We reported previously that long-chain fatty acids are potent inhibitors of mammalian DNA polymerase . At present, based on information available from the NMR structure of the N-terminal 8-kDa domain, we examined the structural interaction with the 8-kDa domain using two species, C 18 -linoleic acid (LA) or C 24 -nervonic acid (NA). In the 8-kDa domain with LA or NA, the structure that forms the interaction interface included helix-1, helix-2, helix-4, the three turns (residues 1-13, 48 -51, and 79 -87) and residues adjacent to an ⍀-type loop connecting helix-1 and helix-2 of the same face. No significant shifts were observed for any of the residues on the opposite side of the 8-kDa domain. The NA interaction interface on the amino acid residues of the 8-kDa domain fragment was mostly the same as that of LA, except that the shifted cross-peaks of Leu-11 and Thr-79 were significantly changed between LA and NA. The 8-kDa domain bound to LA or NA as a 1:1 complex with a dissociation constant (K D ) of 1.02 or 2.64 mM, respectively.We reported previously that long-chain fatty acids strongly inhibited the activities of mammalian DNA polymerase ␣ (pol ␣) 1 and DNA polymerase  (pol ) in vitro and plant DNA polymerases, albeit less potently, but that at the concentrations used, the fatty acids hardly influenced the activities of prokaryotic DNA polymerases or other DNA metabolic enzymes such as DNase I (1, 2). The most potent inhibitors were fatty acids, which have the following characteristics: hydrocarbon chain containing 18 or more carbons, a free carboxyl end, and the cis-configuration is preferred to the trans-configuration. Fatty acids in the trans-configuration have a much weaker inhibitory effect on pol , and those in which the carboxyl end is chemically modified can lose the inhibitory effect on both pol ␣ and pol . The mode of inhibition by longer chain fatty acids showed the same characteristics, except that the minimum inhibitory doses of these longer chain fatty acids were much lower (2, 3). Lineweaver-Burk plots of the fatty acids indicated that both the substrate (i.e. deoxynucleotide)-binding and the template DNA-binding sites of pol ␣ were nonantagonistically inhibited by the fatty acids, but they were effective as antagonists against the sites of pol . For pol , fatty acids acted by competing with not only the substrate but also the template-primer DNA. In screening inhibitors of eukaryotic DNA polymerase, we also found several natural compounds which inhibited pol  in the same manner as fatty acids (4 -10).Pol  is the smallest known DNA polymerase in animal cells with a molecular mass of 39 kDa, and its structure is highly conserved among mammals (11). This protein has a modular two-domain structure, with apparent flexibility within a protease-sensitive region between residues 82 and 86, which separates the two domains. Treatment with trypsin yields an N-terminal domain fragment (8 kDa), which retains binding affinity for single-stranded DNA (ssDNA), and a C-terminal domain fragment (31 kDa) ...
