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

✍ Scribed by Nohad Gresh

• Publisher: Wiley (John Wiley & Sons)
• Year: 1985
• Tongue: English
• Weight: 825 KB
• Volume: 24
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360240809

✦ Synopsis

Theoretical computations are performed on the binding of aliphatic diamines +H,N-(CHJ,-NH,t (n = 3-71, to the minor groove of a (dAdT),, oligomer held in the EDNA conformation. The computations are performed in the framework of an additive prw cedure 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,(T), N3(A), and O,@) 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 6E 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.