Abstract
Because of its outstanding advantages, DNA strand displacement (DSD) reaction has been widely used for signals processing and molecular logic circuit constructing. Two digital logic circuits are constructed in this paper. One is the encoder circuit with four inputs and two outputs, and the other is the decoder circuit with two inputs and four outputs. Finally, the circuits can be programmed and simulated with the software Visual DSD. The simulated results based on DSD show that the molecular circuits constructed in this paper is reliable and effective, which has wide prospects in logical circuits and nano electronics study.
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References
Păun, G., Rozenberg, G., Salomaa, A.: The Oxford Handbook of Membrane Computing. Oxford University Press Inc., Oxford (2010)
Song, T., Pan, L.: Spiking neural P systems with rules on synapses working in maximum spikes consumption strategy. IEEE Trans. NanoBiosci. 14(1), 38–44 (2015)
Zhang, X., Pan, L., Păun, A.: On the universality of axon P systems. IEEE Trans. Neural Netw. Learn. Syst. 26(11), 2816–2829 (2015). doi:10.1109/TNNLS.2015.2396940
Song, T., Pan, L.: Spiking neural P systems with rules on synapses working in maximum spiking strategy. IEEE Trans. NanoBiosci. 14(4), 465–477 (2015)
Tzn, B., Erko, S.: Structural and electronic properties of unusual carbon nanorods. Quantum Matter 13, 136–148 (2012)
Seeman, N.C.: DNA nanotechnology: novel DNA constructure. Ann. Rev. Biophys. Biomol. Struct. 27, 225–248 (1998)
Mao, C., Sun, W., Seeman, N.C.: Designed two dimensional DNA holliday junction arrays vis-ualized by atomic force microscopy. J. Am. Chem. Soc. 121(23), 5437–5443 (1999)
Mao, C., LaBean, T.H., Reif, J.H.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407(6803), 493–496 (2000)
Stojanovic, M.N.: A deoxyribozyme-based molecular automaton. Biotechnology 21, 1069–1074 (2003)
Elbaz, J., Lioubashevski, O., Wang, F.: All-DNA finite-state automata with finite memory. Nanotechnology 107(51), 21996–22001 (2010)
Song, T., Pan, L., Păun, G.: Asynchronous spiking neural P systems with local synchronization. Inf. Sci. 219, 197–207 (2013)
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nature 429(6990), 423–429 (2004)
Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C.: A DNA-fuelled molecular machine made of DNA. Nature 406(6796), 605–608 (2000)
Turberfield, A.J., Mitchell, J.C., Yurke, B.: DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003)
Yurke, B., Mills, A.P.: Using DNA to power nanostructures. Program. Evol. Mach. 4(2), 111–122 (2003)
Zhang, D.Y., Seelig, G.: Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3(2), 103–113 (2011)
Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034), 1196–1201 (2011)
Song, T., Pan, L., Wang, J., et al.: Normal forms of spiking neural P systems with anti-spikes. IEEE Trans. NanoBiosci. 11(4), 352–359 (2012)
Qian, L., Winfree, E., Bruck, J.: Neural network computation with DNA strand displacement cascades. Nature 475(7356), 368–372 (2011)
Qian, L., Winfree, E.: A simple DNA gate motif for synthesizing large-scale circuits. In: Goel, A., Simmel, F.C., SosÃk, P. (eds.) DNA Computing. LNCS, vol. 5347, pp. 70–89. Springer, Heidelberg (2009)
Zhang, D.Y., Andrew, J., Bernard, Y., Winfree, E.: Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318(5853), 1121–1125 (2007)
Zhang, D.Y., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. Am. Chem. Soc. 131(47), 17303–17314 (2009)
Wang, X., Miao, Y., Cheng, M.: Finding motifs in DNA sequences using low-dispersion sequences. J. Comput. Biol. 21(4), 320–329 (2014)
Yurke, B., Mills, A.P.: Using DNA to power nanostructures. Genet. Program. Evol. Mach. 4(2), 111–122 (2003)
Song, T., Pan, L., Jiang, K., et al.: Normal forms for some classes of sequential spiking neural P systems. IEEE Trans. NanoBiosci. 12(3), 255–264 (2013)
Phillips, A., Cardelli, L.: A programming language for composable DNA circuits. Interface 6(4), 419–436 (2009)
Matthew, L., Simon, Y.: Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics 27(22), 3211–3213 (2011)
Lakin, M.R., Youssef, S., Cardelli, L., Phillips, A.: Abstractions for DNA circuit design. J. Royal Soc. Interface 9(68), 470–486 (2012)
Venkataraman, S., Dirks, R.M., Ueda, C.T., Pierce, N.A.: Selective cell death mediated by small conditional RNAs. PNAS 39(107), 16777–16782 (2010)
Eckhoff, G., Codrea, V., Ellington, A.D., Chen, X.: Beyond allostery: catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier. J. Syst. Chem. 1(1), 1–6 (2010)
Su, Y., Pan, L.: Identification of logic relationships between genes and subtypes of non-small cell lung cancer. PLoS One 9(4), 94664 (2014)
Wang, X., Miao, Y.: GAEM: a hybrid algorithm incorporating GA with EM for planted edited motif finding problem. Curr. Bioinf. 9(5), 463–469 (2014)
Kim, V.N.: MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6(5), 376–385 (2005)
Carthew, R.W., Sontheimer, E.J.: Origins and mechanisms of miRNAs and siRNAs. 136(4), 642-655 (2009)
Shi, X., Wang, Z., Deng, C., Song, T., Pan, L., Chen, Z.: A novel bio-sensor based on DNA strand displacement. PLoS One 9(10), e108856 (2014)
Acknowledgements
This work is supported by the NSFC (No. U1304620, 61472372, 61272022), Innovation Scientists and Technicians Troop Construction Projects of Henan (Grant No. 124200510017), and Innovation Scientists and Techni-cians Troop Construction Projects of Zhengzhou (Grant No. 131PLJRC648), Basic and Frontier technologies Research Program of Henan Province (132300410183), Innovation Scientists and Technicians Troop Construction Projects of Henan Province(154200510 012).
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Wang, Z., Cai, Z., Sun, Z., Wang, Y., Cui, G. (2015). The Design of Digital Circuit Based on DNA Strand Displacement Reaction. In: Gong, M., Linqiang, P., Tao, S., Tang, K., Zhang, X. (eds) Bio-Inspired Computing -- Theories and Applications. BIC-TA 2015. Communications in Computer and Information Science, vol 562. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-49014-3_41
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DOI: https://doi.org/10.1007/978-3-662-49014-3_41
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