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RNA aptamers that specifically bind to a 16S ribosomal RNA decoding region construct
1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 45 Shattuck Street, Boston, MA 02115, USA.
Nucleic Acids Research
|July 25, 2000
Summary
Researchers selected RNA aptamers that bind to the 16S rRNA A-site, a key region for translation. The tightest binding aptamer, 109.2-3, uses a loop-loop "kissing" motif for Watson-Crick base pairing.
Area of Science:
- Molecular Biology
- Biochemistry
- Genetics
Background:
- RNA-RNA recognition is vital for biological processes like translation.
- Interactions can occur via Watson-Crick base pairing or tertiary structures.
- Understanding in vitro selection of RNA-RNA binding is crucial.
Purpose of the Study:
- To investigate RNA-RNA binding events selected in vitro.
- To identify RNA aptamers that bind to the 16S rRNA A-site.
- To elucidate the binding mechanism between aptamers and the 16S rRNA A-site.
Main Methods:
- In vitro selection from RNA libraries.
- Characterization of aptamer-rRNA interactions.
- Site-directed mutagenesis to probe binding mechanisms.
Main Results:
- A single family of RNA aptamers was selected from two library sizes.
- The aptamer 109.2-3 showed tight binding to the 16S rRNA A-site.
- Binding involved complementary stem-loop regions, suggesting a loop-loop 'kissing' interaction via Watson-Crick base pairing.
Conclusions:
- RNA aptamer 109.2-3 specifically binds the 16S rRNA A-site through a loop-loop 'kissing' motif.
- Watson-Crick base pairing in stem-loop regions mediates this high-affinity interaction.
- Other structural motifs in the decoding region did not exhibit high-affinity binding.