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  Structure and internal dynamics of short RNA duplexes determined by a combination of pulsed EPR methods and MD simulations

Gauger, M., Heinz, M., Halbritter, A.-L.-J., Stelzl, L. S., Erlenbach, N., Hummer, G., et al. (2024). Structure and internal dynamics of short RNA duplexes determined by a combination of pulsed EPR methods and MD simulations. Angewandte Chemie, International Edition in English, e202402498. doi:10.1002/anie.202402498.

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 Creators:
Gauger, Maximilian1, Author
Heinz, Marcel2, Author                 
Halbritter, Anna-Lena J.3, Author
Stelzl, Lukas S.4, 5, 6, 7, Author
Erlenbach, Nicole1, Author
Hummer, Gerhard2, 8, Author                 
Sigurdsson, Snorri Th3, Author
Prisner, Thomas1, Author
Affiliations:
1Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt, Frankfurt am Main, Germany, ou_persistent22              
2Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              
3Science Institut, University of Iceland, Reykjavik, Iceland, ou_persistent22              
4Faculty of Biology, Johannes Gutenberg Universtity Mainz, Mainz, Germany, ou_persistent22              
5KOMET 1, Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany, ou_persistent22              
6Institute of Quantitative and Computational Bioscience (IQCB), Johannes Gutenberg University Mainz, Mainz, Germany, ou_persistent22              
7Institute of Molecular Biology (IMB), Mainz, Germany, ou_persistent22              
8Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany, ou_persistent22              

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Free keywords: ENDOR spectroscopy, EPR spectroscopy, molecular dynamics, PELDOR/DEER spectroscopy, RNA structure/dynamics
 Abstract: We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20 base-pair long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm and singly fluorine labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state-of-the-art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high-precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.

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Language(s): eng - English
 Dates: 2024-03-242024-02-032024-03-252024-03-26
 Publication Status: Published online
 Pages: 11
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1002/anie.202402498
BibTex Citekey: gauger_structure_2024
 Degree: -

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Title: Angewandte Chemie, International Edition in English
  Abbreviation : Angew. Chem., Int. Ed. Engl.
Source Genre: Journal
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Publ. Info: Weinheim : Wiley-VCH
Pages: - Volume / Issue: - Sequence Number: e202402498 Start / End Page: - Identifier: ISSN: 0570-0833
CoNE: https://pure.mpg.de/cone/journals/resource/0570-0833