Mechanism of intermolecular purine-purine-pyrimidine triple helix stabilization by comb-type polylysine graft copolymer at physiologic potassium concentration

We previously reported a novel strategy to stabilize purine motif tripler DNA within a mammalian gene promoter at physiologically relevant pH, temperature, and potassium (K+) concentrations by a comb-type poly(L-lysine)-graft-dextran copolymer [Ferdous et al., (1998) Nucleic Acids Res. 26, 3949-3954]. Here we describe the major contribution(s) of the copolymer to stabilize the purine motif tripler DNA at physiological K+ concentrations. Self-aggregation through guanine-quartet formation of guanine-rich (G-rich) tripler-forming oligonucleotides (TFOs) has long been proposed for K+-mediated inhibition of the purine motif triplex formation. However, this was not the case for the severe inhibitory effect of K+ observed under our reaction conditions. Rather significant decrease in rate of tripler formation involving a G-rich TFO was a major factor to confer K+ inhibition. Interestingly, in the presence of the copolymer the rate of tripler formation was tremendously increased and K+-induced dissociation of preformed triplexes was not observed. Moreover, the triplex-promoting/stabilizing efficiency of the copolymer was amazingly higher than that of physiological concentrations of spermine. An absolute increase in binding constant of the TFO to the target duplex could therefore be the predominant mechanistic source for the copolymer-mediated tripler stabilization under physiological conditions in vitro.