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

Chem Biol. 2000 Nov;7(11):845-54. doi: 10.1016/s1074-5521(00)00033-8.


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.

MeSH terms

  • Amides
  • Animals
  • Binding, Competitive
  • Cloning, Molecular
  • Electrophoresis, Polyacrylamide Gel
  • Kinetics
  • Magnesium / metabolism
  • Models, Biological
  • Molecular Mimicry
  • Molecular Structure
  • Oligoribonucleotides / genetics
  • Oligoribonucleotides / metabolism*
  • Phosphoric Acids
  • RNA, Catalytic / antagonists & inhibitors*
  • RNA, Catalytic / genetics
  • RNA, Catalytic / metabolism*
  • Tetrahymena thermophila / enzymology*
  • Tetrahymena thermophila / genetics


  • Amides
  • Oligoribonucleotides
  • Phosphoric Acids
  • RNA, Catalytic
  • phosphoramidic acid
  • Magnesium