Rapid in vitro evolution of bacteriophage
T7, T3, and SP6 RNA polymerase promoters was achieved by a method
that allows continuous enrichment of DNAs that contain functional
promoter elements. This method exploits the ability of a special
class of nucleic acid molecules to replicate continuously in
the presence of both a reverse transcriptase and a DNA-dependent
RNA polymerase. Replication involves the synthesis of both RNA
and cDNA intermediates. The cDNA strand contains an embedded
promoter sequence, which becomes converted to a functional double-stranded
promoter element, leading to the production of RNA transcripts.
Synthetic cDNAs, including those that contain randomized promoter
sequences, can be used to initiate the amplification cycle. However,
only those cDNAs that contain functional promoter sequences are
able to produce RNA transcripts. Furthermore, each RNA transcript
encodes the RNA polymerase promoter sequence that was responsible
for initiation of its own transcription. Thus, the population
of amplifying molecules quickly becomes enriched for those templates
that encode functional promoters. Optimal promoter sequences
for phage T7, T3, and SP6 RNA polymerase were identified after
a 2-hour amplification reaction, initiated in each case with
a pool of synthetic cDNAs encoding greater than 1010
promoter sequence variants.
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