, P., Choi, H. M. T., Calvert, C. R. and Pierce, N. A. (2008) Programming biomolecular self-assembly pathways. Nature 451 318322.
Yurke, B. and Mills, A. P. Jr. (2003) Using DNA to Power Nanostructures. Genetic Programming and Evolvable Machines Archive 4 (2)111122.
Zhang, D. Y. (2010) Dynamic DNA strand displacement circuits, Ph.D. Dissertation, California Institute of Technology. (Available at
Zhang, D. Y. (2011) Journal of the American Chemical Society 133 (4)10771086.
Zhang, D. Y., Turberfield, A. J., Yurke, B. and Winfree, E. (2007) Engineering Entropy-driven Reactions and Networks Catalyzed by DNA. Science 318 11211125.
Zhang, D. Y. and Seelig, G. (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chemistry 3 103113.
Zhang, D. Y. and Winfree, E. (2009) Control of DNA Strand Displacement Kinetics Using Toehold Exchange. Journal of the American Chemical Society 131 (47)1730317314.
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Mathematical Structures in Computer Science
  • ISSN: 0960-1295
  • EISSN: 1469-8072
  • URL: /core/journals/mathematical-structures-in-computer-science
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