Citation: YU Chun-Miao, WANG Ye-Sheng, ZHU Zhen-Tong, LI Bing-Ling. Structure Analysis of Large Size Assembly with Solid-state Nanopore[J]. Chinese Journal of Analytical Chemistry, ;2023, 51(5): 842-850. doi: 10.19756/j.issn.0253-3820.231088 shu

Structure Analysis of Large Size Assembly with Solid-state Nanopore

1.
State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China;
2.
Shool of Applied Chemistry and Engineering, University of Science & Technology of China, Hefei 230026, China;
3.
Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, Northwest Normal University, Lanzhou 730070, China

Corresponding author: LI Bing-Ling, binglingli@ciac.ac.cn
Received Date: 9 March 2023
Revised Date: 27 March 2023

Fund Project: Supported by the National Natural Science Foundation of China (Nos. 22074136, 22004102) and the Cooperation Funding of Changchun with Chinese academy of sciences (No. 21SH16).

In recent years, with the rapid development of nanopore sequencing technique, more attention are paid to nanopore. With the development of nucleic acid amplification techniques, the function of DNA has been expanded from a carrier of genetic information to a programmable functional material, and the need for the characterization of DNA assembly is increasingly emerging. However, traditional characterization methods are often unable to provide comprehensive structural information of DNA assembly, and some methods cannot be used in a homogeneous environment. Therefore, a variety of technologies should be combined to complete the characterization. Solid-state nanopore is a kind of characterization method that can complement existing techniques. Taking a four-hairpin hybridization chain reaction (HCR) as the model, the dumbbell and the G-quadruplex on the side-chain of HCR duplex concatamers in homogeneous solution were distinguished in this study. The current offset of the single-side dumbbell structure assembly was about 10 pA, while in the presence of K⁺, the current offset of the G-quadruplex structure assembly increased nearly 4 times. Moreover, the reaction process and reaction products of the concatenated hybridization chain reaction(C-HCR) were analyzed in detail, and the difference in current of assemblies was obviously detected. With the increase of dimension of structure, the current offset increased exponentially. This study paved the way for the subsequent detection of more levels of cascade hybridization chain reaction system. Solid-state nanopores were expected to be an effective means of characterizing DNA nanostructure, such as analyzing finer nanostructures or distinguishing mixed nanostructures in complex samples.
- Solid-state nanopore,
- Hybridization chain reaction,
- Concatenated hybridization chain reaction,
- Nucleic acid assembly
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