FIGURE 3.

Comparison between computed and experimentally derived cleavage barriers for nucleotides from three different motifs. Correlation between computed ΔG^‡ barriers (with specific color for each motif) and barriers derived from experiments (black, pseudo free energies, see Materials and Methods for details) for nucleotides from uGAAAg tetraloop (A), GC-duplex (B), and cUUCGg tetraloop (C). Both computed and experimentally derived ΔG^‡ barriers are displayed as deviations from the corresponding median value. Note that in-line probing data for a uniform GC-duplex are not available, but equivalent G–C base pairs are expected to have similar ΔG^‡ barriers (deviations from the median are set to zero in the figure). Unpaired nucleotides from tetraloops are underlined (see Supplemental Fig. S1 for nucleotide labeling).