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Updated: Jul 26, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
Secondary structure mapping of an RNA ligand that has high affinity for the MetJ repressor protein and interference
A McGregor1, J B Murray, C J Adams
1Department of Biochemistry and Genetics, The University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom.
Abstract:
The secondary structure of an RNA aptamer, which has a high affinity for the Escherichia coli MetJ repressor protein, has been mapped using ribonucleases and with diethyl pyrocarbonate. The RNA ligand is composed of a stem-loop with a highly structured internal loop. Interference modification showed that the bases within the internal loop, and those directly adjacent to it, are important in the binding of the RNA ligand to MetJ. Most of the terminal stem-loop could be removed with little effect on the binding. Ethylation interference suggests that none of the phosphate groups are absolutely essential for tight binding. The data suggest that the MetJ binding site on the aptamer is distinct from that of the natural DNA target, the 8-base pair Met box.
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