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Published in:
Logic Operation Model of the Complementer Based on Two-Domain DNA Strand Displacement Read chapter Read first chapter

2017 | OriginalPaper | Chapter

A Circuit Simplification Mechanism Based on DNA Combinatorial Strands Displacement

Authors : Xuncai Zhang, Feng Han, Yanfeng Wang

Published in: Bio-inspired Computing: Theories and Applications

Publisher: Springer Singapore

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Abstract

Through extensive application of DNA strand displacement technology in the field of molecular computing, we know that the DNA strand of the toehold domain and the branch migration domain are covalently connected to form logical gates in traditional DNA strand displacement circuits. In this paper, we will adopt a composite strand mechanism that the toehold domain and branch migration domain in different single strand form displacing complex, and construct logical gates with combinatorial strand displacement mechanism. After that, a logic gate model is constructed, and the mechanism is verified by the design and simulation of the logical molecular model of the encoder. When the DNA signal strand is input, the signal strand molecule can be output by combination of molecular specific hybridization reaction and intermolecular strand displacement reaction. The results of Visual DSD simulation show the feasibility and accuracy of the encoder logic calculation model designed in this article.

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previous chapter A New Image Encryption Algorithm Based on DNA Dynamic Encoding and Hyper-Chaotic System
next chapter The Design of RNA Biosensors Based on Nano-Gold and Magnetic Nanoparticles
Literature
1.
Mao, C., Labean, T.H., Relf, J.H.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)CrossRef
2.
Penchovsky, R., Breaker, R.R.: Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat. Biotechnol. 23, 1424 (2005)CrossRef
3.
Seelig, G., Soloveichik, D., Zhang, D.Y.: Nucleic acid-based logic circuits. Science 314, 1582–1588 (2006)CrossRef
4.
Zhang, D.Y., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303–17314 (2009)CrossRef
5.
Zhang, D.Y., Seelig, G.: Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103 (2011)CrossRef
6.
Genot, A.J., Zhang, D.Y., Bath, J.: Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. J. Am. Chem. Soc. 133, 2177 (2011)CrossRef
7.
8.
Qian, L., Winfree, E., Bruck, J.: Neural network computation with DNA strand displacement cascades. Nature 475, 368–372 (2011)CrossRef
9.
Zhang, C., Li, D.: Molecular logic computing model based on DNA self-assembly strand branch migration. Chin. Sci. Bull. 58, 32–38 (2013)CrossRef
10.
Abels, S.G., Khisamutdinov, E.F.: Nucleic acid computing and its potentialto transform silicon-based technology. DNA RNA Nanotechnol. 2, 13–22 (2015)CrossRef
11.
Song, T., Zheng, P., Wong, M.L.D.: Design of logic gates using spiking neural P systems with homogeneous neurons and astrocytes-like control. Inf. Sci. 372, 380–391 (2016)CrossRef
12.
Shi, X., Wang, Z., Deng, C., Song, T., Pan, L., Chen, Z.: A novel bio-sensor based on DNA strand displacement. PLoS ONE 9, e108856 (2014)CrossRef
13.
Song, T., Garg, S., Mokhtar, R.: Analog computation by DNA strand displacement circuits. ACS Synth. Biol. 5, 898 (2016)CrossRef
14.
Zhang, C., Yang, J., Xu, J.: Molecular logic computing model based on self-assembly of DNA nanoparticles. Chin. Sci. Bull. 56, 3566–3571 (2011)CrossRef
15.
Shi, X., Lu, W., Wang, Z., Pan, L., Cui, G., Xu, J.: Programmable DNA tile self-assembly using a hierarchical sub-tile strategy. Nanotechnology 25, 075602 (2014)CrossRef
16.
Sun, J., Wu, Y., Cui, G., Wang, Y.: Finite-time real combination synchronization of three complex-variable chaotic systems with unknown parameters via sliding mode control. Nonlinear Dyn. 88, 1677–1690 (2017)CrossRef
17.
Genot, A.J., Bath, J., Turberfield, A.J.: Combinatorial displacement of DNA strands: application to matrix multiplication and weighted sums. Angew. Chem. Int. Ed. Engl. 125, 1227–1230 (2013)CrossRef
18.
Sun, J., Wang, Y., Wang, Y., Shen, Y.: Finite-time synchronization between two complex-variable chaotic systems with unknown parameters via nonsingular terminal sliding mode control. Nonlinear Dyn. 85, 1105–1117 (2016)CrossRefMATHMathSciNet
19.
Jing, Y., Song, Z., Shi, L., Zhang, Q., Zhang, C.: Dynamically arranging gold nanoparticles on DNA origami for molecular logic gates. ACS Appl. Mater. Inter. 8, 22451 (2016)CrossRef
20.
Elbaz, J., Yin, P., Voigt, C.A.: Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nat. Commun. 7, 11179 (2016)CrossRef
21.
Jing, Y., Shuoxing, J., Xiangrong, L., Linqiang, P., Cheng, Z.: Aptamer-binding directed DNA origami pattern for logic gates. ACS Appl. Mater. Inter. 8, 34054–34060 (2016)CrossRef
22.
Mateiu, L., Rannala, B.: Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation. Syst. Biol. 55, 259–269 (2006)CrossRef
23.
Li, W., Yang, Y., Yan, H.: Three-input majority logic gate and multiple input logic circuit based on DNA strand displacement. Nano Lett. 13, 2980 (2013)CrossRef
24.
Alexandru, M., Banu, V., Vellvehi, M.: Design of digital electronics for high temperature using basic logic gates made of 4H-SiC MESFETs. Mater. Sci. Forum 711, 104–108 (2011)CrossRef
25.
Jing, Y., Chen, D., Dong, Y., Shi, L., Pan, L., Cheng, Z.: Logic nanoparticle beacon triggered by the binding-induced effect of multiple inputs. ACS Appl. Mater. Inter. 6, 14486–14492 (2012)
26.
Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Nat. Acad. Sci. USA 107, 5393–5398 (2010)CrossRef
27.
Nasri, A., Boubaker, A., Khaldi, W., Hafsi, B., Kalboussi, A.: Tuning negative differential resistance in a single molecule transistor: designs of logic gates and effects of various oxygen- and hydrogen-induced defects. Dig. J. Nanomater. Bios. 12, 99–110 (2017)
28.
Sun, J., Shen, Y.: Quasi-ideal memory system. IEEE Trans. Cybern. 45, 1353–1362 (2015)CrossRef
29.
Wang, Y., Tian, G., Hou, H., Ye, M., Cui, G.: Simple logic computation based on the DNA strand displacement. J. Comput. Theor. Nanosci. 11, 1975–1982 (2014)CrossRef
30.
Lakin, M.R., Youssef, S., Polo, F., Emmott, S., Phillips, A.: Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics 27, 3211–3213 (2011)CrossRef
Metadata
Title
A Circuit Simplification Mechanism Based on DNA Combinatorial Strands Displacement
Authors
Xuncai Zhang
Feng Han
Yanfeng Wang
Copyright Year
2017
Publisher
Springer Singapore
Book
Bio-inspired Computing: Theories and Applications

Print ISBN: 978-981-10-7178-2

Electronic ISBN: 978-981-10-7179-9

Copyright Year: 2017

DOI
https://doi.org/10.1007/978-981-10-7179-9_23

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