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RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Recognition of tertiary structure in tRNAs by Rh(phen)2phi3+, a new reagent for RNA structure-function mapping
C S Chow1, L S Behlen, O C Uhlenbeck
1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.
Biochemistry
|February 4, 1992
Summary
Rhodium complex Rh(phen)2phi3+ selectively cleaves tRNA at tertiary interaction sites, revealing structural insights. This photoactivated reagent targets accessible major grooves, aiding in probing RNA structural changes and validating tRNA tertiary structure.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Biology
Background:
- Transfer RNAs (tRNAs) are crucial for protein synthesis, exhibiting complex tertiary structures.
- Understanding tRNA structure is vital for deciphering its diverse functions.
- Probing RNA structure often requires specific chemical or enzymatic reagents.
Purpose of the Study:
- To evaluate the rhodium complex Rh(phen)2phi3+ as a novel reagent for probing tRNA tertiary structure.
- To investigate the specificity of Rh(phen)2phi3+ cleavage on different tRNA molecules and mutants.
- To assess the utility of this complex in identifying sites of tertiary interaction within RNAs.
Main Methods:
- Photoactivation of the rhodium complex Rh(phen)2phi3+.
- Cleavage studies on yeast tRNA(Phe), tRNA(Asp), unmodified tRNA(Phe) transcript, and tRNA(Phe) mutants.
- Analysis of cleavage sites to map regions of tertiary interaction.
- Comparison of cleavage patterns in native, unmodified, and chemically modified tRNAs.
Main Results:
- Rh(phen)2phi3+ selectively cleaves tRNA at specific residues involved in tertiary interactions, notably G22, G45, U47, psi 55, and U59 on tRNA(Phe).
- Cleavage patterns were consistent across different tRNAs, highlighting conserved tertiary structural features.
- Cleavage was observed in accessible major groove regions, particularly around triply bonded bases, indicating structural targeting.
- Absence of modified bases or mutations altered cleavage patterns, suggesting sensitivity to structural nuances.
Conclusions:
- Rh(phen)2phi3+ is a sensitive and specific photoactivated reagent for probing tRNA tertiary structure.
- The complex directly targets sites of tertiary interaction, particularly accessible major groove regions.
- Cleavage studies with Rh(phen)2phi3+ provide valuable insights into RNA structural dynamics and the role of modified bases.
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