Breaker, R.R. & Joyce, G.F.

"Emergence of a Replicating Species from an in vitro RNA Evolution Reaction"

Proc. Natl. Acad. Sci. USA, 91, 6093-6097

The technique of self-sustained sequence replication (3SR) allows isothermal amplification of DNA and RNA molecules in vitro. This method relies on the activities of a reverse transcriptase and a DNA-dependent RNA polymerase to amplify specific nucleic acid sequences. We have modified the 3SR protocol to allow selective amplification of RNAs that catalyze a particular chemical reaction. During an in vitro RNA evolution experiment employing this modified system, a unique class of selfish RNAs emerged and replicated to the exclusion of the intended RNAs. Members of this new class of selfish molecules, termed "RNA Z", amplify efficiently despite their inability to catalyze the target chemical reaction. Their amplification requires the action of both reverse transcriptase and RNA polymerase and involves the synthesis of both DNA and RNA replication intermediates. The proposed amplification mechanism for RNA Z involves the formation of a DNA hairpin that functions as a template for transcription by RNA polymerase. This arrangement links the two strands of the DNA, resulting in the production of RNA transcripts that contain an embedded RNA polymerase promoter sequence.