Positively charged oligonucleotides overcome potassium-mediated inhibition of triplex DNA formation

The formation of tripler DNA using unmodified, purine-rich oligonucleotides (ODNs) is inhibited by physiologic levels of potassium, Changing negative phosphodiester bonds in a tripler forming oligonucleotide (TFO) to neutral linkages causes a small increase in tripler formation, When phosphodiester bonds in a TFO are converted to positively-charged linkages the formation of tripler DNA increases dramatically, In the absence of KCI, a 17mer TFO containing 11 positively-charged linkages at a concentration of 0.2 mu M converts essentially all of a 30 bp target duplex to a tripler, Less than 15% of the target duplex is shifted by 2 mu M of the unmodified TFO, In 130 mM KCI, tripler formation is undetectable using the unmodified TFO, while tripler formation is nearly complete with 2 mu M positively-charged TFO, With increasing potassium, TFOs containing a higher proportion of modified linkages show enhanced tripler formation compared with those less modified, In contrast with unmodified TFOs, tripler formation with more heavily modified TFOs can occur in the absence of divalent cations, We conclude that replacement of phosphodiester bonds with positively-charged phosphoramidate linkages results in more efficient tripler formation, suggesting that these compounds may prove useful for in vivo applications.