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Free energy effects of major groove substitutions for each DNA substrate. The ΔΔG = ΔGsub - ΔGunsub values for each DNA are defined in eqs 3-5. Free energy effects of the (A) N5N3, (B) H5H3, and (C) N5N4 substitutions for substrates with 32, 24 and 18 nucleotide scissile strands are shown. We note that changes in the activation barrier (ES → ES‡) arising from each modification may be gleaned by simply adding the bar heights corresponding to ES and ES‡.
