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For a pictorial explanation of alkaline footprint interpretation for the 5′- and 3′-labeled samples, see Supporting Information.
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For a pictorial explanation of alkaline footprint interpretation for the 5′- and 3′-labeled samples, see Supporting Information.
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Polynucleotide kinase treatment ensures the 5′-phosphorylation and 3′-dephosphorylation of all fragments. See Supporting Information for a comparison of base versus aniline catalyzed cleavage mechanisms and products.
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Polynucleotide kinase treatment ensures the 5′-phosphorylation and 3′-dephosphorylation of all fragments. See Supporting Information for a comparison of base versus aniline catalyzed cleavage mechanisms and products.
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Initial rates were quantified in order to avoid complications due to hydrolysis of the bromoacetamide-substrate analogue at longer time points required to observe completion of the alkylation reaction
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An important caveat must be entertained: the affinity label may perturb the hairpin ribozyme active site structure such that apparent pK a of G8 is increased relative to its pKa in the presence of native substrate. Moreover, the 2′-bromoacetamide substrate analogue is not, by definition, a mechanism based inhibitor in that its reactivity is not unmasked as a result of the catalytic mechanism. The positioning of the reactive electrophile where substrate deprotonation normally occurs encourages a mechanistic interpretation for ribozyme alkylation, especially where the alkylation rate shows log-linear increase with pH, as for hammerhead G12 alkylation. Caution must be exercised, however, as the high reactivity of the probe may lead to alkylations that reflect only fortuitous structural positioning, not the involvement of a particular residue in general base catalysis. This is exemplified by the apparently pH-independent alkylations of A6, C7, G8
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