Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Single-molecule correlated chemical probing (smCCP) is a powerful technique for RNA structural analysis.
• smCCP data provides insights into base pairing, conformational ensembles, and tertiary interactions.
• Isolating specific tertiary structure communication from smCCP data has been challenging.

Purpose of the Study:

• To introduce mutual information as a metric for filtering smCCP data.
• To isolate and characterize RNA tertiary structure communication.
• To apply this method to the SAM-III riboswitch and other complex RNAs.

Main Methods:

• Utilized mutual information as a filtering metric for smCCP data.
• Developed an smCCP fingerprint selective for ligand-bound tertiary structures.
• Applied mutual information filters to independent RNA datasets.

Main Results:

• Successfully isolated through-space tertiary interactions in various RNA structures.
• Identified an smCCP fingerprint indicative of concurrent tertiary structure formation and ligand binding.
• Demonstrated the effectiveness of mutual information filtering on complex RNA systems.

Conclusions:

• Mutual information filtering enhances smCCP's capability to discover and characterize RNA tertiary structures.
• This approach allows for the identification of specific higher-order structural states within an ensemble.
• The combined smCCP and mutual information method serves as a valuable tool for RNA structural biology research.