Priority Encoder Based on DNA Strand Displacement

WANG Fang; ZHANG Xinjian; CHEN Xin; LV Shuying; CHEN Congzhou; SHI Xiaolong

doi:10.23919/cje.2022.00.042

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Fang WANG, Xinjian ZHANG, Xin CHEN, et al., “Priority Encoder Based on DNA Strand Displacement,” Chinese Journal of Electronics, vol. 33, no. 6, pp. 1–8, 2024 doi: 10.23919/cje.2022.00.042

Citation:

Fang WANG, Xinjian ZHANG, Xin CHEN, et al., “Priority Encoder Based on DNA Strand Displacement,” Chinese Journal of Electronics, vol. 33, no. 6, pp. 1–8, 2024 doi: 10.23919/cje.2022.00.042

Fang WANG, Xinjian ZHANG, Xin CHEN, et al., “Priority Encoder Based on DNA Strand Displacement,” Chinese Journal of Electronics, vol. 33, no. 6, pp. 1–8, 2024 doi: 10.23919/cje.2022.00.042

Citation:

Fang WANG, Xinjian ZHANG, Xin CHEN, et al., “Priority Encoder Based on DNA Strand Displacement,” Chinese Journal of Electronics, vol. 33, no. 6, pp. 1–8, 2024 doi: 10.23919/cje.2022.00.042

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Priority Encoder Based on DNA Strand Displacement

doi: 10.23919/cje.2022.00.042

1.
Institution of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
2.
Beijing University of Technology, Beijing 100081, China
3.
School of Computer Science, Peking university, Beijing 100871, China

More Information

Author Bio:
Fang WANG received the B.S. degree from Ocean University of China in 2019. She is currently pursuing the Master’s degree in Computer Science at Guangzhou University. Her interests include DNA computing and DNA nano-manufacturing. (Email: 2111906105@e.gzhu.edu.cn)

Xinjian ZHANG Received the B.S. degree from Zhengzhou University in 2019. He is currently pursuing the Master’s degree in Computer Science at Guangzhou University. His interests include DNA computing and bio-computing. (Email: 2111906105@e.gzhu.edu.cn)

Xin CHEN received the B.S. degree from Hunan University of Science and Engineering in 2020. He is currently pursuing the Master’s degree in Computer Science at Guangzhou University. His interests include DNA computing and nanostructure. (Email: 2112006073@e.gzhu.edu.cn)

Shuying LV is currently pursuing a B.S. degree in Aerospace at Beijing University of Technology.Her interests include Aerospace Engineering and mathematical modeling. (Email:1120203335@bit.edu.cn)

Congzhou CHEN received the B.S. degree in Automation from Wuhan University of Science and Technology, Wuhan, China in 2014 and the M.S. degree in Automation from Huazhong University of Science and technology, Wuhan, China in 2016. He is currently a Ph.D. candidate at Peking University, Beijing, China. (Email: chencongzhou@pku.edu.cn)

Xiaolong SHI received his Ph.D.in System Engineering from Huazhong University of Science and technology. He was the tenured professor in Huazhong University of Science and Technology, and now he is the Dean/Professor of the Institute of Computer Science and Technology in Guangzhou University. (Email: xlshi@gzhu.edu.cn)
Corresponding author: Email: xlshi@gzhu.edu.cn
Received Date: 2022-03-17
Accepted Date: 2023-03-14

Available Online: 2024-03-28

Abstract

Abstract

The slow development of traditional computing has prompted a search for new materials to replace silicon-based computers. Bio-computers, which use molecules as the basis of computation, are highly parallel and information capable, attracting a lot of attention. In this study, we designed a NAND logic gate based on the DNA strand displacement mechanism. Further, we assembled a molecular calculation model, a 4-wire-2-wire priority encoder logic circuit, by cascading the proposed NAND gates. Different concentrations of input DNA chains were added into the system, resulting in corresponding output, through DNA hybridization and strand displacement. Therefore, it achieved the function of a priority encoder. Simulation results verify the effectiveness and accuracy of the molecular NAND logic gate and the priority coding system presented in this study. The unique point of this proposed circuit is that we cascaded only one kind of logic gate, which provides a beneficial exploration for the subsequent development of complex DNA cascade circuits and the realization of the logical coding function of information.
- DNA strand displacement,
- Logic circuit,
- NAND gate,
- priority encoder

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References(26)

References

[1]	L. M. Adleman, “Molecular computation of solutions to combinatorial problems,” Science, vol. 266, no. 5187, pp. 1021–1024, 1994. doi: 10.1126/science.7973651
[2]	Y. Benenson, “Biocomputers: From test tubes to live cells,” Molecular BioSystems, vol. 5, no. 7, pp. 675–685, 2009. doi: 10.1039/b902484k
[3]	E. Katz and V. Privman, “Enzyme-based logic systems for information processing,” Chemical Society Reviews, vol. 39, no. 5, pp. 1835–1857, 2010. doi: 10.1039/B806038J
[4]	I. S. de Murieta, J. M. Miro-Bueno, and A. Rodriguez-Paton, “Biomolecular computers,” Current Bioinformatics, vol. 6, no. 2, pp. 173–184, 2011. doi: 10.2174/1574893611106020173
[5]	M. Zhou and S. J. Dong, “Bioelectrochemical interface engineering: Toward the fabrication of electrochemical biosensors, biofuel cells, and self-powered logic biosensors,” Accounts of Chemical Research, vol. 44, no. 11, pp. 1232–1243, 2011. doi: 10.1021/ar200096g
[6]	W. E. Arter, Y. Yusim, Q. Peter, et al., “Digital sensing and molecular computation by an enzyme-free DNA circuit,” ACS Nano, vol. 14, no. 5, pp. 5763–5771, 2020. doi: 10.1021/acsnano.0c00628
[7]	Q. Lin, A. M. Wang, S. Y. Liu, et al., “A DNA tetrahedron-based molecular computation device for the logic sensing of dual microRNAs in living cells,” Chemical Communications, vol. 56, no. 39, pp. 5303–5306, 2020. doi: 10.1039/d0cc01231a
[8]	B. Y. Wang, C. Chalk, and D. Soloveichik, “SIMD\| \| DNA: Single instruction, multiple data computation with DNA strand displacement cascades,” in 25th International Conference on DNA Computing and Molecular Programming, Seattle, WA, USA, pp. 219–235, 2019.
[9]	F. Wang, H. Lv, Q. Li, et al., “Implementing digital computing with DNA-based switching circuits,” Nature Communications, vol. 11, no. 1, article no. 121, 2020. doi: 10.1038/s41467-019-13980-y
[10]	C. Zhang, Y. M. Zhao, X. M. Xu, et al., “Cancer diagnosis with DNA molecular computation,” Nature Nanotechnology, vol. 15, no. 8, pp. 709–715, 2020. doi: 10.1038/s41565-020-0699-0
[11]	G. T. Walker, M. S. Fraiser, J. L. Schram, et al., “Strand displacement amplification—an isothermal, in vitro DNA amplification technique,” Nucleic Acids Research, vol. 20, no. 7, pp. 1691–1696, 1992. doi: 10.1093/nar/20.7.1691
[12]	L. L. Qian and E. Winfree, “Scaling up digital circuit computation with DNA strand displacement cascades,” Science, vol. 332, no. 6034, pp. 1196–1201, 2011. doi: 10.1126/science.1200520
[13]	R. Sarpeshkar, “Analog versus digital: Extrapolating from electronics to neurobiology,” Neural Computation, vol. 10, no. 7, pp. 1601–1638, 1998. doi: 10.1162/089976698300017052
[14]	A. Eshra, S. Shah, T. Q. Song, et al., “Renewable DNA hairpin-based logic circuits,” IEEE Transactions on Nanotechnology, vol. 18, pp. 252–259, 2019. doi: 10.1109/TNANO.2019.2896189
[15]	T. Q. Song, A. Eshra, S. Shah, et al., “Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase,” Nature Nanotechnology, vol. 14, no. 11, pp. 1075–1081, 2019. doi: 10.1038/s41565-019-0544-5
[16]	G. Seelig, D. Soloveichik, D. Y. Zhang, et al., “Enzyme-free nucleic acid logic circuits,” Science, vol. 314, no. 5805, pp. 1585–1588, 2006. doi: 10.1126/science.1132493
[17]	B. M. Frezza, S. L. Cockroft, and M. R. Ghadiri, “Modular multi-level circuits from immobilized DNA-based logic gates,” Journal of the American Chemical Society, vol. 129, no. 48, pp. 14875–14879, 2007. doi: 10.1021/ja0710149
[18]	C. Zhang, J. Yang, and J. Xu, “Circular DNA logic gates with strand displacement,” Langmuir, vol. 26, no. 3, pp. 1416–1419, 2010. doi: 10.1021/la903137f
[19]	L. L. Qian and E. Winfree, “A simple DNA gate motif for synthesizing large-scale circuits,” Journal of the Royal Society Interface, vol. 8, no. 62, pp. 1281–1297, 2011. doi: 10.1098/rsif.2010.0729
[20]	D. Y. Zhang and G. Seelig, “Dynamic DNA nanotechnology using strand-displacement reactions,” Nature Chemistry, vol. 3, no. 2, pp. 103–113, 2011. doi: 10.1038/nchem.957
[21]	B. Yurke, A. J. Turberfield, A. P. Jr. Mills, et al., “A DNA-fuelled molecular machine made of DNA,” Nature, vol. 406, no. 6796, pp. 605–608, 2000. doi: 10.1038/35020524
[22]	B. Yurke and A. P. Mills, “Using DNA to power nanostructures,” Genetic Programming and Evolvable Machines, vol. 4, no. 2, pp. 111–122, 2003. doi: 10.1023/A:1023928811651
[23]	J. J. Mulawka, P. Wasiewicz, and A. Plucienniczak, “Another logical molecular NAND gate system,” in Proceedings of the Seventh International Conference on microelectronics for Neural, Fuzzy and Bio-Inspired Systems, Granada, Spain, pp. 340–345, 1999.
[24]	M. Ruiz-Perez and A. Virazel, “Logic gates made with DNA,” in Innovative Computer Architectures and Concepts Seminar, Citeseer, 2002.
[25]	C. Z. Chen, W. Xiao, J. W. Zhao, et al., “DNA logic circuits based on accurate step function gate,” IEEE Access, vol. 8, pp. 125513–125520, 2020. doi: 10.1109/ACCESS.2020.3003636
[26]	D. Soloveichik, G. Seelig, and E. Winfree, “DNA as a universal substrate for chemical kinetics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 12, pp. 5393–5398, 2010. doi: 10.1073/pnas.0909380107