Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly

Chen，Zhe1,2,3; Cao，Lingyan4; Yun，Keming1,3; Lu，Jingxiong2,5

2024-01-16

10.1021/acsmacrolett.3c00680

ACS Macro Letters   影响因子和分区

2161-1653

Despite 40 years of development of DNA nanotechnology, the fundamental knowledge of the process of DNA strand assembly into targeted nanostructures remains unclear. Study of the dynamic process, especially the competing hybridizations in kinetic traps, provides insight into DNA assembly. In this study, a system of middle-domain first assembly (MDFA) was proposed to enable oligonucleotides to assemble into a 2D DNA monolayer in a pathway-dependent approach. This system was an ideal case to study the dynamic interactions between competing hybridizations during oligonucleotide assembly. Dynamic study revealed the coexistence of the kinetically trapped dead-end byproduct and target product at the early stage of annealing, followed by transformation of the byproduct into the target product by reverse disassembly, due to the equilibrium of the competing hybridizations increasingly favoring the target product pathway. This study offered a better understanding of the assembly pathway of DNA nanostructures for future design.

SCI ; EI

英语

通讯

2-s2.0-85182010998

Scopus

1.School of Forensic Medicine,Shanxi Medical University,Jinzhong,98 University Street, Yuci District, Shanxi,030600,China
2.Research Center for Intelligent Computing Platforms,Zhejiang Laboratory,Hangzhou,311100,China
3.Key Laboratory of Forensic Toxicology of Ministry of Public Security,Jinzhong,98 University Street, Yuci District, Shanxi,030600,China
4.Department of Prosthodontics,Ninth People’s Hospital,Shanghai Jiao Tong University School of Medicine,Shanghai,639 Zhizaoju Road,200011,China
5.Institute of Medi-X,Academy for Advanced Interdisciplinary Studies,Southern University of Science and Technology,Shenzhen,1088 Xueyuan Blvd., Nanshan District, Guangdong,518055,China

Chen，Zhe,Cao，Lingyan,Yun，Keming,et al. Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly[J]. ACS Macro Letters,2024,13(1):94-98.

Chen，Zhe,Cao，Lingyan,Yun，Keming,&Lu，Jingxiong.(2024).Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly.ACS Macro Letters,13(1),94-98.

Chen，Zhe,et al."Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly".ACS Macro Letters 13.1(2024):94-98.