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Structure-Function Analysis of RNAs Generated by In Vivo and In Vitro Selection

Today, the concept of Darwinian evolution plays a significant role in studying structure-function relationships concerning known molecules and in helping to design previously unknown molecules with desired functionalities. Results from in vitro and in vivo selection experiments, however, are often very difficult to interpret, e.g. due to the fact, that molecular answers to applied selection pressures are unforeseen by the experimenter. Here we point out, that secondary structure prediction can be a valid tool in understanding structure-function relationships of functional RNAs from in vitro and in vivo selection experiments. Benefits as well as possible limitations of the approach are discussed.