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 resistance 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 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 precursor. 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 recognition elements have been used to guide design of hexanucleotide mimics of the 5' exon that have backbones modified for nuclease stability. These hexanucleotides bind as much as 100000-fold more tightly to a ribozyme derived from the intron than to a hexanucleotide mimic of the intron's internal guide sequence, r(GGAGGC). Several of these oligonucleotides inhibit precursor self-splicing via a suicide inhibition mechanism. The most promising suicide inhibitor is the ribophosphoramidate rn(GCCUC)rU, which forms more trans-spliced than cis-spliced product at oligonucleotide concentrations of >100 nM at 1 mM Mg(2+). The results indicate that short oligonucleotides modified for nuclease stability can target catalytic RNAs when the elements of tertiary interactions are complex.
Disney
M D
MD
Departments of Chemistry and Pediatrics, University of Rochester, Rochester, New York 14627-0216, USA.
Matray
T
T
Gryaznov
S M
SM
Turner
D H
DH
D001667:Binding, Competitive; D002176:Candida albicans / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development*; D007438:Introns; D008274:Magnesium / Q000737:chemistry; D011089:Polydeoxyribonucleotides / Q000737:chemistry*; D012322:RNA Precursors / Q000037:antagonists & inhibitors / Q000235:genetics; D012326:RNA Splicing; D016337:RNA, Catalytic / Q000037:antagonists & inhibitors* / Q000235:genetics*; D012331:RNA, Fungal / Q000037:antagonists & inhibitors / Q000235:genetics; D012335:RNA, Ribosomal / Q000037:antagonists & inhibitors / Q000235:genetics; D013873:Thionucleotides / Q000737:chemistry*
D011089:Polydeoxyribonucleotides; D012322:RNA Precursors; D016337:RNA, Catalytic; D012331:RNA, Fungal; D012335:RNA, Ribosomal; D013873:Thionucleotides; D008274:Magnesium