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

Abstract:

: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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Dibrov SM,Parsons J,Hermann T

doi

10.1093/nar/gkq159

subject

Has Abstract

pub_date

2010-07-01 00:00:00

pages

4458-65

issue

13

eissn

0305-1048

issn

1362-4962

pii

gkq159

journal_volume

38

pub_type

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