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Updated: Jan 17, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

TiRNA: RNA構造予測と折り畳みにおける温度とイオン効果を考慮した粗視化手法

Xunxun Wang¹, Zouchenyu Zhou¹, Shixiong Yu¹

¹Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.

Nucleic acids research

|January 14, 2026

Abstract:

RNAs play crucial roles in various important biological functions such as gene regulation and catalysis. The functions of RNAs are generally coupled to their structures as well as to the stability of the structure, which can strongly depend on ionic conditions. However, it is still a challenge to make reliable predictions for the structures and stability of RNAs in ion solutions. In this work, we developed a coarse-grained method involving temperature and ion effects for simulating RNA folding and three-dimensional (3D) structure prediction, named TiRNA. Extensive tests demonstrate that TiRNA can make successful predictions for 3D structures of RNAs, including pseudoknots and multi-way junctions, and for thermal stability of RNAs in ion solutions solely from sequences, as compared with the top existing methods. Moreover, TiRNA can also make reliable predictions for 3D structures and stability of RNAs in ion solutions based on inputting secondary structures.

キーワード:

RNA構造予測 RNA折り畳み粗視化シミュレーションイオン効果熱安定性

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RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Nanomanipulation of Single RNA Molecules by Optical Tweezers

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Published on: August 20, 2014

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