基于DNA链置换的两位格雷码减法器分子电路设计

王延峰; 张桢桢; 王盼如; 孙军伟

doi:10.11999/JEIT190880

基于DNA链置换的两位格雷码减法器分子电路设计

doi: 10.11999/JEIT190880

郑州轻工业大学电气信息工程学院郑州 450002

基金项目: 国家重点研发计划中美政府间合作项目(2017YFE0103900)，国家自然科学基金河南联合基金(U1804262)，国家自然科学基金重点项目(61632002)，中原千人计划(204200510003)，食管癌防治国家重点实验室开放基金(K2020-0010, K2020-0011)

详细信息

作者简介:
王延峰：男，1973年生，教授，研究方向为生物启发计算

张桢桢：女，1994年生，硕士生，研究方向为生物启发计算

王盼如：女，1994年生，博士生，研究方向为生物启发计算

孙军伟：男，1984年生，副教授，研究方向为生物启发计算

通讯作者:
孙军伟　junweisun@yeah.net

中图分类号: TP 301
计量
- 文章访问数: 1758
- HTML全文浏览量: 770
- PDF下载量: 73
- 被引次数: 0
出版历程
- 收稿日期: 2019-11-04
- 修回日期: 2020-06-07
- 网络出版日期: 2020-07-11
- 刊出日期: 2020-10-13

Molecular Circuit Design of Two-bit Gray Code Subtracter Based on DNA Strand Displacement

School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China

Funds: The National Key R and D Program of China for International S and T Cooperation Projects (2017YFE0103900), The Joint Funds of the National Natural Science Foundation of China (U1804262), The State Key Program of National Natural Science of China (61632002), The Central Plains Thousand Talents Program (204200510003), The Open Fund of State Key Laboratory of Esophageal Cancer Prevention and Treatment (K2020-0010, K2020-0011)

摘要

摘要: DNA链置换技术具有自发性、并行性、可编程性、动态级联性的特点，在DNA计算中占据重要的地位。DNA链置换技术被广泛的应用于解决数学问题，该文采用格雷码编码方式结合DNA链置换技术设计了两位减法器，扩展DNA减法运算。最后利用Visual DSD软件模拟两位减法器，该电路达到预期的功能，且具有并行性和可扩展性，可与其他生化电路结合使用。
- 分子电路 /
- DNA链置换 /
- 格雷码 /
- 减法器
Abstract: DNA strand displacement technology has the characteristics of spontaneity, parallelism, programmability and dynamic cascade, which is widely used to solve mathematical problems. In this paper, a two-bit subtracter is designed by using Gray code encoding and DNA strand displacement technology to extend the operation of DNA subtraction. Finally, Visual DSD software is used to simulate the two-bit subtracter. The circuit, with the strong parallelism and expansibility, achieves the expected function. It can be used in combination with other biochemical circuits.
- Molecular circuit /
- DNA strand displacement /
- Gray code /
- Subtracter

HTML全文

图 1 DNA链置换反应的过程机理

下载: 全尺寸图片幻灯片

图 2 两位格雷码减法器seesaw门

下载: 全尺寸图片幻灯片

图 3 两位减法器seesaw双轨分子电路

下载: 全尺寸图片幻灯片

图 4 DNA链置换的反应过程机理示意图

下载: 全尺寸图片幻灯片

5 两位格雷码减法器仿真图

下载: 全尺寸图片幻灯片

表 1 两位减法器操作运算的真值表

X₂X₁/减数	U₂U₁/被减数	S₂S₁/差值	B₂/高位借位	X₂X₁/减数	U₂U₁/被减数	S₂S₁/差值	B₂/高位借位
00	00	00	0	11	00	11	0
00	01	10	1	11	01	01	0
00	11	11	1	11	11	00	0
00	10	01	1	11	10	10	1
01	00	01	0	10	00	10	0
01	01	00	0	10	01	11	0
01	11	10	1	10	11	01	0
01	10	11	1	10	10	00	0

下载: 导出CSV

参考文献(20)

XU Jin, QIANG Xiaoli, CHENG 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

SONG Tianqi, GARG S, MOKHTAR R, et al. Analog computation by DNA strand displacement circuits[J]. ACS Synthetic Biology, 2016, 5(8): 898–912. doi: 10.1021/acssynbio.6b00144

THUBAGERE A J, THACHUK C, BERLEANT J, et al. Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components[J]. Nature Communications, 2017, 8: 14373. doi: 10.1038/ncomms14373

ZOU Chengye, WEI Xiaopeng, ZHANG Qiang, et al. Solution of equations based on analog DNA strand displacement circuits[J]. IEEE Transactions on Nanobioscience, 2019, 18(2): 191–204. doi: 10.1109/TNB.2019.2897116

SONG Tianqi, GARG S, MOKHTAR R, et al. Design and analysis of compact DNA strand displacement circuits for analog computation using autocatalytic amplifiers[J]. ACS Synthetic Biology, 2018, 7(1): 46–53. doi: 10.1021/acssynbio.6b00390

李佩佳, 石勇, 汪华东, 等. 基于有序编码的核极限学习顺序回归模型[J]. 电子与信息学报, 2018, 40(6): 1287–1293. doi: 10.11999/JEIT170765

LI Peijia, SHI Yong, WANG Huadong, et al. Ordered code-based kernel extreme learning machine for ordinal regression[J]. Journal of Electronics &Information Technology, 2018, 40(6): 1287–1293. doi: 10.11999/JEIT170765

刘伟, 魏志刚, 杜薇, 等. 近阈值电压下可容错的末级缓存结构设计[J]. 电子与信息学报, 2018, 40(7): 1759–1766. doi: 10.11999/JEIT170989

LIU Wei, WEI Zhigang, DU Wei, et al. Fault-tolerant last level cache architecture design at near-threshold voltage[J]. Journal of Electronics &Information Technology, 2018, 40(7): 1759–1766. doi: 10.11999/JEIT170989

KONG Jinglin, ZHU Jinbo, CHEN Kaikai, et al. Specific biosensing using DNA aptamers and nanopores[J]. Advanced Functional Materials, 2019, 29(3): 1807555. doi: 10.1002/adfm.201807555

CUI Yunxi, FENG Xuenan, WANG Yaxin, et al. An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity[J]. Chemical Science, 2019, 10(3): 2290–2297. doi: 10.1039/c8sc05102j

LI Hua, LIU Jin, and GU Hongzhou. Targeting nucleolin to obstruct vasculature feeding with an intelligent DNA nanorobot[J]. Journal of Cellular and Molecular Medicine, 2019, 23(3): 2248–2250. doi: 10.1111/jcmm.14127

KIELAR C, REDDAVIDE F V, TUBBENHAUER S, et al. Pharmacophore nanoarrays on DNA origami substrates as a single-molecule assay for fragment-based drug discovery[J]. Angewandte Chemie, 2018, 130(45): 15089–15093. doi: 10.1002/ange.201806778

TASCIOTTI E. Smart cancer therapy with DNA origami[J]. Nature Biotechnology, 2018, 36(3): 234–235. doi: 10.1038/nbt.4095

CORDEIRO M, OTRELO-CARDOSO A R, SVERGUN D I, et al. Optical and structural characterization of a chronic myeloid leukemia DNA biosensor[J]. ACS Chemical Biology, 2018, 13(5): 1235–1242. doi: 10.1021/acschembio.8b00029

ELBAZ J, LIOUBASHEVSKI O, WANG Fuan, et al. DNA computing circuits using libraries of DNAzyme subunits[J]. Nature Nanotechnology, 2010, 5(6): 417–422. doi: 10.1038/nnano.2010.88

QIAN Lulu and WINFREE E. A simple DNA gate motif for synthesizing large-scale circuits[J]. Journal of the Royal Society Interface, 2011, 8(62): 1281–1297. doi: 10.1098/rsif.2010.0729

QIAN Lulu, WINFREE E, and BRUCK J. Neural network computation with DNA strand displacement cascades[J]. Nature, 2011, 475(7356): 368–372. doi: 10.1038/nature10262

马丽娜, 董亚非, 张成, 等. 基于DNA链置换与荧光标记的0–1规划问题的计算模型[J]. 数学的实践与认识, 2013, 43(11): 152–159. doi: 10.3969/j.issn.1000-0984.2013.11.020

MA Lina, DONG Yafei, ZHANG Cheng, et al. A computing model based on DNA strand replacement/fluorescence labeling for 0–1 programming[J]. Mathematics in Practice and Theory, 2013, 43(11): 152–159. doi: 10.3969/j.issn.1000-0984.2013.11.020

姚莉娜, 田桂花, 叶盟盟, 等. DNA链置换技术的研究现状与展望[J]. 郑州轻工业学院学报: 自然科学版, 2014, 29(1): 15–21. doi: 10.3969/j.issn.2095-476X.2014.01.003

YAO Lina, TIAN Guihua, YE Mengmeng, et al. Current situation and prospect of DNA strand displacement technology[J]. Journal of Zhengzhou University of Light Industry:Natural Science, 2014, 29(1): 15–21. doi: 10.3969/j.issn.2095-476X.2014.01.003

ZOU Chengye, WEI Xiaopeng, ZHANG Qiang, et al. Four-analog computation based on DNA strand displacement[J]. ACS Omega, 2017, 2(8): 4143–4160. doi: 10.1021/acsomega.7b00572

LOPEZ R, WANG Ruofan, and SEELIG G. A molecular multi-gene classifier for disease diagnostics[J]. Nature Chemistry, 2018, 10(7): 746–754. doi: 10.1038/s41557-018-0056-1

施引文献

资源附件(0)

访问统计