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Volume 42 Issue 6
Jun.  2020
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Zhixiang YIN, Zhen TANG, Qiang ZHANG, Jianhong CUI, Jing YANG, Risheng WANG, Shouwei ZHAO, Juli ZHANG. NAND Gate Computational Model Based on the DNA Origami Template[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1355-1364. doi: 10.11999/JEIT190825
Citation: Zhixiang YIN, Zhen TANG, Qiang ZHANG, Jianhong CUI, Jing YANG, Risheng WANG, Shouwei ZHAO, Juli ZHANG. NAND Gate Computational Model Based on the DNA Origami Template[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1355-1364. doi: 10.11999/JEIT190825

NAND Gate Computational Model Based on the DNA Origami Template

doi: 10.11999/JEIT190825
Funds:  The National Natural Science Foundation of China (61672001, 61702008, 11801362), The Natural Science Foundation of Anhui Province (1808085MF193), The Natural Science Research Project of Universities in Anhui Province (KJ2019A0538)
  • Received Date: 2019-10-28
  • Rev Recd Date: 2020-01-17
  • Available Online: 2020-02-19
  • Publish Date: 2020-06-22
  • The essence of NAND gate is the superposition of AND gate and NOT gate. The AND gate operation is performed first, and then the NOT gate is performed. It is the basis of the DNA computer. In order to realize the computing of NAND gate, a NAND gate computational model is established based on the DNA origami template. The inputs of the logic value are completed by the Hybridization Chain Reaction (HCR) on the DNA origami template. The input strands first react with the AND gate region and then react with the NOT gate region. The result of the reaction is shown by dynamically separation of the gold nanoparticles on the DNA origami template. The simulation of the model through Visual DSD shows that the system has the advantages of high feasibility.
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  • ADLEMAN L M. Molecular computation of solutions to combinatorial problems[J]. Science, 1994, 266(5187): 1021–1024. doi: 10.1126/science.7973651
    LIPTON R J. DNA solution of hard computational problems[J]. Science, 1995, 268(5210): 542–545. doi: 10.1126/science.7725098
    SAKAMOTO K, GOUZU H, KOMIYA K, et al. Molecular computation by DNA hairpin formation[J]. Science, 2000, 288(5469): 1223–1226. doi: 10.1126/science.288.5469.1223
    YIN Zhixiang, CUI Jianzhong, YANG Jing, et al. DNA computing model of the integer linear programming problem based on molecular beacon[C]. International Conference on Intelligent Computing, Kunming, China, 2006: 238–247.
    GUO Ping and LIU Lili. A surface-based DNA algorithm for the 0–1 programming problem[C]. The 3rd International Conference on Innovative Computing Information and Control, Dalian, China, 2008.
    QIAN Lulu and WINFREE E. Scaling up digital circuit computation with DNA strand displacement cascades[J]. Science, 2011, 32(6034): 1196–1201.
    YANG Jing, ZHANG Cheng, LIU Shi, et al. A molecular computing model for 0-1 programming problem using DNA nanoparticles[J]. Journal of Computational and Theoretical Nanoscience, 2013, 10(10): 2380–2384. doi: 10.1166/jctn.2013.3218
    LI Fei, LIU Jingming, and LI Zheng. DNA computation based on self-assembled nanoparticle probes for 0-1 integer programming problem[J]. Mathematics and Computers in Simulation, 2018, 151: 140–146. doi: 10.1016/j.matcom.2017.02.004
    YIN Zhixiang, CUI Jianzhong, and YANG Jing. Integer programming problem based on plasmid DNA computing model[J]. Chinese Journal of Electronics, 2017, 26(6): 1284–1288. doi: 10.1049/cje.2017.07.013
    XU Jin, QIANG Xiaoli, ZHANG Kai, et al. A DNA computing model for the graph vertex coloring problem based on a probe graph[J]. Engineering, 2018, 4(1): 61–77. doi: 10.1016/j.eng.2018.02.011
    YURKE B, TURBERFIELD A J, MILLS JR A P, et al. A DNA-fuelled molecular machine made of DNA[J]. Nature, 2000, 406(6796): 605–608. doi: 10.1038/35020524
    DIRKS R M and PIERCE N A. Triggered amplification by hybridization chain reaction[J]. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(43): 15275–15278. doi: 10.1073/pnas.0407024101
    ROTHEMUND P W K. Folding DNA to create nanoscale shapes and patterns[J]. Nature, 2006, 440(7082): 297–302. doi: 10.1038/nature04586
    LAKIN M R, PARKER D, CARDELLI L, et al. Design and analysis of DNA strand displacement devices using probabilistic model checking[J]. Journal of the Royal Society Interface, 2012, 9(72): 1470–1485. doi: 10.1098/rsif.2011.0800
    CONDON A, KIRKPATRICK B, and MAŇUCH J. Reachability bounds for chemical reaction networks and strand displacement systems[J]. Natural Computing, 2014, 13(4): 499–516. doi: 10.1007/s11047-013-9403-8
    MARDIAN R, SEKIYAMA K, and FUKUDA T. DNA strand displacement for stochastic decision making based on immune’s clonal selection algorithm[J]. Information Technologies Knowledge, 2013, 7(1): 34–45.
    YANG Jing, DONG Chen, DONG Yafei, et al. Logic nanoparticle beacon triggered by the binding-induced effect of multiple inputs[J]. ACS Applied Materials & Interfaces, 2014, 6(16): 14486–14492.
    YANG Jing, JIANG Shuoxing, LIU Xiangrong, et al. Aptamer-binding directed DNA origami pattern for logic gates[J]. ACS Applied Materials & Interfaces, 2016, 8(49): 34054–34060.
    PAN Linqiang, WANG Zhiyu, LI Yifan, et al. Nicking enzyme-controlled toehold regulation for DNA logic circuits[J]. Nanoscale, 2017, 9(46): 18223–18228. doi: 10.1039/C7NR06484E
    YANG Jing, WU Ranfeng, LI Yifan, et al. Entropy-driven DNA logic circuits regulated by DNAzyme[J]. Nucleic Acids Research, 2018, 46(16): 8532–8541. doi: 10.1093/nar/gky663
    XU Fei, WU Tingfang, SHI Xiaolong, et al. A study on a special DNA nanotube assembled from two single-stranded tiles[J]. Nanotechnology, 2019, 30(11): 115602. doi: 10.1088/1361-6528/aaf9bc
    PAN Linqiang, HU Yingxin, DING Taoli, et al. Aptamer-based regulation of transcription circuits[J]. Chemical Communications, 2019, 55(51): 7378–7381. doi: 10.1039/C9CC03141C
    WANG Xiaolong, BAO Zhenmin, HU Jingjie, et al. Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction[J]. Biosystems, 2008, 91(1): 117–125. doi: 10.1016/j.biosystems.2007.08.006
    俞洋, 苏邵, 晁洁. 基于“DNA折纸术”设计哈密顿路径问题的解决方案[J]. 中国科学: 化学, 2015, 45(11): 1226–1230. doi: 10.1360/N032015-00035

    YU Yang, SU Shao, and CHAO Jie. A "DNA origami"-based approach to the solution of Hamilton path problem[J]. Scientia Sinica Chimica, 2015, 45(11): 1226–1230. doi: 10.1360/N032015-00035
    俞洋, 苏邵, 晁洁. 基于“DNA折纸术”设计图着色问题的解决方案[J]. 南京大学学报: 自然科学, 2016, 52(4): 656–661.

    YU Yang, SU Shao, and CHAO Jie. A "DNA origami"-based approach to the solution of graph coloring problem[J]. Journal of Nanjing University:Natural Sciences, 2016, 52(4): 656–661.
    YANG Jing, SONG Zhichao, LIU Shi, et al. Dynamically arranging gold nanoparticles on DNA origami for molecular logic gates[J]. ACS Applied Materials & Interfaces, 2016, 8(34): 22451–22456.
    ZHANG Qiang, WANG Xiaobiao, Wang Xiaojun, et al. Solving probability reasoning based on DNA strand displacement and probability modules[J]. Computational Biology and Chemistry, 2017, 71: 274–279. doi: 10.1016/j.compbiolchem.2017.09.011
    CHAO Jie, WANG Jianbang, WANG Fei, et al. Solving mazes with single-molecule DNA navigators[J]. Nature Materials, 2019, 18(3): 273–279. doi: 10.1038/s41563-018-0205-3
    TANG Zhen, YIN Zhixiang, SUN Xia, et al. Dynamically NAND gate system on DNA origami template[J]. Computers in Biology and Medicine, 2019, 109: 112–120. doi: 10.1016/j.compbiomed.2019.04.026
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