A cell-free mRNA decay assay has been adapted to
permit the kinetics of 3′ → 5′
exoribonuclease activities to be monitored in real time.
RNA probes containing 5′ caps and 3′ poly(A)
tails generated by transcription in vitro are 3′
labeled using fluorescein-N6-ATP and poly(A)
polymerase. Release of fluorescein-conjugated adenosine
residues from the 3′ end of the RNA substrate is
monitored by a time-dependent decrease in fluorescence
anisotropy in the presence of cytosolic proteins. To demonstrate
the utility of the assay, an RNA probe was constructed
containing a fragment of the c-myc 3′ untranslated
region and an 85-base poly(A) tail. Following 3′
fluorescein labeling, the rate of 3′-terminal adenosine
excision was monitored in the presence of an S100 cytosolic
extract prepared from K562 erythroleukemia cells. Removal
of the fluorescein-tagged A residues resolved to a first-order
decay function, allowing the rate constant and enzyme-specific
activity to be determined in this extract. Further applications
and advantages of this technology are discussed.