Skip to main content
    • Aa
    • Aa

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.

Linked references
Hide All

This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

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.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Mathematical Structures in Computer Science
  • ISSN: 0960-1295
  • EISSN: 1469-8072
  • URL: /core/journals/mathematical-structures-in-computer-science
Please enter your name
Please enter a valid email address
Who would you like to send this to? *


Full text views

Total number of HTML views: 0
Total number of PDF views: 47 *
Loading metrics...

Abstract views

Total abstract views: 220 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 26th June 2017. This data will be updated every 24 hours.