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

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).

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.
- Rolling circle amplification,
- DNA origami,
- Molecular self-assembly,
- Stability of nano-structures
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