As pathogens continue to evade therapeutical drugs,
a better understanding of the mode of action of antibiotics
continues to have high importance. A growing body of evidence
points to RNA as a crucial target for antibacterial and
antiviral drugs. For example, the aminocyclitol antibiotic
streptomycin interacts with the 16S ribosomal RNA and,
in addition, inhibits group I intron splicing. To understand
the mode of binding of streptomycin to RNA, we isolated
small, streptomycin-binding RNA aptamers via in vitro selection.
In addition, bluensomycin, a streptomycin analogue that
does not inhibit splicing, was used in a counter-selection
to obtain RNAs that bind streptomycin with high affinity
and specificity. Although an RNA from the normal selection
(motif 2) bound both antibiotics, an RNA from the counter-selection
(motif 1) discriminated between streptomycin and bluensomycin
by four orders of magnitude. The binding site of streptomycin
on the RNAs was determined via chemical probing with dimethylsulfate
and kethoxal. The minimal size required for drug binding
was a 46- and a 41-mer RNA for motifs 1 and 2, respectively.
Using Pb2+ cleavage in the presence and absence
of streptomycin, a conformational change spanning the entire
mapped sequence length of motif 1 was observed only when
both streptomycin and Mg2+ were present. Both
RNAs require Mg2+ for binding streptomycin.