The cellular environment stabilizes adenine riboswitch RNA structure

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Studying RNA structure and function in vitro often uses conditions that differ significantly from the intracellular environment.
• The crowded cellular milieu can influence RNA folding and ligand interactions.

Purpose of the Study:

• To investigate the impact of the intracellular environment on RNA structure and ligand binding.
• To compare the in-cell conformation of an RNA aptamer with its in vitro behavior.

Main Methods:

• Utilized selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) in live Escherichia coli cells.
• Examined the adenine riboswitch aptamer domain at single-nucleotide resolution.
• Measured intracellular Mg(2+) concentration.

Main Results:

• The ligand-bound aptamer structure in cells closely resembles its structure in vitro at physiological Mg(2+) concentrations.
• The ligand-free aptamer in cells adopts a conformation more similar to the ligand-bound state than observed in vitro.
• The intracellular environment provides greater stabilization to the aptamer than Mg(2+) alone.

Conclusions:

• The cellular environment profoundly influences RNA structure, promoting more organized conformations.
• In vitro studies may not fully capture the native RNA folding landscape due to environmental differences.
• Intracellular factors play a critical role in stabilizing specific RNA structures.