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10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Probing RNA structure within living cells
Andreas Liebeg1, Christina Waldsich
1Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria.
Methods in Enzymology
|October 16, 2010
Summary
Investigating RNA structure in living cells using chemical probing reveals how the cellular environment impacts RNA folding. This method maps RNA architecture and interactions within its natural biological context.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- RNA folding is crucial for RNA function but is primarily studied in vitro.
- The cellular environment significantly influences in vivo RNA structure compared to in vitro conditions.
- Limited exploration of RNA structure formation within living cells exists.
Purpose of the Study:
- To assess the in vivo structure of catalytic RNAs within the cellular environment.
- To understand how the cellular milieu affects RNA architecture.
- To explore RNA interactions and conformational changes in living cells.
Main Methods:
- Applied chemical probing using dimethyl sulfate to living cells.
- Mapped solvent-accessible RNA bases (N1-A, N3-C) via chemical modification.
- Utilized modification mapping to infer secondary and tertiary RNA structure.
Main Results:
- Determined RNA architecture in vivo, reflecting cellular environmental influences.
- Gained insights into RNA secondary and tertiary structures.
- Identified potential interactions with cellular ligands and conformational dynamics.
Conclusions:
- In vivo chemical probing is a powerful technique for studying RNA structure in its native cellular context.
- This method provides substantial information on RNA architecture and interactions.
- The approach is adaptable for studying RNAs across diverse cell types.
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