Steric and electrostatic effects in DNA synthesis by the SOS-induced DNA polymerases II and IV of XXXX .

@entity1 @entity70804 @entity3884 @entity42636 @entity377 @entity1014 @entity20700 @entity6244 @entity526
The SOS-induced DNA polymerases II and IV (pol II and pol IV, respectively) of @entity526 play important roles in processing lesions that occur in genomic DNA. Here we study how electrostatic and steric effects play different roles in influencing the efficiency and fidelity of DNA synthesis by these two enzymes. These effects were probed by the use of nonpolar shape analogues of @entity1014 , in which substituted @entity70804 replace the polar @entity6244 base. We compared @entity6244 with nonpolar analogues to evaluate the importance of @entity3884 bonding in the polymerase active sites, while we used comparisons among a set of variably sized @entity6244 analogues to measure the role of steric effects in the two enzymes. Steady-state kinetics measurements were carried out to evaluate activities for @entity377 insertion and extension. The results showed that both enzymes inserted nucleotides opposite nonpolar template bases with moderate to low efficiency, suggesting that both polymerases benefit from @entity3884 bonding or other electrostatic effects involving the template base. Surprisingly, however, pol II inserted nonpolar @entity377 ( @entity42636 ) analogues into a primer strand with high (wild-type) efficiency, while pol IV handled them with an extremely low efficiency. Base pair extension studies showed that both enzymes bypass non- @entity3884 -bonding template bases with moderately low efficiency, suggesting a possible beneficial role of minor groove @entity3884 bonding interactions at the N-1 position. Measurement of the two polymerases' sensitivity to steric size changes showed that both enzymes were relatively flexible, yielding only small kinetic differences with increases or decreases in @entity377 size. Comparisons are made to recent data for DNA pol I (Klenow fragment), the archaeal polymerase Dpo4, and @entity1 @entity20700 .
