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Screening for engineered neomycin riboswitches that control translation initiation.

Weigand, Julia E. and Sanchez, Martin and Gunnesch, Ewald-Bernd and Zeiher, Sabrina and Schroeder, Renée and Suess, Beatrix (2008):
Screening for engineered neomycin riboswitches that control translation initiation.
In: RNA (New York, N.Y.), 14 (1), pp. 89-97. ISSN 1469-9001,
[Article]

Abstract

Riboswitches are genetic control elements that regulate gene expression in a small molecule-dependent way. We developed a two-stage strategy of in vitro selection followed by a genetic screen and identified several artificial small molecule-binding riboswitches that respond to the aminoglycoside neomycin. Structure-function relationships and structural probing revealed that they adopt the general neomycin-binding motif. They display no sequence similarities to in vitro selected neomycin aptamers but contain parts of the decoding site that is the binding site for neomycin on the ribosomal RNA. We propose a model of a composed binding pocket of an internal loop as primary docking site and a terminal flaplike loop structure fixing neomycin in a sandwich-like manner. Such binding pockets characterized by multiple contacts between ligand and RNA are described for both natural and engineered riboswitches. We anticipate that combination of in vitro selection and in vivo screening is a useful strategy to identify RNA molecules with a desired functionality.

Item Type: Article
Erschienen: 2008
Creators: Weigand, Julia E. and Sanchez, Martin and Gunnesch, Ewald-Bernd and Zeiher, Sabrina and Schroeder, Renée and Suess, Beatrix
Title: Screening for engineered neomycin riboswitches that control translation initiation.
Language: English
Abstract:

Riboswitches are genetic control elements that regulate gene expression in a small molecule-dependent way. We developed a two-stage strategy of in vitro selection followed by a genetic screen and identified several artificial small molecule-binding riboswitches that respond to the aminoglycoside neomycin. Structure-function relationships and structural probing revealed that they adopt the general neomycin-binding motif. They display no sequence similarities to in vitro selected neomycin aptamers but contain parts of the decoding site that is the binding site for neomycin on the ribosomal RNA. We propose a model of a composed binding pocket of an internal loop as primary docking site and a terminal flaplike loop structure fixing neomycin in a sandwich-like manner. Such binding pockets characterized by multiple contacts between ligand and RNA are described for both natural and engineered riboswitches. We anticipate that combination of in vitro selection and in vivo screening is a useful strategy to identify RNA molecules with a desired functionality.

Journal or Publication Title: RNA (New York, N.Y.)
Journal volume: 14
Number: 1
Divisions: 10 Department of Biology
10 Department of Biology > Synthetic Genetic Circuits
10 Department of Biology > RNA Biochemistry
Date Deposited: 22 Feb 2012 10:32
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