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A model for the study of ligand binding to the ribosomal RNA helix h44

Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome bu...

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Detalles Bibliográficos
Autores principales: Dibrov, Sergey M., Parsons, Jerod, Hermann, Thomas
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910043/
https://www.ncbi.nlm.nih.gov/pubmed/20215440
http://dx.doi.org/10.1093/nar/gkq159
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author Dibrov, Sergey M.
Parsons, Jerod
Hermann, Thomas
author_facet Dibrov, Sergey M.
Parsons, Jerod
Hermann, Thomas
author_sort Dibrov, Sergey M.
collection PubMed
description Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand–RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region.
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spelling pubmed-29100432010-07-27 A model for the study of ligand binding to the ribosomal RNA helix h44 Dibrov, Sergey M. Parsons, Jerod Hermann, Thomas Nucleic Acids Res RNA Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand–RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region. Oxford University Press 2010-07 2010-03-09 /pmc/articles/PMC2910043/ /pubmed/20215440 http://dx.doi.org/10.1093/nar/gkq159 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Dibrov, Sergey M.
Parsons, Jerod
Hermann, Thomas
A model for the study of ligand binding to the ribosomal RNA helix h44
title A model for the study of ligand binding to the ribosomal RNA helix h44
title_full A model for the study of ligand binding to the ribosomal RNA helix h44
title_fullStr A model for the study of ligand binding to the ribosomal RNA helix h44
title_full_unstemmed A model for the study of ligand binding to the ribosomal RNA helix h44
title_short A model for the study of ligand binding to the ribosomal RNA helix h44
title_sort model for the study of ligand binding to the ribosomal rna helix h44
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910043/
https://www.ncbi.nlm.nih.gov/pubmed/20215440
http://dx.doi.org/10.1093/nar/gkq159
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