EXONUCLEOLYTIC PROOFREADING DURING REPLICATION OF REPETITIVE DNA

We are attempting to understand the processes required to accurately r eplicate the repetitive DNA sequences whose instability is associated with several human diseases. Here we test the hypothesis that the cont ribution of exonucleolytic proofreading to frameshift fidelity during replication of repetitive DNA sequences diminishes as the number of re peats in the sequence increases. The error rates of proofreading-profi cient T7, T4, and Pyrococcus furiosis DNA polymerases are compared to their exonuclease-deficient derivatives, for +1 and -1 base errors in homopolymeric repeat sequences of three to eight base pairs. All three exonuclease-deficient polymerases produce frameshift errors during sy nthesis at rates that increase as a function of run length, suggesting the involvement of misaligned intermediates. Their wild-type counterp arts are all much more accurate, suggesting that the majority of the i ntermediates are corrected by proofreading. However, the contribution of the exonuclease to fidelity decreases substantially as the length o f the homopolymeric run increases. For example, the exonuclease enhanc es the frameshift fidelity of T7 DNA polymerase in a run of three A . T base pairs by 160-fold, similar to its contribution to base substitu tion fidelity. However, in a run of eight consecutive A . T base pairs , the exonuclease only enhances frameshift fidelity by 7-fold. A simil ar pattern was observed with T4 and Pfu DNA polymerases. Thus, both po lymerase selectivity and exonucleolytic proofreading efficiency are di minished during replication of repetitive sequences. This may place an increased relative burden on post-replication repair processes to red uce rates of addition and deletion mutations in organisms whose genome contains abundant simple repeat DNA sequences.