Thermodynamic studies on interactions between DNA and dye

• Published in: Thermochimica acta 1994-08, Vol.242, p.65-75
• Main Authors: Kagemoto, Akihiro, Kunihiro, Akira, Baba, Yoshihiro
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Base pair; Biological and medical sciences; Chemical thermodynamics; Chemistry; Cytosine; DNA; Dna, deoxyribonucleoproteins; Dye; Elements, mineral and organic compounds; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; General and physical chemistry; Guanine; Intercalation; Nucleic acids; Thermodynamic properties; Thermodynamics; UVS
• ISSN: 0040-6031; 1872-762X
• DOI: 10.1016/0040-6031(94)85009-7

The interactions in solution between DNA, DNA-I (GC content 26.5%), DNA-II (GC content 42%), and DNA-III (GC content 72%), with various contents of guanine—cytosine base pair (GC content), and 9-amino-acridine (9-AA) or quinacrine with side chains were studied by microcalorimetry and spectrophotometry. The thermodynamic quantities for dye intercalated into adjacent base pairs of DNA were determined. From the results, the Δ G ⊖ values in the DNA-I—, -II—, and -III—9AA systems were estimated to be about −32 kJ, virtually independent of GC content, although the absolute values of Δ H increase with increasing GC content of DNA, suggesting that an interaction between DNA and 9-AA forms a thermodynamically stable complex, depending on the GC content of the DNA. However, the Δ G ⊖ value for the DNA-II—quinacrine system is lower than that for the DNA-I— or DNA-III—quinacrine systems, demonstrating that an interaction between DNA-II and quinacrine forms a thermodynamically stable complex, compared with those in the DNA-I— and DNA-III—quinacrine systems. An analysis for base specificity of dyes accompanying the intercalation was carried out according to Eq. (7) in the text. The thermodynamic quantities for dye intercalated into GC/GC, AT/AT, and GC/AT base pair sequences were estimated. From these results, the most stable base sequence with respect to the intercalation of 9-AA into adjacent base pairs was the AT/AT base pair rather than the GC/GC and AT/GC base pairs, its thermodynamic quantities being about −31 kJ mol −1 for Δ H, 5.0 J K −1 mol −1 for Δ S, and −33 kJ mol −1 for Δ G ⊖. Therefore, 9-AA interacts preferentially with the AT/AT base pair sequence. However, in the quinacrine systems, the most stable base pair for intercalation of quinacrine into adjacent base pairs was the GC/AT base sequence, and its thermodynamic quantities being Δ H ≈ −64 kJ mol −1, Δ S ≈ −12 J K −1 mol −1, and Δ G ⊖ ≈ −68 kJ mol −1 suggesting that interaction between DNA and quinacrine is governed by Δ H, and also, that the interaction mode of quinacrine is different from that of 9-AA.