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Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry
Bin Wang1, Kevin A Wilkinson, Kevin M Weeks
1Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
Biochemistry
|February 23, 2008
Summary
Magnesium ions and tobramycin surprisingly alter yeast transfer RNA (tRNA) folding in complex ways. Single-nucleotide resolution SHAPE chemistry revealed unexpected structural rearrangements and unfolding pathways upon ligand binding.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- RNA structure is sensitive to charged ligands, with ions like Mg(2+) stabilizing native folds.
- Polyvalent cations can either stabilize or disrupt RNA structure, influencing folding pathways.
Purpose of the Study:
- To investigate the effects of Mg(2+) and tobramycin on the folding of Saccharomyces cerevisiae tRNA (Asp).
- To analyze RNA structural rearrangements at single nucleotide resolution using SHAPE chemistry.
Main Methods:
- Single nucleotide resolution SHAPE (Selective 2'-hydroxyl acylation analyzed by primer extension) chemistry.
- Analysis of tRNA (Asp) folding in the presence of varying Mg(2+) concentrations and tobramycin.
Main Results:
- Reduced Mg(2+) concentration induced a structural rearrangement with D- and variable loop pairing in tRNA (Asp).
- Tobramycin binding caused two distinct unfolding transitions: loss of T- and D-loop interactions, followed by D-stem unfolding.
- Both ligands modulated tRNA (Asp) folding in complex, non-hierarchical ways.
Conclusions:
- Ligand binding to RNA can induce complex folding landscapes not explained by simple hierarchical models.
- Single-nucleotide resolution monitoring is crucial for defining intermediate structures in RNA folding.
- This work enhances understanding of RNA-ligand interactions and solution environment effects.
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