Effect of pH on the Stability of DNA Origami

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Effect of pH on the Stability of DNA Origami

Research Article | 更新时间：2021-01-26

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- Effect of pH on the Stability of DNA Origami
- Acta Polymerica Sinica Issue 12, Pages: 1993-2000(2017)
- 作者机构：
  
  1.中国科学院上海应用物理研究所上海 201800
  2.中国科学院大学北京 100049
- 作者简介：
- 基金信息：
- DOI：10.11777/j.issn1000-3304.2017.17064
  CLC：
- Published：20 December 2017，
  
  Received：28 March 2017，
  
  Revised：20 April 2017，
扫描看全文
Wei-na Fang, Chun-hai Fan, Hua-jie Liu. Effect of pH on the Stability of DNA Origami. [J]. Acta Polymerica Sinica (12):1993-2000(2017)
DOI：

Wei-na Fang, Chun-hai Fan, Hua-jie Liu. Effect of pH on the Stability of DNA Origami. [J]. Acta Polymerica Sinica (12):1993-2000(2017) DOI： 10.11777/j.issn1000-3304.2017.17064.

摘要

研究了不同pH环境对2种使用M13链作为骨架链的常见DNA折纸折叠与稳定性的影响，获得了其在pH=4~11这一广泛范围内的耐受性数据.首先观察了在不同pH缓冲液中的三角形DNA折纸自组装折叠行为，发现其合适pH范围为6~9，过高或过低的pH都不能退火形成折纸结构.另一方面，又研究了在标准pH缓冲液中预先制备的DNA折纸，对不同pH环境的耐受性.研究发现，在pH值为5~10的溶液环境中，DNA折纸均保持一定稳定.比较以上2种研究方法获得的结果，可以发现，相比在不同pH缓冲液中从头退火制备，已形成的DNA折纸对酸碱有较好耐受性.另外，研究也发现，长方形折纸和三角形折纸稳定性相似，都能在pH=5~10的环境中保持至少12 h的稳定性.据此，还提出了pH对折纸稳定性的可能影响机理，认为其对氢键的破坏及对DNA链造成的断裂共同导致了DNA折纸结构的破碎.

Abstract

The response of DNA origami nanostructures to pH is systematically investigated from two aspects in this work. At first

self-assembly of DNA origami triangle in different pH buffer was tested by putting M13 scaffold and staple strands into a series of sodium citrate buffer (10 mmol/L with 12.5 mmol/L Mg

2+

)

the as-prepared sample was characterized by AFM. The formation of the origami structure was affected by pH and the structure was observed only in the pH range of 6-9. Tolerance of DNA origami to pH in the external environment was investigated by immersing them (pH=8) into acidic and basic solutions for 2 h at room temperature

followed by characterization of the samples by AFM and 0.5% agarose gel respectively. The AFM results showed that the DNA origami triangle maintained the original structure at pH range of 5-10

and the structure was broken at higher or lower pH. The agarose gel suggested that the most stable state of DNA origami triangle was in pH range of 7-8

where the intensity and mobility of the sample band remained the same. Compared with the origami self-assembled in different pH buffers

the pre-prepared origami showed better resistance to acidic and alkali environments. In order to test the long time-stability of DNA origami

pH value of the prepared triangle origami was adjusted in the range of 5-10 and the reaction time was extended to 12 h. AFM test results indicated that the DNA origami could maintain its original structure for at least 12 h. Another common origami nanostructure was also tested; like origami triangle

rectangle structure showed a similar pH tolerance which could keep the stability at pH range of 5-10 for at least 12 h. The long time pH stability experiment of the triangle and the rectangle structures indicated that the origami structure based on M13 owned a relatively high pH tolerance. Based on the above results

possible mechanism of pH effect on DNA origami stability was also proposed. In the process of the origami preparation

excess H

+

or OH

-

will affect the formation of the hydrogen bond thus affecting the hybridization of DNA double helixes. In the pH tolerance experiment

excessive H

+

or OH

-

will attack the formed hydrogen bonds and make the origami structure floppy. In both aspects

more H

+

or OH

-

will undermine the primary structure of DNA

and eventually affect the formation and stability of DNA origami structures.

关键词

DNA折纸自组装稳定性pH

Keywords

DNA origamiSelf-assemblyStabilitypH

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State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology

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