高级搜索

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

基于DNA折纸基底的与非门计算模型

殷志祥 唐震 张强 崔建中 杨静 王日晟 赵寿为 张居丽

殷志祥, 唐震, 张强, 崔建中, 杨静, 王日晟, 赵寿为, 张居丽. 基于DNA折纸基底的与非门计算模型[J]. 电子与信息学报, 2020, 42(6): 1355-1364. doi: 10.11999/JEIT190825
引用本文: 殷志祥, 唐震, 张强, 崔建中, 杨静, 王日晟, 赵寿为, 张居丽. 基于DNA折纸基底的与非门计算模型[J]. 电子与信息学报, 2020, 42(6): 1355-1364. doi: 10.11999/JEIT190825
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 and 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 and Information Technology, 2020, 42(6): 1355-1364. doi: 10.11999/JEIT190825

基于DNA折纸基底的与非门计算模型

doi: 10.11999/JEIT190825
基金项目: 国家自然科学基金(61672001, 61702008, 11801362),安徽省自然科学基金(1808085MF193),安徽省高校自然科学研究项目(KJ2019A0538)
详细信息
    作者简介:

    殷志祥:男,1966年生,教授,研究方向为DNA计算和DNA自组装

    唐震:男,1994年生,博士生,研究方向为DNA计算和DNA自组装

    张强:男,1971年生,教授,研究方向为生物计算、智能机器人和医疗大数据处理

    崔建中:男,1973年生,博士生,研究方向为DNA计算和DNA自组装

    杨静:女,1980年生,副教授,研究方向为DNA计算和DNA自组装

    王日晟:男,1993年生,博士生,研究方向为DNA计算和DNA自组装

    赵寿为:女,1982年生,博士,研究方向为应用数学

    张居丽:女,1982年生,博士,研究方向为计算数学

    通讯作者:

    唐震 1179145666@qq.com

  • 中图分类号: TP301

NAND Gate Computational Model Based on the DNA Origami Template

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)
  • 摘要: 与非门(NAND)的本质是与门(AND)和非门(NOT)的叠加,先进行与运算,再进行非运算,它是建立DNA计算机的基础。为了实现与非门的计算,该文在DNA折纸基底上建立了一个与非门计算模型,逻辑值的输入是通过在DNA折纸基底上发生有向的杂交链式反应(HCR)来完成的,输入链先经过与门区域再经过非门区域,最后通过DNA折纸基底上是否还保留纳米金颗粒来显示计算结果的真假。利用Visual DSD对该计算模型进行仿真模拟,显示该计算模型具有较好的可行性。
  • 图  1  杂交链式反应基本反应原理

    图  2  构建好的折纸基底示意图

    图  3  输入链示意图

    图  4  输入A=0, B=0后的结果示意图

    图  5  输入A=1, B=0后的结果示意图

    图  6  输入A=0, B=1后的结果示意图

    图  7  输入A=1, B=1后的结果示意图

    图  8  仿真模拟数据图

    图  9  最终产物的DNA链示意图

    表  1  与非门真值表

    A0011
    B0101
    F1110
    下载: 导出CSV
  • 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
  • 加载中
图(9) / 表(1)
计量
  • 文章访问数:  1320
  • HTML全文浏览量:  505
  • PDF下载量:  67
  • 被引次数: 0
出版历程
  • 收稿日期:  2019-10-28
  • 修回日期:  2020-01-17
  • 网络出版日期:  2020-02-19
  • 刊出日期:  2020-06-22

目录

    /

    返回文章
    返回

    官方微信,欢迎关注