Theoretical study of the binding of aliphatic diamines to the minor groove of a B‐DNA (dA‐dT)₁₁ oligomer

Theoretical computations are performed on the binding of aliphatic diamines + H 3 N‐(CH 2 ) n ‐NH ( n = 3–7), to the minor groove of a (dA‐dT) 11 oligomer held in the B‐DNA conformation. The computations are performed in the framework of an additive procedure elaborated recently in this laboratory by means of which the intermolecular DNA–diamine interaction energies and the intramolecular energy variations of the diamine are computed simultaneously. The results of the computations show that the binding of the diamines occurs in well‐defined configurations in which each cationic extremity interacts with specific sites, O 2 (T), N 3 (A), and O 1 ,(S) in the groove, the overall configuration differing according to the length of the diamine. The overall energy balance for complexation is found to depend on the chain length of the diamine, an optimal value for δ E being found for 1,6 diaminohexane. This result is discussed in light of available experimental results of the compared affinities of diamines for the double‐stranded polymer dA ‐ dT .