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Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR

RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of fun...

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Detalles Bibliográficos
Autores principales: Lusky, Orr Simon, Meir, Moran, Goldbourt, Amir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680805/
https://www.ncbi.nlm.nih.gov/pubmed/36425459
http://dx.doi.org/10.1016/j.bpr.2021.100027
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author Lusky, Orr Simon
Meir, Moran
Goldbourt, Amir
author_facet Lusky, Orr Simon
Meir, Moran
Goldbourt, Amir
author_sort Lusky, Orr Simon
collection PubMed
description RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work, we present a methodology for studying large intact RNA biomolecules using homonuclear (15)N solid-state NMR spectroscopy. We show that proton-driven spin-diffusion experiments with long mixing times, up to 16 s, improved by the incorporation of multiple rotor-synchronous (1)H inversion pulses (termed radio-frequency dipolar recoupling pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of guanine-cytosine Watson-Crick basepairs, and beyond these common interactions, we observe a significant contribution of the guanine-uracil wobble basepairs. Moreover, we can differentiate basepaired and non-basepaired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques and possibly structure determination methods.
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spelling pubmed-96808052022-11-23 Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR Lusky, Orr Simon Meir, Moran Goldbourt, Amir Biophys Rep (N Y) Article RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work, we present a methodology for studying large intact RNA biomolecules using homonuclear (15)N solid-state NMR spectroscopy. We show that proton-driven spin-diffusion experiments with long mixing times, up to 16 s, improved by the incorporation of multiple rotor-synchronous (1)H inversion pulses (termed radio-frequency dipolar recoupling pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of guanine-cytosine Watson-Crick basepairs, and beyond these common interactions, we observe a significant contribution of the guanine-uracil wobble basepairs. Moreover, we can differentiate basepaired and non-basepaired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques and possibly structure determination methods. Elsevier 2021-09-29 /pmc/articles/PMC9680805/ /pubmed/36425459 http://dx.doi.org/10.1016/j.bpr.2021.100027 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Lusky, Orr Simon
Meir, Moran
Goldbourt, Amir
Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR
title Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR
title_full Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR
title_fullStr Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR
title_full_unstemmed Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR
title_short Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR
title_sort characterizing hydrogen bonds in intact rna from ms2 bacteriophage using magic angle spinning nmr
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680805/
https://www.ncbi.nlm.nih.gov/pubmed/36425459
http://dx.doi.org/10.1016/j.bpr.2021.100027
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