Orientation preferences of pyrrole - imidazole polyamides in the minor groove of DNA

A study on the orientation of pyrrole was conducted to determine its influence on positive charge, position of positive charge at N- or C-terminus and substitution of the terminal imidazole. The research identified equilibrium association constants for a series of six-ring hairpin polyamides with respect to N and C termini. Results show that second generation design principles on pairing rules optimize sequence specificity of pyrrole-imidazole polyamides for double helical DNA.