Mechanics of DNA Flexibility Visualized by Selective 2′-Amine Acylation at Nucleotide Bulges

We used selective acylation of 2′-amine-substituted nucleotides to visualize local backbone conformations that occur preferentially at bulged sites in DNA duplexes. 2′-Amine acylation reports local nucleotide flexibility because unconstrained 2′-amino nucleotides more readily reach a reactive conformation in which the amide-forming transition state is stabilized by interactions between the amine nucleophile and the adjacent 3′-phosphodiester group. Bulged 2′-amine-substituted cytidine nucleotides react ∼20-fold more rapidly than nucleotides constrained by base-pairing at 35 °C. In contrast, base-paired 2′-amine-substituted nucleotides flanked by a 5′ or 3′ bulge react two- or six-fold more rapidly, respectively, than the perfectly paired duplex. The relative lack of 2′-amine reactivity for nucleotides adjacent to a DNA bulge emphasizes, first, that structural perturbations do not extend significantly into the flanking duplex structure. Second, the exquisite sensitivity towards very local perturbations in nucleic acid structure suggests that 2′-amine acylation can be used to chemically interrogate deletion mutations in DNA. Finally, these data support the mechanical interpretation that the reactive ribose conformation for 2′-amine acylation requires that the base lies out of the helix and in the major groove, a mechanistic insight useful for designing 2′-amine-based sensors.