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Two-domain DNA strand displacement

  • LUCA CARDELLI (a1)
Abstract

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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Y. Benenson , T. Paz-Elizur , R. Adar , E. Keinan , Z. Livneh and E. Shapiro (2001) Programmable and Autonomous Computing Machine made of Biomolecules. Nature 414 (22).

L. Cardelli (2011) Strand Algebras for DNA Computing. Natural Computing 10 (1) 407428.

W. Fontana (2006) Science 314 (8).

S. J. Green , D. Lubrich and A. J. Turberfield (2006) DNA Hairpins: Fuel for Autonomous DNA Devices. Biophysical Journal 91 29662975.

M. Hagiya (2004) Towards Molecular Programming. In: G. Ciobanu and G. Rozenberg (eds.) Modelling in Molecular Biology, Springer-Verlag.

A. Hinton , M. Kwiatkowska , G. Norman and D. Parker (2006) PRISM: A tool for automatic verification of probabilistic systems. In: H. Hermanns and J. Palsberg (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.

A. Phillips and L. Cardelli (2009) A Programming Language for Composable DNA Circuits. Journal of the Royal Society Interface 6 S419–S436.

G. Seelig , D. Soloveichik , D. Y. Zhang and E. Winfree (2006) Enzyme-Free Nucleic Acid Logic Circuits. Science 314 (8).

D. Soloveichik , G. Seelig and E. Winfree (2010) DNA as a Universal Substrate for Chemical Kinetics. PNAS 107 (12) 53935398.

P. Yin , H. M. T. Choi , C. R. Calvert and N. A. Pierce (2008) Programming biomolecular self-assembly pathways. Nature 451 318322.

B. Yurke and A. P. Mills Jr. (2003) Using DNA to Power Nanostructures. Genetic Programming and Evolvable Machines Archive 4 (2) 111122.

D. Y. Zhang (2011) Journal of the American Chemical Society 133 (4) 10771086.

D. Y. Zhang , A. J. Turberfield , B. Yurke and E. Winfree (2007) Engineering Entropy-driven Reactions and Networks Catalyzed by DNA. Science 318 11211125.

D. Y. Zhang and G. Seelig (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chemistry 3 103113.

D. Y. Zhang and E. Winfree (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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