separate biochemical assays (Table 1). The first was
a fluorescence-polarization-based RNA-binding
assay to determine the affinity of each mutant for a
small RNA hairpin [16]. The majority of mutations did
not significantly affect RNA binding, but C290D and
C290E did result in weakened affinities with 4-fold
and 8-fold increases in Kd, respectively. The second
assay was a classical oligo-dT/poly(A) extension
assay that measures the bulk incorporation of
α-
32P-UMP nucleotides upon primer extensions
with 50- to 300-nt-long templates. Activities are
reported as a percentage of the wild-type control
activity that has been set to 100%. Due to the nature
of this extension assay, higher activity is generally
associated with polymerases that can processively
elongate long stretches of RNA in a short amount of
time, which is due to minimizing the number of slow
initiation events. Last, we investigated the ability of
each mutant to undergo three successive rounds of
nucleotide addition in a stepwise nucleotide incorporation
assay using a RNA hairpin substrate similar
to that used in the RNA-binding assay.
The resulting data have been used to divide the
mutant polymerases into three biochemical activity
classes (Table 1). Class I mutants retain the ability to
undergo three rounds of nucleotide addition and
have activities in the poly(A) elongation assay that
differ significantly from that of the wild-type enzyme.