The theory of helix-based RNA folding kinetics and its application

doi:10.1088/1674-1056/abab84

中国物理B ›› 2020, Vol. 29 ›› Issue (10): 108703-.doi: 10.1088/1674-1056/abab84

所属专题： SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

Sha Gong(龚沙)¹, Taigang Liu(刘太刚)², Yanli Wang(王晏莉)², Wenbing Zhang(张文炳)²^,†()

收稿日期:2020-06-29 修回日期:2020-07-30 接受日期:2020-08-01 出版日期:2020-10-05 发布日期:2020-10-05
通讯作者: Wenbing Zhang(张文炳)

The theory of helix-based RNA folding kinetics and its application

Sha Gong(龚沙)¹, Taigang Liu(刘太刚)², Yanli Wang(王晏莉)², and Wenbing Zhang(张文炳)^2,†

¹ Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang 438000, China
² Department of Physics, Wuhan University, Wuhan 430072, China

Received:2020-06-29 Revised:2020-07-30 Accepted:2020-08-01 Online:2020-10-05 Published:2020-10-05
Contact: ^†Corresponding author. E-mail: wbzhang@whu.edu.cn
About author:
†Corresponding author. E-mail: wbzhang@whu.edu.cn
* Project supported by the Science Fund from the Key Laboratory of Hubei Province, China (Grant No. 201932003) and the National Natural Science Foundation of China (Grant Nos. 1157324 and 31600592).

摘要/Abstract

Abstract:

RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requires a conceptual framework to investigate the folding kinetics of RNA molecules, instead of native structures alone. Over the past several decades, many experimental and theoretical methods have been developed to address RNA folding. The helix-based RNA folding theory is the one which uses helices as building blocks, to calculate folding kinetics of secondary structures with pseudoknots of long RNA in two different folding scenarios. Here, we will briefly review the helix-based RNA folding theory and its application in exploring regulation mechanisms of several riboswitches and self-cleavage activities of the hepatitis delta virus (HDV) ribozyme.

Key words: RNA folding kinetics, RNA structure, Riboswitch, HDV ribozyme

中图分类号: (RNA)

87.14.gn

87.15.bd (Secondary structure) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways) 87.18.Cf (Genetic switches and networks)

Sha Gong(龚沙), Taigang Liu(刘太刚), Yanli Wang(王晏莉), Wenbing Zhang(张文炳). [J]. 中国物理B, 2020, 29(10): 108703-.

Sha Gong(龚沙), Taigang Liu(刘太刚), Yanli Wang(王晏莉), and Wenbing Zhang(张文炳)†. The theory of helix-based RNA folding kinetics and its application[J]. Chin. Phys. B, 2020, 29(10): 108703-.

图/表 5

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The theory of helix-based RNA folding kinetics and its application

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