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NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database

Abstract

RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the Biological Magnetic Resonance Data Bank (BMRB) to identify sequences that had no (or limited) chemical shift information. Here, we report the chemical shift assignments for 12 RNA hairpins designed specifically to help populate the BMRB.

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Acknowledgements

This work was supported by National Science Foundation grant MCB-1942398 (to S.C.K.) and by National Institute of General Medical Sciences of the National Institutes of Health grant U54 GM 103297 (to B.A.J.). Research reported in this publication was supported by the University of Michigan BioNMR Core Facility (U-M BioNMR). U-M BioNMR Core is grateful for support from U-M including the College of Literature, Sciences and Arts, Life Sciences Institute, College of Pharmacy and the Medical School along with the U-M Biosciences Initiative.

Funding

This work was supported by National Science Foundation grant MCB-1942398 (to S.C.K.) and by National Institute of General Medical Sciences of the National Institutes of Health grant U54 GM 103,297 (to B.A.J.). Research reported in this publication was supported by the University of Michigan BioNMR Core Facility (U-M BioNMR). U-M BioNMR Core is grateful for support from U-M including the College of Literature, Sciences and Arts, Life Sciences Institute, College of Pharmacy and the Medical School along with the U-M Biosciences Initiative.

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Correspondence to Sarah C. Keane.

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Assigned chemical shifts along with raw NMR data have been deposited in the BMRB. RNA5: 50933, RNA7: 50932, RNA8: 50931, RNA21: 50930, RNA23: 50929, RNA24: 50928, RNA73: 50927, RNA74: 50926, RNA75: 50925, RNA89: 50924, RNA90: 50923, RNA91: 50922.

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Liu, Y., Kotar, A., Hodges, T.L. et al. NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database. Biomol NMR Assign 15, 479–490 (2021). https://doi.org/10.1007/s12104-021-10049-0

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  • DOI: https://doi.org/10.1007/s12104-021-10049-0

Keywords

  • RNA
  • Solution NMR spectroscopy
  • GAGA tetraloop
  • Chemical shift database