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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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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. |
format | Online Article Text |
id | pubmed-9680805 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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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