Automated and assisted RNA resonance assignment using NMR chemical shift statistics
Open access
Autor(in)
Alle anzeigen
Datum
2013-10-01Typ
- Journal Article
ETH Bibliographie
yes
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Abstract
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 H1′/C1′ 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 stem-loop 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. Mehr anzeigen
Persistenter Link
https://doi.org/10.3929/ethz-b-000073863Publikationsstatus
publishedExterne Links
Zeitschrift / Serie
Nucleic Acids ResearchBand
Seiten / Artikelnummer
Verlag
Oxford University PressThema
Nucleic acid structure; RNA characterisation and manipulationOrganisationseinheit
03591 - Allain, Frédéric / Allain, Frédéric
Anmerkungen
It was possible to publish this article open access thanks to a Swiss National Licence with the publisherETH Bibliographie
yes
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