The Formal Language and Design Principles of Autonomous DNA Walker Circuits

ACS Synthetic Biology

Volumn 5, Issue 8, 2016, Pages 878-884

  Boemo, Michael A ^a   Lucas, Alexandra E ^a   Turberfield, Andrew J ^a   Cardelli, Luca ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b MICROSOFT RESEARCH   (United Kingdom)

Author keywords

distributed systems; DNA computation; DNA walkers; logic gates; Petri nets

Indexed keywords

ARTICLE; COMPUTER HEURISTICS; COMPUTER LANGUAGE; DNA DETERMINATION; DNA STRAND; EXPERIMENTAL DESIGN; GENE MAPPING; GEOMETRY; MARKOV CHAIN; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RESTRICTION SITE; GENETICS; MOLECULAR COMPUTER; SOFTWARE;

DNA;

COMPUTERS, MOLECULAR; DNA; SOFTWARE;

EID: 84983347907     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00275     Document Type: Article

References (13)

1. Phillips, A. and Cardelli, L. (2009) A programming language for composable DNA circuits J. R. Soc., Interface 6, S419-S436 10.1098/rsif.2009.0072.focus
2. Lakin, M. R., Youssef, S., Polo, F., Emmott, S., and Phillips, A. (2011) Visual DSD: A design and analysis tool for DNA strand displacement systems Bioinformatics 27, 3211-3213 10.1093/bioinformatics/btr543
3. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., and Shapiro, E. (2004) An autonomous molecular computer for logical control of gene expression Nature 429, 423-429 10.1038/nature02551
4. Yin, P., Turberfield, A. J., Sahu, S., and Reif, J. H. (2005) In DNA Computing (Ferretti, C., Mauri, G., and Zandron, C., Eds.) Lecture Notes in Computer Science, Vol. 3384, pp 426-444, Springer, Berlin, Heidelberg.
5. Bath, J., Green, S. J., and Turberfield, A. J. (2005) A free-running DNA motor powered by a nicking enzyme Angew. Chem. 117, 4432-4435 10.1002/ange.200501262
6. Wickham, S. F. J., Endo, M., Katsuda, Y., Hidaka, K., Bath, J., Sugiyama, H., and Turberfield, A. J. (2011) Direct observation of stepwise movement of a synthetic molecular transporter Nat. Nanotechnol. 6, 166-169 10.1038/nnano.2010.284
7. Rothemund, P. W. K. (2006) Folding DNA to create nanoscale shapes and patterns Nature 440, 297-302 10.1038/nature04586
8. Wickham, S. F. J., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., and Turberfield, A. J. (2012) A DNA-based molecular motor that can navigate a network of tracks Nat. Nanotechnol. 7, 169-173 10.1038/nnano.2011.253
9. Dannenberg, F., Kwiatkowska, M., Thachuk, C., and Turberfield, A. J. (2013) In DNA Computing and Molecular Programming (Soloveichik, D. and Yurke, B., Eds.) Lecture Notes in Computer Science, Vol. 8141, pp 31-45, Springer International Publishing.
10. Lakin, M., Petersen, R., Gray, K. E., and Phillips, A. (2014) In DNA Computing and Molecular Programming (Murata, S. and Kobayashi, S., Eds.) Lecture Notes in Computer Science, Vol. 8727, pp 132-147, Springer International Publishing.
11. Joyner, D., Čertík, O., Meurer, A., Granger, B. E., and Joyner, D. (2011) Open Source Computer Algebra Systems: SymPy ACM Commun. Comput. Algebra 45, 225-234 10.1145/2110170.2110185
12. Kwiatkowska, M., Norman, G., and Parker, D. (2011) PRISM 4.0: Verification of probabilistic real-time systems Proc. 23rd International Conference on Computer Aided Verification 6806, 585-591 10.1007/978-3-642-22110-1-47
13. Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., and Pierce, N. A. (2011) NUPACK: Analysis and design of nucleic acid systems J. Comput. Chem. 32, 170-173 10.1002/jcc.21596