A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme.
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.
Hanna
R L
RL
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
Gryaznov
S M
SM
Doudna
J A
JA
D000577:Amides; D000818:Animals; D001667:Binding, Competitive; D003001:Cloning, Molecular; D004591:Electrophoresis, Polyacrylamide Gel; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008954:Models, Biological; D018716:Molecular Mimicry; D015394:Molecular Structure; D009843:Oligoribonucleotides / Q000235:genetics / Q000378:metabolism*; D010756:Phosphoric Acids; D016337:RNA, Catalytic / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism*; D016808:Tetrahymena thermophila / Q000201:enzymology* / Q000235:genetics
D000577:Amides; D009843:Oligoribonucleotides; D010756:Phosphoric Acids; D016337:RNA, Catalytic; C011067:phosphoramidic acid; D008274:Magnesium