The use of nonnatural nucleotides to probe the contributions of shape complementarity and pi-electron surface area during DNA polymerization.

It is widely accepted that the dynamic behavior of DNA polymerases during translesion DNA synthesis is dependent upon the nature of the DNA lesion and the incoming dNTP destined to be the complementary partner. We previously demonstrated that 5-nitro-1-indolyl-2'-deoxyribose-5'-triphosphate, a nonnatural nucleobase possessing enhanced base-stacking abilities, can be selectively incorporated opposite an abasic site (Reineks, E. Z., and Berdis, A. J. (2004) Biochemistry 43, 393-404.). While the enhancement in insertion presumably reflected the contributions of the pi-electrons present in the nitro group, other physical parameters such as solvation capabilities, dipole moment, surface area, and shape could also contribute. To evaluate these possibilities, a series of 5-substituted indole triphosphates were synthesized and tested for enzymatic incorporation into normal and damaged DNA by the bacteriophage T4 DNA polymerase. The overall catalytic efficiency for the insertion of the 5-phenyl-indole derivative opposite an abasic site is several orders of magnitude greater than the insertion of either the 5-fluoro- or the 5-amino-indole derivative. The generated structure-activity relationship indicates that pi-electrons play the largest role in modulating the catalytic efficiency for insertion opposite this nontemplating DNA lesion. Despite the large size of 5-phenyl-indole, the catalytic efficiency for its insertion opposite natural nucleobases is equal to or greater than that of the 5-fluoro- or 5-amino-indole derivatives. The higher catalytic efficiency reflects a higher binding affinity of 5-phenyl-1-indolyl-2'-deoxyribose-5'-triphosphate and suggests that the polymerase relies on pi-electron surface area rather than shape complementarity as a driving force for polymerization efficiency.