Nucleic Acids Research, Vol 24, Issue 19 3700-3706, Copyright © 1996 by Oxford University Press
H Miyaguchi, H Narita, K Sakamoto and S Yokoyama
A small RNA derived from the decoding region of Escherichia coli 16S rRNA
can bind to antibiotics of aminoglycosides (neomycin and paromomycin) that
act on the small ribosomal subunit [Purohit,P. and Stern,S. (1994) Nature,
370, 659-662]. In the present study, the P-site subdomain was removed from
this decoding region RNA to construct a 27mer RNA (designated as ASR-27),
which includes the A-site-related region (positions 1402-1412 and
1488-1497) of 16S rRNA. Footprint experiments with dimethyl sulfate as a
chemical probe indicated that the ASR-27 RNA can interact with the neomycin
family in the same manner as the decoding region RNA. A mutagenesis
analysis of the ASR-27 RNA revealed that paromomycin binding of ASR-27
involves the C1407.G1494 and C1409-G1491 base pairs, and the internal loop
comprising A1408 and the nucleotides in positions 1492-1493, located
between the two C.G base pairs. In addition, a G or U in position 1495, and
base pairing between positions 1405 and 1496 are also involved. These
structural features were found in a viral RNA element, the Rev-binding site
of human immunodeficiency virus type-1, which may explain why neomycin can
bind to this viral RNA.
ARTICLES
An antibiotic-binding motif of an RNA fragment derived from the A-site- related region of Escherichia coli 16S rRNA
Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Japan.
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