Figure 6.

Correlations between physical features and persistence lengths of base-substituted DNA molecules. Linear correlations with P (measured by cyclization) appear for T_m difference from natural DNA (A), base stacking ΔΔG difference (substituted base minus corresponding natural base) (B), and change in van der Waals volume of groove (51) normalized per residue (C) for diaminopurine- and inosine-substituted DNA. Similar correlations exist from analysis by AFM and optical tweezers. Importantly, these correlations vanish when seven thymine variants (data points numbered 1–7, corresponding to Fig. 7) are included in the analysis. Data for these additional variants were taken from Peters et al. (22); base stacking data were not collected for thymine variants 3, 4, and 7. Uncertainty in P_cyclization is smaller than the symbol size. (D) Thymine variants do not display linear trends in P_AFM; uncertainty is indicated by error bars.