Inhibitory action of C22-fatty acids on DNA polymerases and DNA topoisomerases

We reported previously that unsaturated linear-chain fatty acids of the cis-configuration with a C18-hydrocarbon chain such as linoleic acid (cis-9, 12-octadecadienoic acid, C18:2) could potently inhibit the activity of mammalian DNA polymerases (Biochim Biophys Acta 1308: 256-262, 1996). In this study, we investigated the inhibitory effects of cis-type C22-fatty acids including cis-7,10,13,16,19-docosapentaenoic acid (DPA, C22:5) and cis-4,7,10,13,16,19-docosahexaenoic acid (DHA, C22:6) on mammalian DNA polymerases and human DNA topoisomerases. Cis-13,16-docosadienoic acid (C22:2) was the strongest inhibitor of both DNA polymerases and topoisomerases of all C22-fatty acids tested. The inhibitory tendency by the fatty acids on DNA polymerases was the same as that of DNA topoisomerases, and the second strongest inhibitor was cis-13,16,19-docosatrienoic acid (C22:3). The energy-minimized three-dimensional structures of the fatty acids were calculated and it was found that a length of 19-21 Å and width of more than 7 Å in C22-fatty acid structure were important for enzyme inhibition. The three-dimensional structure of the active site of both DNA polymerases and topoisomerases must have a pocket to join C22:2, and this pocket was 19.41 Å long and 9.58 Å wide.