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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

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Microscale Thermophoresis to Study RNA-RNA Binding Affinity.

Britta Jordan¹, Lisa Nickel¹, Ruth A Schmitz²

¹Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|August 3, 2022

Summary

Microscale thermophoresis (MST) effectively characterizes RNA-RNA binding affinity. This method quantifies interactions between small noncoding RNAs (ncRNAs) and their mRNA targets using minimal sample amounts.

Keywords:

MST Microscale thermophoresis RNA–RNA binding affinity sRNA

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Area of Science:

Molecular Biology
Biophysics

Background:

Studying RNA-RNA interactions is vital for understanding molecular mechanisms, particularly noncoding RNA (ncRNA) interactions.
Microscale thermophoresis (MST), based on the Ludwig-Soret Effect, measures molecular movement in response to temperature gradients.
MST offers a rapid method for detecting and characterizing biomolecular interactions, requiring only small quantities of target and ligand.

Purpose of the Study:

To characterize RNA-RNA binding affinity using Microscale Thermophoresis (MST).
To demonstrate the utility of MST for studying interactions between small noncoding RNAs and their mRNA targets.

Main Methods:

Utilized Microscale Thermophoresis (MST) to analyze binding affinity.
Employed the sRNA41 from Methanosarcina mazei and its target, the 5' UTR of mRNA-MM2089, as a model system.

Main Results:

Successfully characterized the binding affinity between sRNA41 and its native mRNA target.
Demonstrated MST's capability in quantifying RNA-RNA interactions.

Conclusions:

MST is a powerful and efficient technique for evaluating RNA-RNA binding affinity.
The study provides a specific example of ncRNA-mRNA interaction characterization using MST.