Targeting a Pneumocystis carinii group I intron with methylphosphonate oligonucleotides: Backbone charge is not required for binding or reactivity

Pneumocystis carinii is a mammalian pathogen that contains a self-splicing group I intron in its large subunit rRNA precursor. We report the binding o f methylphosphonate/DNA chimeras and neutral methylphosphonate oligonucleot ides to a ribozyme that is a truncated form of the intron. At 15 mM Mg2+, t he nuclease-resistant all-methylphosphonate hexamer, d(AmTmGmAmCm)rU, with a sequence that mimics the 3' end of the precursor's 5' exon, binds with a dissociation constant of 272 nM. The hexamer's dissociation constant for bi nding by base-pairing alone to the ribozyme's binding site sequence is 8.3 mM. Thus there is a 30 000-fold binding enhancement by tertiary interaction s (BETI), which is close to the 60 000-fold enhancement previously observed with the all-ribo hexamer, r(AUGACU). Evidently, backbone charge and 2' hy droxyl groups are not required for BETI. At 3-15 mM Mg2+, the all-methylpho sphonate and DNA oligonucleotides trans-splice to a truncated form of the r RNA precursor, but do not compete with cis-splicing when pG is present. The se results suggest that uncharged or partially charged backbones may be use d to design therapeutics to target RNAs through binding enhancement by tert iary interactions and suicide inhibition strategies.