Background: Phosphoramidate oligonucleotide analogs containing N3′–P5′ linkages share many structural properties with natural nucleic acids and can be recognized by some RNA-binding proteins. Therefore, if the N–P bond is resistant to nucleolytic cleavage, these analogs may be effective substrate analog 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 phosphoramidate oligonucleotides but is unable to cleave the N3′–P5′ bond. Although it adopts an A-form helical structure, the deoxyribo-phosphoramidate analog, like DNA, does not dock efficiently into the ribozyme catalytic core. In contrast, the ribo-phosphoramidate analog docks similarly to the native RNA substrate, and behaves as a competitive inhibitor of the group I intron 5′ splicing reaction.
Conclusions: Ribo-N3′–P5′ phosphoramidate oligonucleotides are useful tools for structural and functional studies of ribozymes as well as protein–RNA interactions.
