Bacteriophage T4 DNA polymerase

Bacteriophage T4 DNA polymerase is a DNA polymerase associated with bacteriophage T4. It extends an existing paired strand end in the $5^{\prime }\to 3^{\prime }$ direction using a DNA template and deoxynucleoside triphosphates. A primer supplies the extendable end. The enzyme also has $3^{\prime }\to 5^{\prime }$ exonuclease activity, supporting DNA polymerase proofreading; the characterized enzyme lacks a $5^{\prime }\to 3^{\prime }$ exonuclease function.^[ref]

Extension and removal are competing chemical outcomes, not contradictory strand directions. A simplified kinetic example assigns rates $k_{\mathrm{ext}}$ and $k_{\mathrm{exo}}$ to two possible exits from one enzyme–strand-end state. If both exits have exponential waiting times, the probability that extension happens first isStipulated rates $100$ and $1{\mathrm{s}}^{-1}$ give $P_{\mathrm{ext}}\approx 0.990$; rates $0.1$ and $10{\mathrm{s}}^{-1}$ give approximately $0.0099$. These illustrative numbers show how slowing extension relative to removal can favor proofreading. They are not measured constants for this enzyme or a complete model of its active-site transitions.

The same protein also supplied a historical binding target. In their 1990 primary study, C. Tuerk and L. Gold selected RNA sequences that bound T4 DNA polymerase, finding distinct selected sequences with equivalent binding constants.^[ref] Measuring binding to a protein and measuring its catalytic DNA synthesis answer different experimental questions. The selected RNA is an aptamer; it is not itself the polymerase.