Automated and assisted RNA resonance assignment using NMR chemical shift statistics

The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed r
The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson– Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H10/C10 chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stemloop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs.
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Metadaten
Author:Thomas Aeschbacher, Elena Schmidt, Markus Blatter, Christophe Maris, Olivier Duss, Frédéric Allain, Peter Güntert, Mario Schubert
URN:urn:nbn:de:hebis:30:3-444225
DOI:http://dx.doi.org/10.1093/nar/gkt665
Pubmed Id:http://www.ncbi.nlm.nih.gov/pubmed?term=23921634
Parent Title (English):Nucleic Acids Research
Publisher:Oxford University Press
Place of publication:London
Document Type:Article
Language:English
Year of Completion:2013
Date of first Publication:2013/08/05
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2017/09/21
Volume:41
Issue:18 e172
Pagenumber:14
Note:
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
HeBIS PPN:425145832
Institutes:Biochemie und Chemie
Frankfurt Institute for Advanced Studies (FIAS)
Dewey Decimal Classification:570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - Namensnennung-Nicht kommerziell 3.0

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