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Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides

Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational excha...

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Autores principales: Wilson, Alex L., Outeiral, Carlos, Dowd, Sarah E., Doig, Andrew J., Popelier, Paul L. A., Waltho, Jonathan P., Almond, Andrew
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814580/
https://www.ncbi.nlm.nih.gov/pubmed/36703475
http://dx.doi.org/10.1038/s42004-020-0298-x
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author Wilson, Alex L.
Outeiral, Carlos
Dowd, Sarah E.
Doig, Andrew J.
Popelier, Paul L. A.
Waltho, Jonathan P.
Almond, Andrew
author_facet Wilson, Alex L.
Outeiral, Carlos
Dowd, Sarah E.
Doig, Andrew J.
Popelier, Paul L. A.
Waltho, Jonathan P.
Almond, Andrew
author_sort Wilson, Alex L.
collection PubMed
description Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational exchange. Here, a framework is presented that predicts Raman spectra using mixtures of sub-spectra corresponding to major conformers calculated using classical and ab initio molecular dynamics. Experimental optimization allowed purines and pyrimidines to be characterized as predominantly syn and anti, respectively, and ribose into exchange between equivalent south and north populations. These measurements are in excellent agreement with Raman spectroscopy of ribonucleosides, and previous experimental and computational results. This framework provides a measure of ribonucleoside solution populations and conformational exchange in RNA subunits. It complements other experimental techniques and could be extended to other molecules, such as proteins and carbohydrates, enabling biological insights and providing a new analytical tool.
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spelling pubmed-98145802023-01-10 Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides Wilson, Alex L. Outeiral, Carlos Dowd, Sarah E. Doig, Andrew J. Popelier, Paul L. A. Waltho, Jonathan P. Almond, Andrew Commun Chem Article Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational exchange. Here, a framework is presented that predicts Raman spectra using mixtures of sub-spectra corresponding to major conformers calculated using classical and ab initio molecular dynamics. Experimental optimization allowed purines and pyrimidines to be characterized as predominantly syn and anti, respectively, and ribose into exchange between equivalent south and north populations. These measurements are in excellent agreement with Raman spectroscopy of ribonucleosides, and previous experimental and computational results. This framework provides a measure of ribonucleoside solution populations and conformational exchange in RNA subunits. It complements other experimental techniques and could be extended to other molecules, such as proteins and carbohydrates, enabling biological insights and providing a new analytical tool. Nature Publishing Group UK 2020-05-06 /pmc/articles/PMC9814580/ /pubmed/36703475 http://dx.doi.org/10.1038/s42004-020-0298-x Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Wilson, Alex L.
Outeiral, Carlos
Dowd, Sarah E.
Doig, Andrew J.
Popelier, Paul L. A.
Waltho, Jonathan P.
Almond, Andrew
Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides
title Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides
title_full Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides
title_fullStr Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides
title_full_unstemmed Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides
title_short Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides
title_sort deconvolution of conformational exchange from raman spectra of aqueous rna nucleosides
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814580/
https://www.ncbi.nlm.nih.gov/pubmed/36703475
http://dx.doi.org/10.1038/s42004-020-0298-x
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