ArticleJournal of biomolecular NMR2012
A procedure to validate and correct the 13C chemical shift calibration of RNA datasets.
Article in Journal of biomolecular NMR, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- A suite of macrocyclic peptide inhibitors and substrate probes for arginine methyltransferases.Chemical science · 2026Article
- Elucidating microRNA-34a organisation within human Argonaute-2 by dynamic nuclear polarisation-enhanced magic angle spinning NMR.Nucleic acids research · 2024Article
- Characterization of conformational heterogeneity via higher-dimensionality, proton-detected solid-state NMR.Journal of biomolecular NMR · 2022Article
- Synthesis of [7-Monatshefte fur chemie · 2022Article
- Mutate-and-chemical-shift-fingerprint (MCSF) to characterize excited states in RNA using NMR spectroscopy.Nature protocols · 2021Review
- Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.RNA (New York, N.Y.) · 2020Article
- Solution NMR readily reveals distinct structural folds and interactions in doublyScience advances · 2020Article
- Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase.ACS chemical biology · 2019Article
- Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.Journal of biomolecular NMR · 2018Article
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic acids research · 2017Article
- NMRFx Processor: a cross-platform NMR data processing program.Journal of biomolecular NMR · 2016Article
- Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.Journal of biomolecular NMR · 2015Article
- A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA.The journal of physical chemistry. B · 2014Article
- Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10.Journal of biomolecular NMR · 2014Article
- Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments.Journal of biomolecular NMR · 2014Article
- Standardization of RNA chemical mapping experiments.Biochemistry · 2014Article
- Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.Nucleic acids research · 2014Article
- Automated and assisted RNA resonance assignment using NMR chemical shift statistics.Nucleic acids research · 2013Article
- Peakmatch: a simple and robust method for peak list matching.Journal of biomolecular NMR · 2013Article
- Database proton NMR chemical shifts for RNA signal assignment and validation.Journal of biomolecular NMR · 2013Article
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3 authors.
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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 (13)C NMR data of RNAs. Our procedure uses five (13)C 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 (13)C calibration and detect errors or inconsistencies in RNA (13)C 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-(13)C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable (13)C 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 (13)C chemical shift data. This is demonstrated by a clear relationship between ribose (13)C 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 RNA.
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