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) (tripler 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 tripler. The experimental results support the interaction model suggested previously (Wilson et al. Biochemistry 1993, 32, 10614).