M. Hendrix et al., DIRECT OBSERVATION OF AMINOGLYCOSIDE-RNA INTERACTIONS BY SURFACE-PLASMON RESONANCE, Journal of the American Chemical Society, 119(16), 1997, pp. 3641-3648
The specificity of neomycin B and related aminoglycoside antibiotics i
n their interaction with the Rev responsive element (RRE) of HIV-1 mRN
A has been studied by directly observing the aminoglycoside-RNA comple
xes using surface plasmon resonance. Several different RNA sequences,
each with a biotin tag, have been prepared using T7 RNA polymerase-cat
alyzed transcription of synthetic DNA templates and have been immobili
zed on a streptavidin-coated surface for the binding study, The result
s indicate that neomycin B is not specific for the G-rich bubble regio
n in RRE. Rather, it appears to interact with three different sites, e
ach with a submicromolar dissociation constant, within the 67-nucleoti
de domain II of RRE. Further analysis of neomycin B binding with three
short synthetic RNA hairpins showed binding with submicromolar affini
ty and 1:1 stoichiometry in each case. This suggests that neomycin B m
ay generally bind with this affinity to regular A-form RNA or hairpin
loops. The approach described here is generally useful for understandi
ng the fundamental interactions involved in the specific recognition o
f nucleic acids by small molecules which is the basis of rational drug
design.