Hydrogen bonding in deoxyribonucleic acid base recognition. 2. Deoxyribonucleic acid binding studies of acridine alkylamides.

A series of derivatives of 2-methoxy-6-chloro-9-aminoacridine bearing side chains terminated by various groups, such as carboxamide, N-methylcarboxamide, N,N-dimethylcarboxamide, methyl ester, and methyl were synthesized. The interaction of these intercalating dyes with DNA of various GC content was studied comparatively by using equilibrium dialysis and fluorescence spectroscopy. The results showed that the compounds bearing a chain terminated by a free carboxamide group could interact specifically with GC-rich DNA provided that the length and conformation of the side chain were appropriate. From these results in hand as well as those reported in the preceding paper (NMR studies at the minihelix level) it is thought that the G specificity of these compounds arises from their ability to form hydrogen bonds between the terminal carboxamide group borne by their side chain and the NH2 and N3 of the adjacent guanine located in the small grove.