The interaction of mefloquine (4), two of its analogues, 5 and 6, quinacrine (2), chloroquine (l), and quinine (3) with DNA has been investigated using difference spectroscopy, spectral shifts in the presence of DNA, viscometric titrations with sonicated calf thymus DNA and Col El plasmid superhelical DNA, and Tm measurements. The results from these experiments indicate that quinolines with the methanolamine side chain at position 4 cannot intercalate with DNA if they have another bulky substituent (such as trifluoromethyl) at position 2. Mefloquine (4), which has been found to be clinically effective against chloroquine-resistant Plasmodium falciparum, completely clears parasitemia in a single dose. This drug contains trifluoromethyl substituents at positions 2 and 8 of the quinoline nucleus and binds to DNA only weakly by electrostatic attraction at low ionic strength. Similar compounds such as 5 and quinine (3) without bulky substituents at position 2 can intercalate with DNA, but this interaction is not correlated in any apparent manner with antimalarial activity. Even intercalating quinolinemethanolamines bind weakly to DNA relative to compounds such as quinacrine (2), ethidium, and daunorubicin which are thought to exert their medicinal effects through in vivo intercalation with DNA. These results, taken collectively, strongly suggest that interaction with DNA is not involved in the antimalarial action of the quinolinemethanolamines analyzed in these experiments.