Synergistic stabilization of triplex by combination of comb-type cationic copolymer and oligo-N3'-->P5' phosphoramidates.

Abstract

In the present study, we describe rapid formation of stable pyrimidine motif triplex at physiological pH. The triplex formation was achieved by the synergistic effect of poly(L-lysine)-graft-dextran (PLL-g-Dex) copolymer and N3'-->P5' phosphoramidate (PN) backbone modification of triplex-forming oligonucleotide (TFO). Either the PLL-g-Dex copolymer or the PN modification alone increased the binding constant by nearly two orders of magnitude for the triplex formation at neutral pH. The combination of both stabilizing factors that was the triplex formation with the PN TFO in the presence of the copolymer increased the binding constant by nearly four orders of magnitude. The kinetic study indicated that the copolymer increased the association rate constant, whereas the PN modification decreased the dissociation rate constant. No negative interference between these stabilizing effects was observed. The kinetically orchestrated effects in which the copolymer and the PN TFO contribute to distinct ingredients in triplex equilibrium achieved the rapid formation of the stable triplex.