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 Delta 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 Delta 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 Delta 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 Delta H, 5.0 J K-1 mol(-1) for Delta S, and -33 kJ mol(-1) for Delta 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 Delta H approximate to - 64 kJ mol(-1), Delta S approximate to - 12 J K-1 mol(-1), and Delta G(-) approximate to - 68 kJ mol(-1) suggesting that interaction between DNA and quinacrine is governed by Delta H, and also, that the interaction mode of quinacrine is different from that of 9-AA.