Rational combination of strategies to achieve synergistic stabilization of triplex

The combination of two stabilizing strategies to increase stability of nucleic acid assembly is not always resulted in synergistic effect. In the present study, to explore the rational way to select the combination for synergistically stabilizing strategies, we examined the kinetic effects of different triplex-stabilizing strategies, poly(L-lysine)-graft-dextran (PLL-g-Dex) copolymer and N3'-->P5' phosphoramidate (PN) backbone modification of triplex-forming oligonucleotide (TFO). The former increased the association rate constant, whereas the latter decreased the dissociation rate constant in triplex equilibrium. Each strategy increased the binding constant of the triplex formation by nearly two orders of magnitude. The combination of both stabilizing strategies, which was the triplex formation with PN TFO in the presence of the copolymer, increased the binding constant by nearly four orders of magnitude, implying successful synergy of their activities. The kinetically orchestrated effects in which the copolymer and the PN modification contribute to distinct ingredients in triplex equilibrium achieved the observed synergistic stabilization. We conclude that kinetic analyses of stabilizing effects enable us to select a rational combination of stabilizing strategies.