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We are referring to the 2′-deoxynucleotides in the various base-pairs with a single- or two-letter abbreviation. For example, A = 2′-deoxyadenosine and Z = 2′-deoxyturbercidin.
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We assume that the conditions of the hydroxyl radical footprinting provide the base for cleavage at the abasic site generated by MutY. The band with retarded mobility with respect to the position of the "A" results from incomplete base treatment, since these conditions are not as basic as used in the MutY assay to visualize the glycosylase activity.
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