The polymerase chain reaction (PCR) is one of the most important reactions in molecular biology. The detailed mechanistic studies of the polymerase chain reaction have revealed a complex sequence of reversible reactions that involve intermediaries and activated complexes. The DNA polymerase does not merely facilitate the insertion of dNMP (deoxynucleotide monophosphates), but it also performs rapid screening of substrates to ensure a high degree of fidelity. The main result of this study is an expression for the average extension rate of the enzyme. The model is versatile and additional complexities, such as the type of nucleotide to be inserted, the GC content of the sequence in the vicinity of the insertion site, and the topology of the template, such as kinks and hairpins, are easy to incorporate. The insertion of incorrect nucleotides into the sequence is also addressed. Expressions to predict error frequencies are presented. It is shown that a relation exists between error frequency and extension rate: the error frequency is a minimum when the extension rate is optimal. © 2005 American Institute of Chemical Engineers AIChE J, 2006
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