Abstract
DNA strand displacement has been widely used in designing the molecular logic circuit, nanomedicine and molecular automata and so on. In this article, the two-digit full subtractor is designed by DNA strand displacement reaction and has been verified by the simulation of DNA strand displacement. The accuracy of simulation results is further confirmed that DNA strand displacement is a valid method for the research of logical bio-chemical circuit. The multi-digit full subtractor could be used in biological computer in the future.
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References
Beaver, D.: Computing with DNA. J. Comput. Biol. 3, 254–257 (1996)
Xu, J., Qiang, X., Yang, Y., et al.: An unenumerative DNA computing model for vertex coloring problem. IEEE Trans. Nanobiosci. 10, 94–98 (2011)
Chen, Y.J., Dalchau, N., Srinivas, N., et al.: Programmable chemical controllers made from DNA. Nature Nanotechnol. 8, 755–762 (2013)
Yurke, B., Turberfield, A.J., Mills, A.P., et al.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)
Mao, C., LaBean, T.H., Reif, J.H., et al.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)
Santini, C.C., Bath, J., Turberfield, A.J., et al.: A DNA network as an information processing system. Int. J. Mol. Sci. 13, 5125–5137 (2012)
Shin, J.C.S., Pierce, N.A.: A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–10835 (2004)
Lund, K., Manzo, A.J., Dabby, N., et al.: Molecular robots guided by prescriptive land-scapes. Nature 465, 206–210 (2010)
Rahul, C., Jaswinder, S., Yan, L., Sherri, R., Hao, Y.: DNA self-assembly for nanomedicine. Adv. Drug. Deliver. Rev. 62, 617–625 (2010)
Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314, 1585–1588 (2006)
Lederman, H., Macdonald, J., Stephanovic, D., Stojanovic, M.N.: Deoxyribozymebased three-input logic gates and construction of a molecular full adder. Biochemistry 45, 1194–1199 (2006)
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 2010. LNCS, vol. 6518, pp. 25–36. Springer, Heidelberg (2011). doi:10.1007/978-3-642-18305-8_3
Qian, L., Winfree, E.: A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface 8, 1281–1297 (2011)
Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011)
Zhang, D.Y., Seelig, G.: Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103–113 (2011)
Zhang, C., Ma, L.N., Dong, Y.F., et al.: Molecular logic computing model based on DNA self-assembly strand branch migration. Chinese. Sci. Bull. 58, 32–38 (2013)
Shi, X.L., Lu, W., Wang, Z.Y., Pan, L.Q., Cui, G.Z., Xu, J., LaBean, T.H.: Programmable DNA tile self-assembly using a hierarchical sub-tile strategy. Nanotechnology 25(7), 075602 (2014)
Shi, X.L., Wang, Z.Y., Deng, C.Y., Song, T., Pan, L.Q., Chen, Z.H.: A novel bio-sensor based on DNA strand displacement. PLoS ONE 9(10), e108856 (2014). doi:10.1371/journal.pone.0108856
Yang, J., Dong, C., Dong, Y.F., Liu, S., Pan, L.Q., Zhang, C.: Logic nanoparticle beacon triggered by the binding-induced effect of multiple inputs. ACS Appl. Mater. Interfaces 6(16), 14486–14492 (2014)
Xu, J.: Probe machine. IEEE Trans. Neural Netw. Learn. Syst. 27(7), 1405–1416 (2016)
Wang, Y., Tian, G., Hou, H., et al.: Simple logic computation based on the DNA strand displacement. J. Comput. Theor. Nanosci. 11, 1975–1982 (2014)
Cui, G., Zhang, J., Cui, Y., et al.: DNA strand-displacement digital logic circuit with fluorescence resonance energy transfer detection. J. Comput. Theor. Nanosci. 12, 2095–2100 (2015)
Zhang, D.Y., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303–17314 (2009)
Zhang, D.Y.: Towards domain-based sequence design for DNA strand displacement reactions. In: Sakakibara, Y., Mi, Y. (eds.) DNA 2010. LNCS, vol. 6518, pp. 162–175. Springer, Heidelberg (2011). doi:10.1007/978-3-642-18305-8_15
Yurke, B., Mills, A.P.: Using DNA to power nanostructures. Genet. Program. Evol. Mach. 4, 111 (2003). doi:10.1023/A:1023928811651
Lakin, M.R., Youssef, S., Polo, F., Emmott, S., et al.: Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics 27, 3211–3213 (2011)
Lakin, M.R., Petersen, R., Gray, K.E., Phillips, A.: Abstract modelling of tethered DNA circuits. In: Murata, S., Kobayashi, S. (eds.) DNA 2014. LNCS, vol. 8727, pp. 132–147. Springer, Heidelberg (2014). doi:10.1007/978-3-319-11295-4_9
Song, T., Pan, L.: Spiking neural P systems with request rules. Neurocomputing 193(12), 193–200 (2016)
Song, T., Liu, X., Zhao, Y., Zhang, X.: Spiking neural P systems with white hole neurons. IEEE Trans. Nanobiosci. (2016). doi:10.1109/TNB.2016.2598879
Song, T., Pan, Z., Wong, D.M., Wang, X.: Design of logic gates using spiking neural P systems with homogeneous neurons and astrocytes-like control. Inf. Sci. 372, 380–391 (2016)
Wang, X., Song, T., Gong, F., Pan, Z.: On the computational power of spiking neural P systems with self-organization. Scientific reports. doi:10.1038/srep27624
Shi, X., Wu, X., Song, T., Li, X.: Construction of DNA nanotubes with controllable diameters and patterns by using hierarchical DNA sub-tiles. Nanoscale 8, 14785–14792 (2016). doi:10.1039/C6NR02695H
Acknowledgments
The work is supported by the State Key Program of the National Natural Science Foundation of China (Grant No. 61632002), the National Natural Science Foundation of China (Grant Nos. 61472371, 61472372, 61572446, 61602424 and 61603348), China Postdoctoral Science Foundation funded project (Grant No. 2015M570641 and 2016T90687), Basic and Frontier Technology Research Program of Henan Province (Grant No. 162300410220), Key Program of Higher Education of China Henan Province (Grant No. 17A120005) and the Science Foundation of for Doctorate Research of Zhengzhou University of Light Industry (Grant No. 2014BSJJ044).
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Sun, J., Li, X., Huang, C., Cui, G., Wang, Y. (2016). Two-Digit Full Subtractor Logical Operation Based on DNA Strand Displacement. In: Gong, M., Pan, L., Song, T., Zhang, G. (eds) Bio-inspired Computing – Theories and Applications. BIC-TA 2016. Communications in Computer and Information Science, vol 681. Springer, Singapore. https://doi.org/10.1007/978-981-10-3611-8_3
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DOI: https://doi.org/10.1007/978-981-10-3611-8_3
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