phosphoramidite and Hepatitis-D

Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p K

Topics: DNA; Hepatitis D; Hepatitis Delta Virus; Humans; Nucleic Acid Conformation; Oligonucleotides; Organophosphorus Compounds; Protons; RNA, Catalytic; RNA, Viral; Substrate Specificity