DNA Structural Selectivity of Binding by the Pol I DNA Polymerases from Escherichia coli and Thermus aquaticus

• Main Author: Wowor, Andy James Budiman
• Other Authors: LiCata, Vince J.
• Format: Others
• Language: en
• Published: LSU 2009
• Subjects: Biochemistry (Biological Sciences)
• Online Access: http://etd.lsu.edu/docs/available/etd-11112009-121622/

Understanding the thermodynamics of substrate selection by DNA Polymerase I is important for characterizing the balance between replication and repair for this enzyme <I>in vivo</I>. Due to their sequence and structural similarities, Klenow and Klentaq, the large fragments of the Pol I DNA polymerases from <I>Escherichia coli</I> and <I>Thermus aquaticus</I>, are considered functional homologues. Klentaq, however, does not have a functional proofreading site. Examination of the DNA binding thermodynamics of Klenow and Klentaq to different DNA structures: single-stranded DNA (ss-DNA), primer-template DNA (pt-DNA), and blunt-end double-stranded DNA (ds-DNA) show that the binding selectivity pattern is similar when examined across a wide range of salt concentration, but can differ significantly at any individual salt concentration. For both proteins, binding of ss-DNA shifts from weakest to tightest binding of the three structures as the salt concentration increases. Both Klenow and Klentaq release 2-3 more ions when binding to pt-DNA and ds-DNA than when binding to ss-DNA. Both of these non-sequence specific binding proteins exhibit relatively large heat capacity changes (ΔC_p) upon DNA binding, however, Klenow exhibits significant differences in the ΔC_p of binding to pt-DNA versus ds-DNA, while Klentaq does not, suggesting that Klenow and Klentaq discriminate between these two structures differently. Taken together, the ΔG, ΔC_p, and salt dependence patterns suggest that the two polymerases bind ds-DNA very differently, but that both bind pt-DNA and ss-DNA similarly, despite the absence of a proofreading site in Klentaq. Structural data from the electrophoretic mobility shift assay (EMSA) also support a striking difference between ds-DNA binding for Klenow and Klentaq. In EMSA, all ds-DNA/Klenow complexes show a time dependent shift from a slower to a faster moving complex while pt-DNA/Klenow complexes (both matched and mismatched) are found only in the fast moving complex. In contrast, all DNA/Klentaq complexes are observed in a slower moving complex only. Several potential molecular models for correlating the thermodynamics and the structural data are discussed. The thermodynamic differences among the different DNA structural preferences for the two polymerases suggest that the <I>in vivo</I> functions of these two largely homologous polymerases are somewhat different and respond differently to environmental conditions.