Binding of threading intercalator to nucleic acids: thermodynamic analyses.

Abstract

The constant melting temperature upon the change in the oligonucleotide concentration showed that the oligonucleotide d(CGCTTTGCG) formed a intramolecular hairpin rather than a duplex with an internal loop. We examined the thermodynamic properties of the interaction between the threading intercalator, naphthalene diimides designated as NDI, and a series of hairpin oligonucleotides, d(CGCTnGCG) (n = 3, 4, 5, and 6) designated as CGCn. A complex with a molar ratio of 1:1 was formed between NDI and CGCn. Because the observed negative entropy change was unfavorable for the binding of NDI to CGCn, the binding was driven by the large negative enthalpy change. All of the thermodynamic parameters for the threading intercalation were not significantly changed by the difference in the loop length n. The stem region rather than the loop region of CGCn is mainly involved in the binding of NDI.