FIGURE 9.

Proposed mechanism for substrate binding with the help of G/T-rich DNA P2 oligo extensions. (A) Secondary structure of the polymerase ribozyme Pol1e (black) with the proposed interaction between the P2 oligo (blue) and the single-stranded portion of the primer/template (green). The example uses template T50c and the P2 oligo 5′-GGCGCC-ext 3. See the legend of Figure 1 for more details. (B) Correlation between the predicted base-pairing stability and polymerization efficiency. The base-pairing stabilities between the P2 oligo 3′-extensions and the single-stranded portions of the primer/templates were estimated by the UNAfold algorithm. All 23 P2 oligos with 60% G and 40% T in their 3′-extension were used. Template T21 (open circles) resulted in a high polymerization efficiency with weak template/P2 oligo interactions, presumably because T21 interacts directly with the polymerase ribozyme. The linear regression was fitted to the values of templates T50a (blue circles), T50b (red triangles), and T50c (green squares). The linear regression coefficients r are shown, together with p, which describes the likelihood that no correlation exists. For the three templates combined, the linear regression coefficient was −0.575 (p < 0.0001).