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

Liu, Yaping; Kotar, Anita; Hodges, Tracy L.; Abdallah, Kyrillos; Taleb, Mallak H.; Bitterman, Brayden A.; Jaime, Sara; Schaubroeck, Kyle J.; Mathew, Ethan; Morgenstern, Nicholas W.; Lohmeier, Anthony; Page, Jordan L.; Ratanapanichkich, Matt; Arhin, Grace; Johnson, Breanna L.; Cherepanov, Stanislav; Moss, Stephen C.; Zuniga, Gisselle; Tilson, Nicholas J.; Yeoh, Zoe C.; Johnson, Bruce A.; Keane, Sarah C.

doi:10.1007/s12104-021-10049-0

Article
Published: 27 August 2021

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

Yaping Liu¹^na1,
Anita Kotar^1,5^na1,
Tracy L. Hodges¹,
Kyrillos Abdallah¹,
Mallak H. Taleb¹,
Brayden A. Bitterman¹,
Sara Jaime¹,
Kyle J. Schaubroeck¹,
Ethan Mathew¹,
Nicholas W. Morgenstern¹,
Anthony Lohmeier¹,
Jordan L. Page¹,
Matt Ratanapanichkich¹,
Grace Arhin¹,
Breanna L. Johnson¹,
Stanislav Cherepanov¹,
Stephen C. Moss¹,
Gisselle Zuniga¹,
Nicholas J. Tilson¹,
Zoe C. Yeoh²,
Bruce A. Johnson³ &
Sarah C. Keane ORCID: orcid.org/0000-0003-3206-9048^1,4

Biomolecular NMR Assignments volume 15, pages 479–490 (2021)Cite this article

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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.

Author information

Yaping Liu and Anita Kotar have contributed equally to this work.

Authors and Affiliations

Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
Yaping Liu, Anita Kotar, Tracy L. Hodges, Kyrillos Abdallah, Mallak H. Taleb, Brayden A. Bitterman, Sara Jaime, Kyle J. Schaubroeck, Ethan Mathew, Nicholas W. Morgenstern, Anthony Lohmeier, Jordan L. Page, Matt Ratanapanichkich, Grace Arhin, Breanna L. Johnson, Stanislav Cherepanov, Stephen C. Moss, Gisselle Zuniga, Nicholas J. Tilson & Sarah C. Keane
Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
Zoe C. Yeoh
Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
Bruce A. Johnson
Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
Sarah C. Keane
Current Address: Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
Anita Kotar

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Yaping Liu
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Anita Kotar
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Tracy L. Hodges
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Kyrillos Abdallah
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Mallak H. Taleb
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Brayden A. Bitterman
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Sara Jaime
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Kyle J. Schaubroeck
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Ethan Mathew
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Nicholas W. Morgenstern
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Anthony Lohmeier
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Jordan L. Page
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Matt Ratanapanichkich
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Grace Arhin
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Breanna L. Johnson
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Stanislav Cherepanov
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Stephen C. Moss
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Gisselle Zuniga
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Nicholas J. Tilson
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Zoe C. Yeoh
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Bruce A. Johnson
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Sarah C. Keane
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Correspondence to Sarah C. Keane.

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Availability of data and material

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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Received: 24 May 2021
Accepted: 22 August 2021
Published: 27 August 2021
Issue Date: October 2021
DOI: https://doi.org/10.1007/s12104-021-10049-0

Keywords

RNA
Solution NMR spectroscopy
GAGA tetraloop
Chemical shift database