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Direct Selection Strategy for Isolating Aptamers with pH-Sensitive Binding Activity
journal contribution
posted on 2018-12-06, 00:00 authored by Chelsea
K. L. Gordon, Michael Eisenstein, Hyongsok Tom SohAn
aptamer reagent that can switch its binding affinity in a pH-responsive
manner would be highly valuable for many biomedical applications including
imaging and drug delivery. Unfortunately, the discovery of such aptamers
is difficult and only a few have been reported to date. Here we report
the first experimental strategy for generating pH-responsive aptamers
through direct selection. As an exemplar, we report streptavidin-binding
aptamers that retain nanomolar affinity at pH 7.4 but exhibit a ∼100-fold
decrease in affinity at pH 5.2. These aptamers were generated by incorporating
a known streptavidin-binding DNA motif into an aptamer library and
performing FACS-based screening at multiple pH conditions. Upon structural
analysis, we found that one aptamer’s affinity-switching behavior
is driven by a noncanonical G-A base-pair that controls its folding
in a highly pH-dependent manner. We believe our strategy could be
readily extended to other aptamer-target systems because it does not
require a priori structural knowledge of the aptamer or the target.
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pH-dependent mannernoncanonical G-A base-pairpH 5.2.nanomolar affinityDirect Selection Strategystreptavidin-binding DNA motifaptamer reagentreport streptavidin-binding aptamerspH-responsive aptamerspH 7.4pH-responsive manneraptamer libraryaptamer-target systemspH-Sensitive Binding Activitydrug deliverybinding affinitypH conditionsFACS-based screening
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