The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in basic researches and application studies in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP , theoretical studies of the fidelity issue are still lacking. Kinetic models which considered explicitly both the polymerase pathway and the exonuclease (proofreading ) pathway were proposed since 1970s', but so far there was no rigorous treatment of such models . In this paper, we propose a new  kinetic model of the exonuclease proofreading mechanism, based on some recent experimental observations  . We present a rigorous analytical treatment of the  steady-state kinetic equations including higher-order terminal effects , and then apply the results to the fidelity problem of some real DNAPs . Our results show good agreements with previous intuitive estimate of some DNAPs' fidelity under bio-relevant conditions .
The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite few theoretical studies on the fidelity issue . The first model which explicitly considered both sites was proposed in 1970s' and the basic idea was widely accepted by later models. However, all these models did not systematically and rigorously investigate the dominant factor on DNAP fidelity, i.e, the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity . In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations , which includes previous models as special cases . We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs , which are in good agreements with previous intuitive estimates given by experimentalists .
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