Oligoribonucleotides containing a photocaged 2'-amino-5'--phophorothiolate linkage have potential applications as therapeutic agents and biological probes to investigate the RNA structure and function. We envisioned that oligoribonucleotides containing a 2'-amino-5'--phosphorothiolate linkage could provide an approach to identify the general base within catalytic RNAs by chemogenetic suppression. To enable preliminary tests of this idea, we developed synthetic approaches to a dinucleotide, trinucleotide, and oligoribonucleotide containing a photocaged 2'-amino-5'--phosphorothiolate linkage. We incorporated the photocaged 2'-amino-5'--phosphorothiolate linkage into an oligoribonucleotide substrate for the hepatitis delta virus (HDV) ribozyme and investigated the pH dependence of its cleavage following UV irradiation both in the presence and absence of the ribozyme. The substrate exhibited a pH-rate profile characteristic of the modified linkage but reacted slower when bound to the ribozyme. Cleavage inhibition by the HDV ribozyme could reflect a non-productive ground-state interaction with the modified substrate's nucleophilic 2'-NH or a poor fit of the modified transition state at the ribozyme's active site.
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| http://dx.doi.org/10.1021/acs.joc.1c01059 | DOI Listing |
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