Stabilization of DNA triple-helix formation by appended cationic peptides.

We have investigated the impact of appended cationic peptides on the triplex-forming and thermal-stabilizing abilities of an oligonucleotide "third strand" using a homopurine-homopyrimidine 37-mer as the host duplex target. The family of appended cationic peptides studied here contains arginine, lysine, ornithine, and diaminobutyric acid, with the residues being linked through either their alpha-amino or side chain amino groups. On the basis of optical melting profiles, we find that peptides with different amino acid compositions, but with four positive charges in common, are able to enhance, in a similar manner, the triplex-forming capability of an oligonucleotide. We note the implications of these results for the rational design of third-strand probes.