Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNAArg from Romanomermis culicivorax

doi:10.1088/1674-1056/ac1e1e

中国物理B ›› 2021, Vol. 30 ›› Issue (10): 108203-108203.doi: 10.1088/1674-1056/ac1e1e

Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNA^Arg from Romanomermis culicivorax

Yan-Hui Li(李彦慧)^1,2, Zhen-Sheng Zhong(钟振声)^1,2,†, and Jie Ma(马杰)^1,2

1 School of Physics, Sun Yat-sen University, Guangzhou 510275, China;
2 State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China

收稿日期:2021-07-09 修回日期:2021-08-04 接受日期:2021-08-17 出版日期:2021-09-17 发布日期:2021-10-08
通讯作者: Zhen-Sheng Zhong E-mail:zhongzhsh@mail.sysu.edu.cn
基金资助:
Project supported by the Natural Science Foundation of Guangdong Province, China (Grant No. 2017A030310085) and the Science and Technology Planning Project of Guangdong Province, China (Grant No. 2018A050506034).

Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNA^Arg from Romanomermis culicivorax

Yan-Hui Li(李彦慧)^1,2, Zhen-Sheng Zhong(钟振声)^1,2,†, and Jie Ma(马杰)^1,2

1 School of Physics, Sun Yat-sen University, Guangzhou 510275, China;
2 State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China

Received:2021-07-09 Revised:2021-08-04 Accepted:2021-08-17 Online:2021-09-17 Published:2021-10-08
Contact: Zhen-Sheng Zhong E-mail:zhongzhsh@mail.sysu.edu.cn
Supported by:
Project supported by the Natural Science Foundation of Guangdong Province, China (Grant No. 2017A030310085) and the Science and Technology Planning Project of Guangdong Province, China (Grant No. 2018A050506034).

摘要/Abstract

摘要： The mechanical stability of tRNAs contributes to their biological activities. The mitochondrial tRNA^Arg from Romanomermis culicivorax is the shortest tRNA ever known. This tRNA lacks D- and T-arms, represents a stem-bulge-stem architecture but still folds into a stable tertiary structure. Although its structure had been reported, studies on its mechanical folding and unfolding kinetic characteristics are lacking. Here, we directly measured the single-molecule mechanical folding and unfolding kinetics of the armless mt tRNA^Arg by using optical tweezers in different solution conditions. We revealed a two-step reversible unfolding pathway: the first and large transition corresponds to the unfolding of acceptor stem and bulge below 11 pN, and the second and small transition corresponds to the unfolding of anticodon arm at 12 pN-14 pN. Moreover, the free energy landscapes of the unfolding pathways were reconstructed. We also demonstrated that amino acid-chelated Mg²⁺(aaCM), which mimics the intracellular solution condition, stabilizes the bulge of mitochondrial tRNA^Arg possibly by reducing the topological constraints or stabilizing the possible local non-canonical base pairings within the bulge region. Our study revealed the solution-dependent mechanical stability of an armless mt tRNA, which may shed light on future mt tRNA studies.

关键词: mitochondrial tRNA, mechanical stability, singlemolecule manipulation, amino acid-chelated Mg²⁺

Abstract: The mechanical stability of tRNAs contributes to their biological activities. The mitochondrial tRNA^Arg from Romanomermis culicivorax is the shortest tRNA ever known. This tRNA lacks D- and T-arms, represents a stem-bulge-stem architecture but still folds into a stable tertiary structure. Although its structure had been reported, studies on its mechanical folding and unfolding kinetic characteristics are lacking. Here, we directly measured the single-molecule mechanical folding and unfolding kinetics of the armless mt tRNA^Arg by using optical tweezers in different solution conditions. We revealed a two-step reversible unfolding pathway: the first and large transition corresponds to the unfolding of acceptor stem and bulge below 11 pN, and the second and small transition corresponds to the unfolding of anticodon arm at 12 pN-14 pN. Moreover, the free energy landscapes of the unfolding pathways were reconstructed. We also demonstrated that amino acid-chelated Mg²⁺(aaCM), which mimics the intracellular solution condition, stabilizes the bulge of mitochondrial tRNA^Arg possibly by reducing the topological constraints or stabilizing the possible local non-canonical base pairings within the bulge region. Our study revealed the solution-dependent mechanical stability of an armless mt tRNA, which may shed light on future mt tRNA studies.

Key words: mitochondrial tRNA, mechanical stability, singlemolecule manipulation, amino acid-chelated Mg²⁺

中图分类号: (Single molecule manipulation of proteins and other biological molecules)

82.37.Rs

87.14.gn (RNA) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways) 87.15.La (Mechanical properties)

Yan-Hui Li(李彦慧), Zhen-Sheng Zhong(钟振声), and Jie Ma(马杰). Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNA^Arg from Romanomermis culicivorax[J]. 中国物理B, 2021, 30(10): 108203-108203.

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Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNA^Arg from Romanomermis culicivorax

Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNA^Arg from Romanomermis culicivorax

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