RNA Diels−Alderases:  Relationships between Unique Sequences and Catalytic Function

A group of eight unique RNA sequences isolated from a single in vitro selection experiment were characterized based on their Diels−Alderase properties. Five of the eight isolates contain a 10-base conserved region, while the remaining three do not share any sequence similarities with any of the others. This series of RNA Diels−Alderases displayed k cat and K m values that spanned 74 and 80-fold ranges, respectively. These values appeared to compensate for one another, as the value of k cat/K m varied by only 5-fold among the isolates studied. Product inhibition experiments revealed a general trend between affinity for the cycloaddition product and catalytic ability as measured by k cat. The activities of each of the RNA Diels−Alderases were completely dependent on the presence of cupric ion. In addition, all of the RNA catalysts demonstrated a high degree of substrate selectivity, even for structurally and electronically similar dienophiles. Overall, the data demonstrate how a variety of RNA sequences can solve a specific chemical problem. The information gathered provides a foundation from which to build our understanding of how sequence, structure, and function are interrelated. Such knowledge could be applied to create new catalysts, both large and small.