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DNA Polymerase: an Active Machine

DNA polymerases catalyze the polymerization of deoxyribonucleotides (dNTPs) using a template DNA strand. In the basic model for DNA polymerase action, the polymerase first binds to a primer/template. Then, a dNTP binds loosely to the complex. Binding of the correct nucleotide leads to a conformational change, which converts the loose ternary complex into a tight activated complex capable of undergoing chemical bond formation. After chemistry occurs, the pyrophosphate product is released and the DNA product is either translocated or dissociated.

Upon dNTP binding DNA polymerase forms a closed ternary complex.

In this Paper of the Week, Paul J. Rothwell and Gabriel Waksman describe a series of fluorescence resonance energy transfer (FRET) analyses that characterize DNA binding and dNTP incorporation by DNA polymerases. Their data indicate that there is a step that occurs before dNTP binding, which differs for all four nucleotides. Because the only difference between the primer/template-polymerase complexes is the templating base, the templating base must play an important role in initial ground state selection. From these experiments, the authors suggest that the polymerase is a very active machine that reads the template base to decide what incoming dNTP is correct, rather than a relatively passive player that views all base pairs similarly and selects them based on common features.

FOOTNOTES

See referenced article, J. Biol. Chem. 2007, 282, 28884-28892

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