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The conformation of a conserved stem-loop structure in ribosomal RNA
P H van Knippenberg1, H A Heus
1Department of Biochemistry, State University of Leiden, The Netherlands.
Journal of Biomolecular Structure & Dynamics
|October 1, 1983
Summary
Investigating conserved RNA stem-loops in small ribosomal subunits reveals methylation destabilizes the structure. Melting initiates at the ends and junction, with basepair changes significantly impacting stability.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- Small ribosomal subunits contain a conserved stem-loop RNA structure near their 3' end.
- This structure features a nine-basepair stem with a conserved A-UU-G junction and a Gm6(2)AM6(2)A sequence in the loop.
Purpose of the Study:
- To investigate the structural and thermal stability characteristics of conserved 3' end stem-loop RNA structures from small ribosomal subunits.
- To elucidate the impact of specific modifications, such as adenine dimethylation and basepair substitutions, on hairpin stability.
Main Methods:
- Utilized UV-optics, micro-calorimetry, and 500 MHz-NMR spectroscopy.
- Studied fragments of approximately 50 nucleotides cleaved from the 3' ends of small ribosomal subunit RNAs using bacteriocins.
Main Results:
- Dimethylation of adenine residues within the loop destabilizes the hairpin structure due to increased base stacking.
- Hairpin melting initiates from both the ends and the central A-UU-G junction.
- Basepair substitutions exhibit a substantial and unexpected influence on the thermal stability of the RNA hairpin.
Conclusions:
- The conserved stem-loop structure's stability is sensitive to modifications within the loop and stem.
- Understanding these structural dynamics is crucial for comprehending ribosomal RNA function and evolution.