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. Author manuscript; available in PMC: 2011 Mar 30.
Published in final edited form as: Biochemistry. 2010 Mar 30;49(12):2753–2762. doi: 10.1021/bi902200n

FIGURE 2. Double-mutant cycles for individual reaction steps.

FIGURE 2

Reactions for WT (EA261OH) or 2′-deoxy A261 (EA261H) ribozyme with AUCG or AUCI. AUCX represents either AUCG or AUCI. The numbers next to each arrow represent the functional effect (ΔΔG in kcal/mol) of either replacing the 2′-hydroxyl group of residue A261 with a 2′-H residue (horizontal arrows) or ablating the exocyclic amine of AUCG, by use of AUCI as the nucleophile (vertical arrows). Values of ΔΔΔGint are calculated by subtracting the value on the right from the value on the right or, equivalently, the value on the bottom from the value on the top. The individual reaction steps (defined in Scheme 2) are as follows: (A) nucleophile binding to the open complex; (B) nucleophile binding to the closed complex; (C) docking of the oligonucleotide substrate S with bound nucleophile; and (D) the chemical step. ΔΔG values are from the rate and equilibrium constants of Tables 2, 3, and 4, and were rounded to a single decimal place to take in account the experimental errors.