Pyrimidine-purine-pyrimidine triplex DNA stabilization in the presence of tetramine and pentamine analogues of spermine

Abstract

The formation and stability of triplex DNA were investigated in the presence of a number of tetramine (+4) and pentamine (+5) derivatives of spermine with altered spacing between the positive charges and bis(ethyl) substitution of pendant amino groups. Thermal denaturation profiles were measured for the duplex and triplex forms of poly[d(TC)].poly[d(GA)] and poly(dA).poly(dT); in both cases the pentamines were more effective than the tetramines in increasing the melting temperature (Tm) of the triplexes. Some structural effects were evident, although bisethylation of the polyamines had only a minor effect on the Tm of pyrimidine-purine-pyrimidine triplexes. Relative association constants to poly(dT).poly(dA).poly(dT) and poly[d(AT)] were measured by an ethidium competition assay. These results demonstrated tighter binding of the pentamines by a factor of up to 10-fold, but bisethylation consistently decreased the relative association constants to the triplex. A third assay involving transmolecular triplex formation between separated pyrimidine-purine tracts in plasmid DNA was also employed. Again the pentamines promoted triplex formation at lower concentrations than the tetramines but structural effects were very important in determining the degree of triplex formation. These results may be important for the design of suitable ligands to stabilize triplex DNA in antigene therapeutics and to elucidate the mechanism of action of polyamine analogues as antitumor drugs.