Polymerases from the Pol I family which are able to efficiently use ddNTPs have demonstrated a much
improved performance when used to sequence
DNA. A number of mutations have been made to the
gene coding for the Pol II family
DNA polymerase from the archaeon Pyrococcus furiosus with the aim of improving ddNTP utilisation. "Rational" alterations to amino acids likely to be near the dNTP
binding site (based on sequence homologies and structural information) did not yield the desired level of selectivity for ddNTPs. However, alteration at four positions (Q472, A486, L490 and Y497) gave rise to variants which incorporated ddNTPs better than the
wild type, allowing sequencing reactions to be carried out at lowered ddNTP:dNTP ratios.
Wild type Pfu-Pol required a ddNTP:dNTP ratio of 30:1; values of 5:1 (Q472H), 1:3 (L490Y), 1:5 (A486Y) and 5:1 (Y497A) were found with the four mutants; A486Y representing a 150-fold improvement over the
wild type. A486, L490 and Y407 are on an alpha-
helix that lines the dNTP binding groove, but the side chains of the three amino acids point away from this groove; Q472 is in a loop that connects this alpha-
helix to a second long
helix. None of the four amino acids can contact the dNTP directly. Therefore, the increased selectivity for ddNTPs is likely to arise from two factors: 1) Small overall changes in conformation that subtly alter the
nucleotide triphosphate
binding site such that ddNTPs become favoured; 2) interference with a
conformational change that may be critical both for the polymerisation step and discrimination between different
nucleotide triphosphates.