Qbetter SELEX: putting the Spiegelman monsters behind bars

RNA SELEX is a very cumbersome method that has remained largely unchanged for over two decades. By using the sequential combination of reverse transcription, PCR and RNA transcription many lengthy steps are necessary for the amplification that may also include a strong bias for certain sequences in the selection. The RNA replicase from phage Qβ can amplify template RNA exponentially with the exceptional speed of 10¹⁰ copies in 10 minutes at room temperature and would thus be a perfect system to be combined with SELEX. However in such an isothermal amplification the so-called Spiegelman monsters quickly supersede slower and potentially more interesting variants. Earlier attempts to harness the power of Qβ replicase for SELEX have failed due to this problem. In order to compensate for this strong bias we have created a new approach in which highly replication-competent libraries are amplified in emulsions. Our accelerated method termed Qbetter SELEX has been shown to yield specific RNA aptamers in just 3 selection rounds in combination with next generation sequencing for analysis. The evolved clones are very good templates for Qβ replicase which is also useful for the sensitive detection of minute target quantities in a simple assay.