In vitro selection of a 5′-purine ribonucleotide transferase ribozyme

Here we report in vitro selection of a novel ribozyme that catalyzes the 5′-nucleotidyl transfer reaction forming the 2′–5′ phosphodiester bond. This ribozyme was retrieved as a sole sequence in the pool enriched for the 5′-triphosphate-dependent activities in incorporating ATP-γS. The originally selected ribozyme consisting of 109-nucleotide (nt) was miniaturized to 45-nt M4 ribozyme via a series of mutation studies, and based on this mini-ribozyme a trans-acting system was constructed. One of the most challenging tasks in our study was to determine the chemistry occurring at the 5′-ppp site. We utilized various analytical methods including MALDI-TOF analysis of the product generated by the trans-acting system and elucidated the chemistry to be 3′→5′ mononucleotide extension forming the 2′–5′ phosphodiester bond. Interestingly, M4 ribozyme promiscuously accepts a variety of purine nucleotides bearing 5′-mono-, di- and triphosphates as substrates. This remarkable ability of M4 ribozyme would lead us to the development of a new tool for the 5′-modification of RNAs with unique chemical groups.