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Secondary structure mapping of an RNA ligand that has high affinity for the MetJ repressor protein and interference modification analysis of the protein-RNA complex

Lookup NU author(s): Professor Bernard Connolly


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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.

Publication metadata

Author(s): McGregor A, Murray JB, Adams CJ, Stockley PG, Connolly BA

Publication type: Article

Publication status: Published

Journal: Journal of Biological Chemistry

Year: 1999

Volume: 274

Issue: 4

Pages: 2255-2262

Print publication date: 22/01/1999

ISSN (print): 0021-9258

ISSN (electronic):

Publisher: American Society for Biochemistry and Molecular Biology, Inc.


DOI: 10.1074/jbc.274.4.2255

PubMed id: 9890988


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