Dataset Information

Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy.

ABSTRACT: Base pairs are fundamental building blocks of RNA. The base pairs of low stability are often critical in RNA functions. Here, we develop a solid-state NMR-based water-RNA exchange spectroscopy (WaterREXSY) to characterize RNA in solid. The approach uses different chemical exchange rates between iminos and water to evaluate base pair stability; the less stable ones would exchange more frequently, leading to stronger cross-peaks on WaterREXSY. Applied to the riboA71-adenine complex (the 71nt-aptamer domain of add adenine riboswitch from Vibrio vulnificus), the U47⋅U51 base pair, which is critical in ligand binding, was found to be less stable than other base pairs. The imino-water exchange rates of U47 at different temperatures are about 500-800 s^-1, indeed indicative of low stability. This implies a highly complex and plastic triad involving U47⋅U51 and that the opening of the U47⋅U51 base pair may be the early stage of ligand release.

SUBMITTER: Zhao S

PROVIDER: S-EPMC9619310 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy.

Zhao Sha S Li Xinming X Wen Ziyang Z Zou Mengbing M Yu Ge G Liu Xiangyang X Mao Jiafei J Zhang Lixin L Xue Yi Y Fu Riqiang R Wang Shenlin S

iScience 20221010 11

Base pairs are fundamental building blocks of RNA. The base pairs of low stability are often critical in RNA functions. Here, we develop a solid-state NMR-based water-RNA exchange spectroscopy (WaterREXSY) to characterize RNA in solid. The approach uses different chemical exchange rates between iminos and water to evaluate base pair stability; the less stable ones would exchange more frequently, leading to stronger cross-peaks on WaterREXSY. Applied to the riboA71-adenine complex (the 71nt-aptam ...[more]

PMID: 36325062

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Dataset Information

Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy.

Publications

Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy.

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