designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions
In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction....
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| Veröffentlicht in: | Nucleic acids research 2009-02, Vol.37 (3), p.e23-e23 |
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| container_title | Nucleic acids research |
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| creator | Shiohara, Tomoaki Saito, Hirohide Inoue, Tan |
| description | In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction. This allows us to select the binding sequence against a targeted internal loop as well as a linker region optimized for binding of the two binding sites. After the selection, the aptamers bound with dissociation constants in the nanomolar range, thereby forming a stable complex with the target RNA. Thus this method enables identification of aptamers for a specific binding site together with a linker for cooperative binding of the two RNAs. It appears that our new method can be applied generally to select RNAs that adhere tightly to a target RNA via two specific sites. The method can also be applicable for further engineering of both natural and artificial RNAs. |
| doi_str_mv | 10.1093/nar/gkn1012 |
| format | Article |
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| ispartof | Nucleic acids research, 2009-02, Vol.37 (3), p.e23-e23 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Aptamers, Nucleotide - chemistry Base Sequence Binding Sites Genetic Engineering Methods Online Molecular Sequence Data Nucleic Acid Conformation RNA - chemistry |
| title | designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions |
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