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Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA

Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove (13)C-(13)C dipolar couplings that complicate (13)C relaxation analyses. While these phenomena are well documented for sites with adjacent (13)C nuclei (e.g. ribose...

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Autores principales: Olenginski, Lukasz T., Dayie, Theodore K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131303/
https://www.ncbi.nlm.nih.gov/pubmed/33914223
http://dx.doi.org/10.1007/s10858-021-00368-8
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author Olenginski, Lukasz T.
Dayie, Theodore K.
author_facet Olenginski, Lukasz T.
Dayie, Theodore K.
author_sort Olenginski, Lukasz T.
collection PubMed
description Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove (13)C-(13)C dipolar couplings that complicate (13)C relaxation analyses. While these phenomena are well documented for sites with adjacent (13)C nuclei (e.g. ribose C1′), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) (13)C-(13)C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-(13)C/(15)N]-ATP or selectively [2-(13)C]-ATP labeled RNAs. Our simulations predict non-negligible (13)C-(13)C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R(1)) relaxation rates in [U-(13)C/(15)N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R(1) measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-(13)C/(15)N]-ATP or [2-(13)C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range (13)C-(13)C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R(1) rates in terms of motional models for large RNAs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10858-021-00368-8.
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spelling pubmed-81313032021-05-24 Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA Olenginski, Lukasz T. Dayie, Theodore K. J Biomol NMR Article Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove (13)C-(13)C dipolar couplings that complicate (13)C relaxation analyses. While these phenomena are well documented for sites with adjacent (13)C nuclei (e.g. ribose C1′), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) (13)C-(13)C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-(13)C/(15)N]-ATP or selectively [2-(13)C]-ATP labeled RNAs. Our simulations predict non-negligible (13)C-(13)C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R(1)) relaxation rates in [U-(13)C/(15)N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R(1) measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-(13)C/(15)N]-ATP or [2-(13)C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range (13)C-(13)C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R(1) rates in terms of motional models for large RNAs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10858-021-00368-8. Springer Netherlands 2021-04-29 2021 /pmc/articles/PMC8131303/ /pubmed/33914223 http://dx.doi.org/10.1007/s10858-021-00368-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Olenginski, Lukasz T.
Dayie, Theodore K.
Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA
title Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA
title_full Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA
title_fullStr Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA
title_full_unstemmed Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA
title_short Quantifying the effects of long-range (13)C-(13)C dipolar coupling on measured relaxation rates in RNA
title_sort quantifying the effects of long-range (13)c-(13)c dipolar coupling on measured relaxation rates in rna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131303/
https://www.ncbi.nlm.nih.gov/pubmed/33914223
http://dx.doi.org/10.1007/s10858-021-00368-8
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