A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme

Background: Phosphoramidate oligonucleotide analogs containing N3'-P5' link ages share many structural properties with natural nucleic acids and can be recognized by some RNA-binding proteins. Therefore, if the N-P bond is res istant to nucleolytic cleavage, these analogs may be effective substrate an alog inhibitors of certain enzymes that hydrolyze RNA. We have explored the ability of the Tetrahymena group I intron ribozyme to bind and cleave DNA and RNA phosphoramidate analogs. Results: The Tetrahymena group I ribozyme efficiently binds to phosphoramid ate oligonucleotides but is unable to cleave the N3'-P5' bond. Although it adopts an A-form helical structure, the deoxyribo-phosphoramidate analog, l ike DNA, does not dock efficiently into the ribozyme catalytic core. In con trast, the ribophosphoramidate analog docks similarly to the native RNA sub strate, and behaves as a competitive inhibitor of the group I intron 5' spl icing reaction. Conclusions: Ribo-N3'-P5' phosphoramidate oligonucleotides are useful tools for structural and functional studies of ribozymes as well as protein-RNA interactions.