Synthetic Nucleotides as Probes of DNA Polymerase Specificity

Figure 1

Comparison of the overall folds of (a) a replicative DNA polymerase, Bacillus stearothermophilus DNA pol I [30], and (b) a Y family DNA polymerase, Sulfolobus solfataricus Dpo4 [31]. The respective thumb domains are shown in green, palm domains are in red, and fingers domains are in blue. The little finger domain unique to the Y family DNA polymerases is in purple [31]. The “vestigial” exonuclease domain of Bs pol I has been omitted for clarity [32]. (c) Polymerase catalyzed DNA replication (phosphoryl transfer) reaction. Polymerization of DNA occurs at a free 3′ hydroxyl group of the deoxyribose. Polymerases use a divalent magnesium ion (Me²⁺) to coordinate the negative charges of both the phosphate groups and the aspartic acid or glutamic acid in the active site of the polymerase [26].