LETTERS the T7 DNA polymerase ternary complex are directly applicable to KF. A similar orientation for bound DNA was also obtained when we superposed the pol-ß carboxylate triad onto the appropriate acidic residues (Asp610, Glu615 and Asp785) of another DNA polymerase, Taq polymerase (PDB entry 1tau), whose DNA-bound structure has been solved7 (Fig. 5).

We would, however, like to caution that, in spite of the generally uniform mode of DNA binding, the polymerases can exhibit enzyme-specific differences in the absolute positions of individual nucleotides within the bound TP. Thus, when DNA in the pol-ß–DNA complex is superposed onto the KF and Taq polymerase structures, steric hindrance with the J-helix regions of these enzymes is noted. Furthermore, DNA that is bound in the vicinity of the polymerase active site appears to deviate from the normal B-DNA structure. For example, within the HIV-1-RT–DNA complex, five or six base pairs of DNA that are proximal to the primer terminus have an A-DNA-like geometry. In pol-ß–DNA complexes, only two or three bases assume such a conformation. Local adaption at or near the active center of a DNA polymerase might have occurred during evolution,