Molecular mechanical simulations on double intercalation of 9-amino acridine into d(CGCGCGC) X d(GCGCGCG): analysis of the physical basis for the neighbor-exclusion principle.

Abstract

The neighbor-exclusion principle is one of the most general and interesting rules describing intercalative DNA binding by small molecules. It suggests that such binding can only occur at every other base-pair site, reflecting a very large negative cooperativity in the binding process. We have carried out molecular mechanics and molecular dynamics simulations to study intercalation complexes between 9-amino acridine and the base-paired heptanucleotide d(CGCGCGC) d(GCGCGCG), in which the neighbor-exclusion principle was both obeyed and violated. Our studies find no stereochemical preference that favors the neighbor-exclusion-obeying structures over the neighbor-exclusion-violating structures. Alternative explanations for the existence of the neighbor-exclusion principle are vibrational entropy effects that we calculate to favor the more flexible neighbor-exclusion models over the more rigid neighbor-exclusion-violating models and polyelectrolyte (counterion release) effects.The neighbor-exclusion principle proposed by Crothers (1) is one of the most general rules for intercalative binding of planar drugs to DNA. According to this principle, every second (next-neighbor) intercalation site along the length of the DNA double helix remains unoccupied. Experimental evidence for this principle has been found in fiber diffraction studies on nucleic acid fibers bound to metallointercalative agents (2, 3), in single-crystal studies (4-8) on complexes between dinucleoside monophosphates complexed with intercalating drugs, and solution studies on binding of ethidium ion to oligonucleotides of ribose and deoxyribose sugars (9). Based on earlier crystallographic studies (4-6) that suggested mixed sugar puckering at the intercalation site, a stereochemical basis for the neighbor-exclusion principle was proposed. However, this mixed sugar puckering scheme has not been shown to be essential for creating intercalating sites in double-helical DNA through several crystal structure and model building studies (7-11).The first evidence suggesting violation of the neighborexclusion model was obtained from viscometric studies (12-14) on interactions between bi-and triderivatives of acridine and DNA, where it was suggested that a single base pair was sandwiched between two acridines. 1H NMR studies on the binding of a series of bis(acridine) compounds to d(AT)5d(AT)5, in which the two acridine rings were linked through linker chains of various lengths, found no evidence of violation of the neighbor-exclusion principle (15,16).However, it was also noted that these studies have not ruled out violation of the neighbor-exclusion principle under different salt conditions and temperatures or a different nucleotide sequence (15). It has been postulated (17) that the anticooperativity of ethidium binding to DNA could be explained without reference to the neighbor-exclusion rule and is solely due to polyelectrolyte effects.Why do some simple monofunctional intercalators such as 9-amino acridine not intercalate at neighboring sites and viol...

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