Differential Effects of Cyclopolyamines on the Stability and Conformation of Triplex DNA

Linear polyamines are excellent promoters of triplex DNA formation. The effects of structural rigidization of polyamines on triplex DNA stability are not known at present. We wished to develop a series of polyamine analogs as secondary ligands for triplex DNA stabilization for antigene applications. To accomplish this goal, we synthesized cyclopolyamines by interconnecting the two amino or imino groups of linear polyamines with a —(CH₂)_n–bridge (n = 3,4,5). Melting temperature (T_m) data showed that [4,3]-spermine and [4,4]-spermine stabilized poly(dA) · 2poly(dT) triplex at >25 μM concentrations (T_m = 71°C at 100 μM). The dTm/dlog [polyamine] values for these compounds were 26 and 40, respectively. [4,3]-Spermine and [4,4]-spermine also stabilized triplex DNA formed by a purine-motif triplex-forming oligonucleotide, TG₃ TG₄ TG₄ TG₃ T with its target duplex, as determined by T_m, circular dichroism (CD) spectroscopy, and electrophoretic mobility shift assay (EMSA). In contrast, [4,4]-putrescine and [4,5]-putrescine as well as [4,5]-spermine had no triplex DNA stabilizing effect. CD spectra also showed triplex DNA aggregation and Ψ-DNA formation at >100 μM [4,3]-spermine. These data demonstrate that structural rigidization of linear polyamines has a profound effect on their ability to stabilize triplex DNA and provoke conformational transitions.