Abstract
We present a computing model based on the DNA strand displacement technique which performs Bayesian inference. The model will take single stranded DNA as input data, representing the presence or absence of a specific molecular signal (evidence). The program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different DNA complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded DNA species whose relative proportion represents the application of Bayes’ Law: the conditional probability of the disease given the signal. The models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adar, R., Benenson, Y., Linshiz, G., Rosner, A., Tishby, N., Shapiro, E.: Stochastic computing with biomolecular automata. Proceedings of the National Academy of Sciences of the United States of America 101(27), 9960–9965 (2004)
Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266(5187), 1021–1024 (1994)
Benenson, Y., Adar, R., Paz-Elizur, T., Livneh, Z., Shapiro, E.: DNA molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA 100(5), 2191–2196 (2003)
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nature 429, 423–429 (2004)
Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414(6862), 430–434 (2001)
Cardelli, L.: Strand Algebras for DNA Computing. In: Deaton, R., Suyama, A. (eds.) DNA 15. LNCS, vol. 5877, pp. 12–24. Springer, Heidelberg (2009)
Chiniforooshan, E., Doty, D., Kari, L., Seki, S.: Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. In: Sakakibara, Y., Mi, Y. (eds.) DNA 16 2010. LNCS, vol. 6518, pp. 25–36. Springer, Heidelberg (2011)
Cho, E.J., Lee, J.W., Ellington, A.D.: Applications of Aptamers as Sensors. Annual Review of Analytical Chemistry 2(1), 241–264 (2009)
Frezza, B.M., Cockroft, S.L., Ghadiri, M.R.: Modular multi-level circuits from immobilized DNA-based logic gates. J. Am. Chem. Soc. 129(48), 14875–14879 (2007)
Lim, H.-W., Lee, S.H., Yang, K.-A., Lee, J.Y., Yoo, S.-I., Park, T.H., Zhang, B.-T.: In vitro molecular pattern classification via dna-based weighted-sum operation. Biosystems 100(1), 1–7 (2010)
Lipton, R.J.: DNA solution of hard computational problems. Science 268(5210), 542–545 (1995)
Minsky, M.: Steps toward artificial intelligence. Proceedings of the IRE 49(1), 8–30 (1961)
Sainz de Murieta, I., Rodríguez-Patón, A.: DNA biosensors that reason. Biosystems (in press, 2012)
Pearl, J.: Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference, 1st edn. Morgan Kaufmann (September 1988)
Ran, T., Kaplan, S., Shapiro, E.: Molecular implementation of simple logic programs. Nature Nanotechnology 4(10), 642–648 (2009)
Rodríguez-Patón, A., Larrea, J.M., Sainz de Murieta, I.: Inference with DNA Molecules. In: Calude, C.S., Hagiya, M., Morita, K., Rozenberg, G., Timmis, J. (eds.) Unconventional Computation. LNCS, vol. 6079, p. 192. Springer, Heidelberg (2010)
Rodríguez-Patón, A., Sainz de Murieta, I., Sosík, P.: Autonomous Resolution Based on DNA Strand Displacement. In: Cardelli, L., Shih, W. (eds.) DNA 17 2011. LNCS, vol. 6937, pp. 190–203. Springer, Heidelberg (2011)
Russell, S., Norvig, P.: Artificial Intelligence: A Modern Approach, 2nd edn. Prentice Hall series in artificial intelligence. Prentice Hall (December 2002)
Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314(5805), 1585–1588 (2006)
Shortliffe, E.H., Buchanan, B.G.: A model of inexact reasoning in medicine. Mathematical Biosciences 23(3-4), 351–379 (1975)
Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences 107(12), 5393–5398 (2010)
Takahashi, K., Yaegashi, S., Kameda, A., Hagiya, M.: Chain Reaction Systems Based on Loop Dissociation of DNA. In: Carbone, A., Pierce, N.A. (eds.) DNA 11. LNCS, vol. 3892, pp. 347–358. Springer, Heidelberg (2006)
Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406(6796), 605–608 (2000)
Zhang, B.-T., Jang, H.-Y.: A Bayesian Algorithm for In Vitro Molecular Evolution of Pattern Classifiers. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 2004. LNCS, vol. 3384, pp. 458–467. Springer, Heidelberg (2005)
Zhang, D.Y., Winfree, E.: Dynamic allosteric control of noncovalent dna catalysis reactions. Journal of the American Chemical Society 130(42), 13921–13926 (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Sainz de Murieta, I., Rodríguez-Patón, A. (2012). Probabilistic Reasoning with a Bayesian DNA Device Based on Strand Displacement. In: Stefanovic, D., Turberfield, A. (eds) DNA Computing and Molecular Programming. DNA 2012. Lecture Notes in Computer Science, vol 7433. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32208-2_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-32208-2_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-32207-5
Online ISBN: 978-3-642-32208-2
eBook Packages: Computer ScienceComputer Science (R0)