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Theoretical study of the binding of aliphatic diamines to the minor groove of a B‐DNA (dA‐dT) 11 oligomer
Author(s) -
Gresh Nohad
Publication year - 1985
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360240809
Subject(s) - oligomer , diamine , chemistry , intramolecular force , minor groove , intermolecular force , dna , groove (engineering) , affinities , stereochemistry , crystallography , computational chemistry , polymer chemistry , organic chemistry , molecule , materials science , biochemistry , metallurgy
Theoretical computations are performed on the binding of aliphatic diamines + H 3 N‐(CH 2 ) n ‐NH 3 +( 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 .