Binding enhancement by tertiary interactions and suicide inhibition of a Candida albicans group I intron by phosphoramidate and 2 '-O-methyl hexanucleotides

Candida albicans is one of many infectious pathogens that are evolving resi stance to current treatments. RNAs provide a large class of targets for new therapeutics for fighting these organisms. One strategy for targeting RNAs uses short oligonucleotides that exhibit binding enhancement by tertiary A BSTRACT: interactions in addition to Watson-Crick pairing. A potential RNA target in C. albicans is the self-splicing group I intron in the LSU rRNA p recursor. The recognition elements that align the 5' exon splice site for a ribozyme derived from this precursor are complex [Disney, M. D., Haidaris, C. G., and Turner, D. H. (2001) Biochemistry 40, 6507-6519]. These recogni tion elements have been used to guide design of hexanucleotide mimics of th e 5' exon that have backbones modified for nuclease stability. These hexanu cleotides bind as much as 100000-fold more tightly to a ribozyme derived fr om the intron than to a hexanucleotide mimic of the intron's internal guide sequence, r(GGAGGC). Several of these oligonucleotides inhibit precursor s elf-splicing via a suicide inhibition mechanism. The most promising suicide inhibitor is the ribophosphoramidate rn(G (C) under bar CUC)rU, which form s more trans-spliced than cis-spliced product at oligonucleotide concentrat ions of >100 nM at 1 mM Mg2+. The results indicate that short oligonucleoti des modified for nuclease stability can target catalytic RNAs when the elem ents of tertiary interactions are complex.