In vitro suicide inhibition of self-splicing of a group I intron from Pneumocystis carinii by an N3 '-> P5 ' phosphoramidate hexanucleotide

Binding enhancement by tertiary interactions is a strategy that takes advan tage of the higher order folding of functionally important RNAs to bind sho rt nucleic acid-based compounds tightly and more specifically than possible by simple base pairing, For example, tertiary interactions enhance binding of specific hexamers to a group I intron ribozyme from the opportunistic p athogen Pneumocystis carinii by 1,000- to 100,000-fold relative to binding by only base pairing, One such hexamer, d(AnTnGnAnCn)rU, contains an N3' -- > P5' phosphoramidate deoxysugar-phosphate backbone inj that is resistant t o chemical and enzymatic decay. Here, it is shown that this hexamer is also a Suicide inhibitor of the intron's self-splicing reaction in vitro. The h examer is ligated in trans to the 3' exon of the precursor, producing dead- end products. At 4 mM Mg2+, the fraction of trans-spliced product is greate r than normally spliced product at hexamer concentrations as low as 200 nM. This provides an additional level of specificity for compounds that can ex ploit the catalytic potential of complexes with RNA targets.