E. coli K-12琥珀酸脱氢酶sdhC基因纳米锥的设计及自组装

doi:10.16085/j.issn.1000-6613.2019-0808

摘要/Abstract

摘要：

采用DAEDALUS软件，以E. coli K-12 MG1655的琥珀酸脱氢酶复合体C亚基编码酶基因sdhC的双链DNA为脚手架链，进行一个边长为17.68 nm的正四面锥设计，并最终通过核酸自组装反应获得了sdhC基因的纳米锥聚合体。利用琼脂糖凝胶电泳、扫描电子显微镜和透射电子显微镜对多组样品进行化学组分和形貌分析，同时利用原子力显微镜液下成像法测定了核酸聚合体的三维尺度。结果表明：DAEDALUS软件设计出的16条订书钉链，确实将624 bp的sdhC双链DNA中的一条链折叠成了平均边长为19.05nm的正四面锥，与预设模型仅相差1.37nm，证明普通基因的双链DNA可以替代M13mp18单链核酸作为DNA折纸的核酸材料，为构建核酸纳米材料提供了一种新方法。

关键词: DNA折纸术, 纳米材料, 琥珀酸脱氢酶, 脱氧核糖核酸, 自组装

Abstract:

E.coli K-12 MG1655 succinate dehydrogenase gene, sdhC (encoding membrane protein sdhC), a double-stranded DNA, was used as a scaffold to design a 17.68nm tetrahedron with DAEDALUS software. The sdhC DNA strand self-assembled into a nanocone polymer exactly as similar as the front design. The morphology, structure and chemical composition of the samples from several experiments were assayed by agarose gel electrophoresis, scanning electron microscope and transmission electron microscopy, at the same time, the three-dimensional structure was imaged by high-resolution atomic force microscope in liquid. The results showed 16 staple strands designed by DAEDALUS folded the 624 bp double-stranded DNA of sdhC gene into nanocones with an average length of 19.05nm, which is only 1.37nm difference with the prediction. This study provides a new method for constructing nucleic acid nanomaterial with common genetic sequences beside M13mp18 in DNA origami.

Key words: DNA origami, nanomaterials, succinate dehydrogenase, DNA, self-assembly

中图分类号:

TB381

周末,刘彦君,佟欣瑞,董延甲,吴欣瑜,王迎香,应明. E. coli K-12琥珀酸脱氢酶sdhC基因纳米锥的设计及自组装[J]. 化工进展, 2020, 39(2): 679-685.

Mo ZHOU,Yanjun LIU,Xinrui TONG,Yanjia DONG,Xinyu WU,Yingxiang WANG,Ming YING. Self-assemble of gene nanocone with sdhC DNA sequence of E. coli K-12[J]. Chemical Industry and Engineering Progress, 2020, 39(2): 679-685.

图/表 9

参考文献 16

1	WILLIAMS S, LUND K, LIN C, et al. Tiamat: a three-dimensional editing tool for complex DNA structures[C]//ASHISH G, FRIEDRICH C S., PETR S.14th International Meeting on DNA Computing. Berlin Heidelberg, Germany: Springer-Verlag. 2009: 90-101.
2	ZHU J, WEI B, YUAN Y, et al. UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation[J]. Nucleic Acids Research, 2009, 37(7): 2164-2175.
3	ANDERSEN E S. DNA origami design of dolphin-shaped structures with flexible tails[J]. ACS Nano, 2008, 2(6): 1213-1218.
4	ANDERSEN E S, DONG M, NIELSE M M, et al. Self-assembly of a nanoscale DNA box with a controllable lid[J]. Nature, 2009, 459(7243): 73-76.
5	DOUGLAS S M, MARBLESTONE A H, TERAPITTAYANON S, et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno[J]. Nucleic Acids Research, 2009, 37(15): 5001-5006.
6	CASTRO C E, KILCHHERR F, KIM D N, et al. A primer to scaffolded DNA origami[J]. Nature Methods, 2011, 8(3): 221-229.
7	VENEZIANO R, RATANALERT S, ZHANG K, et al. Designer nanoscale DNA assemblies programmed from the top down[J]. Science, 2016, 352(6293): 1534.
8	JUN H, ZHANG F, HEPHERD T, et al. Autonomously designed free-form 2D DNA origami[J]. Science Advances, 2019, 5(1): eaav0655.
9	QIAN L L,WANG Y, ZHANG Z, ZHAO J, et al. Analogic China map constructed by DNA[J]. Chinese Science Bulletin, 2006, 51(24): 2973-2976.
10	ANDERSEN E S. Prediction and design of DNA and RNA structures[J]. New Biotechnology, 2010, 27(3):184-193.
11	KOPPERGER E, LIST J, MADHIRA S, et al. A self-assembled nanoscale robotic arm controlled by electric fields[J]. Science, 2018, 359(6373): 296.
12	LI S, JIANG Q, LIU S, et al. A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo[J]. Nature Biotechnology, 2018, 36: 258-264.
13	SHEN L Y, YING M, SHAO S, et al. Photo-luminescent characteristics of carboxyl-CdSe quantum dots synthesized[J]. Journal of Chemical and Pharmaceutical Research, 2015, 7(9): 514-517.
14	SHEN B, LINKO V, TAPIO K, et al. Plasmonic nanostructures through DNA-assisted lithography[J]. Science Advances, 2018, 4(2): eaap8978.
15	YING M, ZHANG F, BAN R. Optimization of riboflavin production from ccpA Mutant Bacillus subtilis 24A1/pMX45[J]. Transactions of Tianjin University, 2006, 6(12): 415-419.
16	ROTHEMUND P W K. Folding DNA to create nanoscale shapes and patterns[J]. Nature, 2006, 440(7082): 297-302.

位置	碱基序列
1～117	TGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC
118～507	ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGGCGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCTTCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTCAAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGATGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTACTGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAA
508～624	GCAACGCCTCCGCATTAGGACGCAATGGCGTACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTTTTTCGCTACCAGTGGCG

位置	碱基序列
1～117	TGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC
118～507	ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGGCGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCTTCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTCAAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGATGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTACTGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAA
508～624	GCAACGCCTCCGCATTAGGACGCAATGGCGTACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTTTTTCGCTACCAGTGGCG

位置	类型	订书钉链碱基序列	碱基数
AD棱	Clip^①	GGTCTGTAGG_{（168-159）}TGCGGGTCAGACA_（13-1）CGCCACTG_{（624-617）}GGGAACCGGAT_{（179-169）}	42
	Pin^②	TCCAGATTAA_{（158-149）}CCGGTCTGCT_（23-14）	20
AC棱	Clip	GAGCGTCAGG_{（584-575）}GCTTCGAATGTTTCTTCCAGA_{（431-411）}TAAATGATGTA_{（595-585）}	42
	Pin	ACGATAGCGG_{（574-565）}GCGTTTACCC_{（441-432）}	20
BC棱	Hook1^③	CCATAAT_{（470-463）}CTGATAAATTTGA_{（492-478）}CGAAAAGCACG_{（321-314）}	31
	Hook2	ACAGTAAT_{（313-306）}TCCTGCGAGAAGTGA_{（337-322）}GAAGCTGC_{（477-471）}	31
AB棱	Clip	TACGACGACG_{（378-369）}ACACCGGAAACGCGATGGAGA_{（2211-201）}TGGCGAATACC_{（389-379）}	42
	Pin	TGATACGCCA_{（368-359）}AAAGGTGATC_{（231-222）}	20
CD棱	Hook1	TTACCTGG_（52-45）ACGGGCACAGAGGTT_（76-61）AGTCCTAA_{（528-522）}	31
	Hook2	TGCGGAGG_{（521-514）}CATGTACGCCATTGC_{（543-529）}ACTTTCTG_（60-53）	31
BD棱	Hook1	AGAAGCCA_{（260-253）}TCAGGGGAAGAGAGGC_{（284-269）}ACGCCCA_{（112-106）}	31
	Hook2	CATGCTGT_（105-98）TTCTTATCATGAATA_{（127-113）}TGGTACCC_{（268-261）}	31
A顶点	Convex^④	TAGCCAAAATCTTTTTCATCATCATG_{（410-390）}ATGGACGCTATTTTTTCGCCGTGATG_{（200-180）}GTAGCGAAAAATTTTT ACCGACCATA_{（616-596）}	78
B顶点	Convex	GAGCGGTAAGGTTTTTATGCCCCACA_{（358-338）}GCGGAAGCTTGTTTTTCTCGAAACCT（305-285）CAGCAGGATGC TTTTTCCACTGCAAC_{（252-232）}	78
C顶点	Convex	CGTTGCTTACCTTTTTATACGAGGAC_{（513-493）}AACAAAGGAGATTTTTTTTTGGCGGA_{（462-442）} TAGCGCGAACGTTTTTAGGATGAAAT_{（564-544）}	78
D顶点	Convex	TCTTATTATTCTTTTTCCTGGGGACT_（97-77）AGACGTCGGGATTTTTTTTCCTTCCT_（44-24） CAGGTCTTTGTTTTTTTTTTTCACAT_{（148-128）}	78

位置	类型	订书钉链碱基序列	碱基数
AD棱	Clip^①	GGTCTGTAGG_{（168-159）}TGCGGGTCAGACA_（13-1）CGCCACTG_{（624-617）}GGGAACCGGAT_{（179-169）}	42
	Pin^②	TCCAGATTAA_{（158-149）}CCGGTCTGCT_（23-14）	20
AC棱	Clip	GAGCGTCAGG_{（584-575）}GCTTCGAATGTTTCTTCCAGA_{（431-411）}TAAATGATGTA_{（595-585）}	42
	Pin	ACGATAGCGG_{（574-565）}GCGTTTACCC_{（441-432）}	20
BC棱	Hook1^③	CCATAAT_{（470-463）}CTGATAAATTTGA_{（492-478）}CGAAAAGCACG_{（321-314）}	31
	Hook2	ACAGTAAT_{（313-306）}TCCTGCGAGAAGTGA_{（337-322）}GAAGCTGC_{（477-471）}	31
AB棱	Clip	TACGACGACG_{（378-369）}ACACCGGAAACGCGATGGAGA_{（2211-201）}TGGCGAATACC_{（389-379）}	42
	Pin	TGATACGCCA_{（368-359）}AAAGGTGATC_{（231-222）}	20
CD棱	Hook1	TTACCTGG_（52-45）ACGGGCACAGAGGTT_（76-61）AGTCCTAA_{（528-522）}	31
	Hook2	TGCGGAGG_{（521-514）}CATGTACGCCATTGC_{（543-529）}ACTTTCTG_（60-53）	31
BD棱	Hook1	AGAAGCCA_{（260-253）}TCAGGGGAAGAGAGGC_{（284-269）}ACGCCCA_{（112-106）}	31
	Hook2	CATGCTGT_（105-98）TTCTTATCATGAATA_{（127-113）}TGGTACCC_{（268-261）}	31
A顶点	Convex^④	TAGCCAAAATCTTTTTCATCATCATG_{（410-390）}ATGGACGCTATTTTTTCGCCGTGATG_{（200-180）}GTAGCGAAAAATTTTT ACCGACCATA_{（616-596）}	78
B顶点	Convex	GAGCGGTAAGGTTTTTATGCCCCACA_{（358-338）}GCGGAAGCTTGTTTTTCTCGAAACCT（305-285）CAGCAGGATGC TTTTTCCACTGCAAC_{（252-232）}	78
C顶点	Convex	CGTTGCTTACCTTTTTATACGAGGAC_{（513-493）}AACAAAGGAGATTTTTTTTTGGCGGA_{（462-442）} TAGCGCGAACGTTTTTAGGATGAAAT_{（564-544）}	78
D顶点	Convex	TCTTATTATTCTTTTTCCTGGGGACT_（97-77）AGACGTCGGGATTTTTTTTCCTTCCT_（44-24） CAGGTCTTTGTTTTTTTTTTTCACAT_{（148-128）}	78

[1]	杨莹, 侯豪杰, 黄瑞, 崔煜, 王兵, 刘健, 鲍卫仁, 常丽萍, 王建成, 韩丽娜. 利用煤焦油中酚类物质Stöber法制备碳纳米球用于CO₂吸附[J]. 化工进展, 2023, 42(9): 5011-5018.
[2]	吴亚, 赵丹, 方荣苗, 李婧瑶, 常娜娜, 杜春保, 王文珍, 史俊. 用于复杂原油乳液的高效破乳剂开发及应用研究进展[J]. 化工进展, 2023, 42(8): 4398-4413.
[3]	尹新宇, 皮丕辉, 文秀芳, 钱宇. 特殊浸润性材料在防治油气管道中水合物成核与聚集的应用[J]. 化工进展, 2023, 42(8): 4076-4092.
[4]	徐沛瑶, 陈标奇, KANKALA Ranjith Kumar, 王士斌, 陈爱政. 纳米材料用于铁死亡联合治疗的研究进展[J]. 化工进展, 2023, 42(7): 3684-3694.
[5]	许春树, 姚庆达, 梁永贤, 周华龙. 氧化石墨烯/碳纳米管对几种典型高分子材料的性能影响[J]. 化工进展, 2023, 42(6): 3012-3028.
[6]	张晨宇, 王宁, 徐洪涛, 罗祝清. 纳米颗粒强化传热的多级潜热储热器性能评价[J]. 化工进展, 2023, 42(5): 2332-2342.
[7]	陈少华, 王义华, 胡强飞, 胡坤, 陈立爱, 李洁. 电化学修饰电极在检测Cr(Ⅵ)中的研究进展[J]. 化工进展, 2023, 42(5): 2429-2438.
[8]	殷铭, 郭晋, 庞纪峰, 吴鹏飞, 郑明远. 铜催化剂在涉氢反应中的失活机制和稳定策略[J]. 化工进展, 2023, 42(4): 1860-1868.
[9]	葛伟童, 廖亚龙, 李明原, 嵇广雄, 郗家俊. Pd-Fe/MWCNTs双金属催化剂制备及其脱氯动力学[J]. 化工进展, 2023, 42(4): 1885-1894.
[10]	万茂华, 张小红, 安兴业, 龙垠荧, 刘利琴, 管敏, 程正柏, 曹海兵, 刘洪斌. MXene在生物质基储能纳米材料领域中的应用研究进展[J]. 化工进展, 2023, 42(4): 1944-1960.
[11]	司银芳, 胡语婕, 张凡, 董浩, 佘跃惠. 生物合成氧化锌纳米颗粒材料及其抗菌应用[J]. 化工进展, 2023, 42(4): 2013-2023.
[12]	郭帅帅, 陈锦路, 金梁程龙, 陶醉, 陈小丽, 彭国文. 基于海水提铀的多孔芳香框架材料研究进展[J]. 化工进展, 2023, 42(3): 1426-1436.
[13]	陈仪, 郭耀励, 叶海星, 李宇璇, 牛青山. 二维纳米材料在渗透汽化脱盐膜中的应用[J]. 化工进展, 2023, 42(3): 1437-1447.
[14]	薛博, 杨婷婷, 王雪峰. 聚苯胺/碳纳米管气敏材料的研究进展[J]. 化工进展, 2023, 42(3): 1448-1456.
[15]	郝旭波, 牛宝联, 郭昊天, 徐祥和, 张忠斌, 李应林. 相变微胶囊改性及其在光热转换中的应用[J]. 化工进展, 2023, 42(2): 854-871.