1 research outputs found
Direct Observation of Aminoglycoside–RNA Binding by Localized Surface Plasmon Resonance Spectroscopy
RNA is involved in fundamental biological functions when
bacterial
pathogens replicate. Identifying and studying small molecules that
can interact with bacterial RNA and interrupt cellular activities
is a promising path for drug design. Aminoglycoside (AMG) antibiotics,
prominent natural products that recognize RNA specifically, exert
their biological functions by binding to prokaryotic ribosomal RNA
and interfering with protein translation, ultimately resulting in
bacterial cell death. The decoding site, a small internal loop within
the 16S rRNA, is the molecular target for the AMG antibiotics. The
specificity of neomycin B, a highly potent AMG antibiotic, to the
ribosomal decoding RNA site, was previously studied by observing AMG–RNA
complexes in solution. Here, we study this interaction using localized
surface plasmon resonance (LSPR) transducers comprising gold island
films prepared by evaporation on glass and annealing. Small molecule
AMG receptors were immobilized on the Au islands via polyethylene
glycol (PEG)-thiol linkers, and the interaction with target RNA in
solution was studied by monitoring the change in the LSPR optical
response upon binding. The results show high-affinity binding of neomycin
to 27-nucleotide model A-site RNA sequence in the nanomolar range,
while no specific binding is observed for synthetic RNA oligomers
(e.g., poly-U). The impact of specific base substitutions in the A-site
RNA constructs on binding affinity and selectivity is determined quantitatively.
It is concluded that LSPR is a powerful tool for providing molecular
insight into small molecule–RNA interactions and for the design
and screening of selective antimicrobial drugs