Figure 2: Sequence- and position-dependent thermodynamic and kinetic parameters describing the Watson–Crick to Hoogsteen transition.

(a) Free-energy difference (ΔG_WC−HG) and (b) forward free-energy barrier (ΔG^‡_WC−HG) for the Watson–Crick to Hoogsteen transition as derived from a two-state analysis of the R_1ρ data. Error bars represent experimental uncertainty (one s.d.) estimated from propagation of errors from monoexponential fitting of duplicate R_1ρ data and analysis of signal-to-noise. Average and standard deviations for dinucleotide steps are shown using white bars. Horizontal lines denote bps with same triplet sequence and positions relative to nearest terminal end. X axis labels denote the triple sequence context (‘XYZ’) with Hoogsteen base pair in the middle; the position relative to the closest terminal end (‘−n’), and name of duplex as denoted in Fig. 1b. Correlation between (c) ΔG^‡_WC−HG and ΔG_WC−HG as well as (d) ΔG^‡_HG−WC and ΔG_WC−HG. A·T and G·C⁺ base pairs are shown in red and blue, respectively. The best line of fit and corresponding Pearson coefficient (R) are shown. (e) Free-energy diagram of the Watson–Crick to Hoogsteen transition depicting relative variations in free energy of Watson–Crick, transition and Hoogsteen states.