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

Journal Article · Thu Sep 02 04:00:00 EDT 2010 · Nucleic Acids Res.

DOI:https://doi.org/10.1093/nar/gkq159· OSTI ID:1002622

Dibrov, Sergey M; Parsons, Jerod; Hermann, Thomas ^[1]

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1. UCSD

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.

• Research Organization: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
• Sponsoring Organization: USDOE
• OSTI ID: 1002622
• Journal Information: Nucleic Acids Res., Journal Name: Nucleic Acids Res. Journal Issue: (13) ; 2010 Vol. 38; ISSN 0305-1048; ISSN NARHAD
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

36 MATERIALS SCIENCE
ANTIBIOTICS
CRYSTAL STRUCTURE
FLUORESCENCE
MODIFICATIONS
MONITORS
MUTATIONS
OLIGONUCLEOTIDES
RESOLUTION
RIBOSOMAL RNA
RIBOSOMES
RNA
STRUCTURAL MODELS