Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy
Sha Zhao,
Xinming Li,
Ziyang Wen,
Mengbing Zou,
Ge Yu,
Xiangyang Liu,
Jiafei Mao,
Lixin Zhang,
Yi Xue,
Riqiang Fu,
Shenlin Wang
Affiliations
Sha Zhao
College of Chemistry and Molecular Engineering, Beijing NMR Center, Peking University, Beijing, 100871, China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
Xinming Li
Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
Ziyang Wen
College of Chemistry and Molecular Engineering, Beijing NMR Center, Peking University, Beijing, 100871, China
Mengbing Zou
College of Chemistry and Molecular Engineering, Beijing NMR Center, Peking University, Beijing, 100871, China
Ge Yu
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
Xiangyang Liu
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
Jiafei Mao
Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
Lixin Zhang
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
Yi Xue
Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Corresponding author
Riqiang Fu
National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA; Corresponding author
Shenlin Wang
College of Chemistry and Molecular Engineering, Beijing NMR Center, Peking University, Beijing, 100871, China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; State Key Laboratory of Medicinal Chemical Biology, NanKai University, Tianjin 300071, China; Corresponding author
Summary: 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.
