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The well-studied interaction between the MS2 coat
protein and its cognate hairpin was used to test the utility
of the methylphosphonate linkage as a phosphate analog.
A nitrocellulose filter binding assay was used to measure
the change in binding affinity upon introduction of a single
methylphosphonate stereoisomer at 13 different positions
in the RNA hairpin. Comparing these data to the available
crystal structure of the complex shows that all phosphates
that are in proximity to the protein show a weaker binding
affinity when substituted with a phosphorothioate and control
positions show no change. However, in two cases, a methylphosphonate
isomer either increased or decreased the binding affinity
where no interaction can be detected in the crystal structure.
It is possible that methylphosphonate substitutions at
these positions affect the structure or flexibility of
the hairpin. The utility of the methylphosphonate substitution
is compared to phosphate ethylation and phosphorothioate
substitution experiments previously performed on the same
system.
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