A procedure to validate and correct the Superscri

Authors: Thomas Aeschbacher Mario Schubert Frédéric HT Allain

Publish Date: 2012/01/18

Volume: 52, Issue: 2, Pages: 179-190

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Abstract

Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information Proper calibration is indispensable to extract such information from chemical shifts Whereas a variety of procedures exist to verify the chemical shift calibration for proteins no such procedure is available for RNAs to date We present here a procedure to analyze and correct the calibration of 13C NMR data of RNAs Our procedure uses five 13C chemical shifts as a reference each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank In 49 datasets we could evaluate the 13C calibration and detect errors or inconsistencies in RNA 13C chemical shifts based on these chemical shift reference values More than half of the datasets 27 out of those 49 were found to be improperly referenced or contained inconsistencies This large inconsistency rate possibly explains that no clear structure–13C chemical shift relationship has emerged for RNA so far We were able to recalibrate or correct 17 datasets resulting in 39 usable 13C datasets 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets We can now search for structure–chemical shift relationships with this improved list of 13C chemical shift data This is demonstrated by a clear relationship between ribose 13C shifts and the sugar pucker which can be used to predict a C2′ or C3′endo conformation of the ribose with high accuracy The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures and the extraction of restraints for structure calculations of RNAWe like to thank Olivier Duss for providing spectra of the two stemloops FZL2 and FZL4 Wolfgang Bermel and Peter Schmieder for helpful discussions concerning chemical shift referencing Further we are grateful to Peter Lukavsky for beneficial discussions of the C1′ chemical shift dependence on the ribose pucker and Fred Damberger for his comments on the manuscript We thank Ryan Mackay and Lawrence P McIntosh for their help regarding chemical shift calibration with Varian software This work was supported by SNFNCCR structural biology

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