DNA纳米折纸带的制备及pH值对其结构稳定性的影响研究

引用本文: 陶晴, 陈谦, 卞晓军, 刘刚, 颜娟. DNA纳米折纸带的制备及pH值对其结构稳定性的影响研究[J]. 分析化学, 2021, 49(5): 743-751. doi: 10.19756/j.issn.0253-3820.201706 shu

Citation: TAO Qing, CHEN Qian, BIAN Xiao-Jun, LIU Gang, YAN Juan. Preparation of DNA Origami Belt and Effect of pH on Its Stability[J]. Chinese Journal of Analytical Chemistry, 2021, 49(5): 743-751. doi: 10.19756/j.issn.0253-3820.201706 shu

DNA纳米折纸带的制备及pH值对其结构稳定性的影响研究

陶晴 ^1, ,
陈谦 ^1, ,
卞晓军 ^1, ,
刘刚 ^2, ,
颜娟 ^{1,
,}

1.
上海海洋大学食品学院, 上海水产品加工及贮藏工程技术研究中心, 农业部水产品贮藏保鲜质量安全风险评估实验室(上海), 上海 201306;
2.
上海市计量测试技术研究院生物计量实验室, 上海 201203

通讯作者: 颜娟,E-mail:j-yan@shou.edu.cn

基金项目:
国家自然科学基金项目（Nos.21775102，21775104）和上海市自然科学基金项目（No.20ZR1424100）资助。

摘要: 以滚环扩增技术制备的含有多个拷贝单元的长单链DNA为脚手架链，与互补的3条订书钉短链通过分子自组装实现长链与短链在特定位置的互补，进而折叠出DNA纳米折纸带。借助SYBR Green染料，采用实时荧光定量PCR技术原理以及原子力显微镜成像技术，通过检测反应液中的荧光信号强度判断体系中是否存在双链结构，并通过原子力显微镜成像技术更直观考察纳米带形貌变化。考察了pH值对纳米带稳定性的影响，结果表明，在中性条件（pH=7）下，纳米带稳定性良好，其荧光信号强度在24 h内均明显优于其它pH条件处理组；对酸碱环境的耐受性较差，在极端pH环境（pH=3，pH=11）下，即使瞬时（<10 s）作用于纳米带，也会引起溶液荧光信号强度迅速下降。原子力显微镜成像和琼脂糖凝胶电泳结果表明，极端pH环境（pH=3）对纳米带的形态的破坏作用是持续且不可逆的，随着时间延长，宽度约16 nm、长度可达微米级的纳米带逐渐变短、变细，推测在此过程中，维持DNA纳米带双链结构的氢键断裂，核苷酸之间磷酸二酯键和核苷酸内部的糖苷键发生水解，致使DNA纳米折纸带逐渐碎片化。

关键词:

English

Preparation of DNA Origami Belt and Effect of pH on Its Stability

TAO Qing ^1, ,
CHEN Qian ^1, ,
BIAN Xiao-Jun ^1, ,
LIU Gang ^2, ,
YAN Juan ^{1,
,}

1.
Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation(Shanghai), College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
2.
Laboratory of Biometrology, Shanghai Institute of Metrology and Testing Technology, Shanghai 201203, China

Corresponding author: YAN Juan, j-yan@shou.edu.cn

Received Date: 26 November 2020
Revised Date: 27 January 2021
Fund Project:
Supported by the National Natural Science Foundation of China (Nos.21775102, 21775104) and the Natural Science Foundation of Shanghai Municipal (No.20ZR1424100).

Abstract: The long single-stranded DNA containing multiple copy units prepared by rolling circle amplification technique was used as a scaffold strand. The scaffold strands were hybridized to three short staple strands at special positions by the molecular self-assembly and formed DNA origami belt. On the basis of the principle of SYBR Green real-time fluorescence quantitative PCR method and atomic force microscopy (AFM) imaging technology, the formation of double-stranded structure was examined by the change of fluorescence signal intensity in the reaction solution while the morphology of DNA belts was observed by AFM straightly. The effect of pH on the stability of DNA belt was studied, and its performance of pH-resistant in the wide range of pH=3-11 was obtained. DNA belts exhibited the best stability in neutral pH enviroment (pH=7), which showed a significantly higher fluorescence signal than that of other groups within 24 h. DNA belts had poor resistance to acid and alkali environment, especially extreme pH conditions (pH=3, pH=11). At extreme pH, even instantaneous treatments (<10 s) could have significant effects on the DNA belts, causing a rapid decrease in the fluorescence signal intensity of the solution. Further, the characterization results of AFM and agarose gel showed that the morphological destruction of DNA belts in extreme pH environment (pH=3) was a continuous and irreversible process. The DNA belts with a width of 16 nm and a length of micrometer became shorter and thinner with the processing time. It was speculated that the hydrogen bond which held the double-stranded structure of DNA belts was broken first, and then the phosphodiester linkage between nucleotides as well as the glycoside bond inside nucleotide, resulting in broken DNA belts in pieces finally.

Key words:

1. [1]
  CAO Y, FATEMI V, DEMIR A, FANG S A, TOMARKEN S L, LUO J Y, SANCHEZ-YAMAGISHI J D, WATANABE K, TANIGUCHI T, KAXIRAS E, ASHOORI R C, JARILLO-HERRERO P. Nature, 2018, 556(7699):80-84.
2. [2]
  LONDONO-CALDERON A, HOSSEN M M, PALO P E, BENDICKSON L, VERGARA S, NILSEN-HAMILTON M, HILLIER A C, PROZOROV T. Small Methods, 2019, 3(12):1900393.
3. [3]
  SEEMAN N C. Annu. Rev. Biophys. Biomol. Struct., 1998, 27(1):225-248.
4. [4]
  SA-ARDYEN P, VOLOGODSKII A V, SEEMAN N C. Biophys. J., 2003, 84(6):3829-3837.
5. [5]
  FU T J, SEEMAN N C. Biochemistry, 1993, 32(13):3211-3220.
6. [6]
  YAN H, LABEAN T H, FENG L P, REIF J H. Proc. Natl. Acad. Sci. U.S.A., 2003, 100(14):8103-8108.
7. [7]
  ZHANG H L, WANG Y, ZHANG H, LIU X G, ANTONY L, HUANG Q L, WANG F, CHAO J, LIU H J, LI J, SHI J Y, ZUO X L, WANG L H, WANG L H, CAO X Y, CARLOS B, TIAN Z Q, FAN C H. Nat. Commun., 2019, 10(1):1006.
8. [8]
  GOODMAN R P, BERRY R M, TURBERFIELD A J. Chem. Commun (Camb)., 2004, (12):1372-1373.
9. [9]
  GOODMAN R P, SCHAAP I A T, TARDIN C F, ERBEN C M, BERRY R M, SCHMIDT C F, TURBERFIELD A J. Science, 2005, 310(5754):1661-1665.
10. [10]
  ROTHEMUND P W. Nature, 2006, 440(7082):297-302.
11. [11]
  CUTLER J I, AUYEUNG E, MIRKIN C A. J. Am. Chem. Soc., 2012, 134(3):1376-1391.
12. [12]
  MELA I, VALLEJO-RAMIREZ P P, MAKARCHUK S, CHRISTIE G, BAILEY D, HENDERSON R M, SUGIYAMA H, ENDO M, KAMINSKI C F. Angew. Chem., Int. Ed., 2020, 59(31):12698-12702.
13. [13]
  ZHANG Q, JIANG Q, LI N, DAI L R, LIU Q, SONG L L, WANG J Y, LI Y Q, TIAN J, DING B Q, DU Y. ACS Nano, 2014, 8(7):6633-6643.
14. [14]
  PAN Q S, NIE C P, YAN L H, YI J T, LIU C, ZHANG J, HE M M, HE M Y, CHEN T T, CHU X. ACS Appl. Mater. Interfaces, 2020, 12(1):400-409.
15. [15]
  YAN J, HU C Y, WANG P, LIU R, ZUO X L, LIU X, SONG S P, FAN C H, HE D N, SUN G. ACS Appl. Mater Interfaces, 2014, 6(22):20372-20377.
16. [16]
  KLEIN W P, ROLCZYNSKI B S, OLIVER S M, ZADEGAN R, BUCKHOUT-WHITE S, ANCONA M G, CUNNINGHAM P D, MELINGER J S, VORA P M, KUANG W, MEDINTZ L L, DÍAZ SEBASTIÁN A. ACS Appl. Nano Mater., 2020, 3(4):3323-3336.
17. [17]
  CHAO J, ZHANG H L, XING Y K, LI Q, LIU H J, WANG L H, WANG L J, FAN C H. Nat. Protoc., 2018, 13(7):1569-1585.
18. [18]
  MODI S, SWETHA M G, GOSWAMI D, GUPTA G D, MAYOR S, KRISHNAN Y. Nat. Nanotechnol., 2009, 4(5):325-330.
19. [19]
  FANG W N, XIE M, HOU X L, LIU X G, ZUO X L, CHAO J, WANG L H, FAN C H, LIU H J, WANG L H. J. Am. Chem. Soc., 2020, 142(19):8782-8789.
20. [20]
  REN K W, XU Y F, LIU Y, YANG M, JU H X. ACS Nano, 2018, 12(1):263-271.
21. [21]
  ZHU Fu-Lin, BIAN Xiao-Jun, TIAN Run, LI Liang, YAN Juan, LIU Gang. Chin. J. Anal. Chem., 2020, 48(4):473-483. 朱福琳, 卞晓军, 田润, 李亮, 颜娟, 刘刚. 分析化学, 2020, 48(4):473-483.
22. [22]
  ZHANG Y A, WANG F, CHAO J, XIE M, LIU H J, PAN M C, KOPPERGER E, LIU X G, LI Q, SHI J Y, WANG L H, HU J, WANG L H, FRIEDRICH C S, FAN C H. Nat. Commun., 2019, 10:5469.
23. [23]
  ZHANG Q, LIN S Y, SHI S R, ZHANG T, MA Q Q, TIAN T R, ZHOU T F, CAI X X, LIN Y F. ACS Appl. Mater. Interfaces, 2018, 10(4):3421-3430.
24. [24]
  SIMON S M. Therapeutic Focus, 1999, 4(1):32-38.
25. [25]
  ZHANG Z H, LIU Z C, TIAN Y. iScience, 2020, 23(7):101344-101362.
26. [26]
  FANG Wei-Na, FAN Chun-Hai, LIU Hua-Jie. Acta Polym. Sin., 2017, 12:1993-2000. 方维娜, 樊春海, 柳华杰. 高分子学报, 2017, 12:1993-2000.
27. [27]
  DU Y M, ZHOU Y Y, WEN Y L, BIAN X J, XIE Y Y, ZHANG W J, LIU G, YAN J. Microchim. Acta, 2019, 186(12):840-850.
28. [28]
  YAN J, SONG S P, LI B, ZHANG Q Z, HUANG Q, ZHANG H, FAN C H. Small, 2010, 6(22):2520-2525.
29. [29]
  YAN J, HU C Y, WANG P, LIU R, ZUO X L, LIU X W, SONG S P, FAN C H, HE D N, SUN G. Angew. Chem., Int. Ed., 2015, 54(8):2431-2435.
30. [30]
  OUYANG X Y, LI J, LIU H J, ZHAO B, YAN J, HE D N, FAN C H, CHAO J. Methods, 2014, 67(2):198-204.

扫一扫看文章

计量

PDF下载量: 10
文章访问数: 1081
HTML全文浏览量: 190

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

DNA纳米折纸带的制备及pH值对其结构稳定性的影响研究

通讯作者: 颜娟,E-mail:j-yan@shou.edu.cn

English

Preparation of DNA Origami Belt and Effect of pH on Its Stability

Corresponding author: YAN Juan, j-yan@shou.edu.cn

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

DNA纳米折纸带的制备及pH值对其结构稳定性的影响研究

通讯作者: 颜娟,E-mail:j-yan@shou.edu.cn

English

Preparation of DNA Origami Belt and Effect of pH on Its Stability

Corresponding author: YAN Juan, j-yan@shou.edu.cn

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

文章相关

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs