Synthesis and structure-DNA binding relationship analysis of DNA triple-helix specific intercalators.

4-[N-(Aminoalkyl)amino]-2-arylquinolines with conformational freedom around positions 2 and 4 of the quinoline stabilize strongly poly(dT.dA.dT) (triplex DNA) and bind weakly to poly-(dA.dT) (duplex DNA). Basicity of N1 of the quinoline parallels the interaction strength of these compounds with the triple-helical DNA structure suggesting that N1 of the quinoline is protonated in the complex with the DNA triplex. The experimental results support the interaction model suggested previously.