The cytotoxic alpha anomer of adenosine, generated in situ, must be recognized and repaired to maintain genomic stability. Endonuclease IV is a member of the base excision repair (BER) enzyme family that acts on abasic sites but also has the auxiliary function of removing the alpha anomeric adenosine. We have employed enzymatic, thermodynamic, and structural studies on DNA duplexes containing a central alpha-anomeric adenosine to investigate the role of the DNA structure on recognition and catalysis by Endo IV. The NMR solution structure of a DNA decamer duplex establishes that the single alpha-anomeric adenosine is intrahelical and stacks in a reverse Watson-Crick fashion. However, its presence confers significant changes to the global duplex conformation. This results from a kink of the helical axis into the major groove and an opening of the minor groove emanating from the alpha-anomeric site. The helical kink has been confirmed from residual dipolar coupling data for obtained at natural 13C abundance. The global structural changes caused by this lesion place the DNA along the conformational path leading to the DNA structure observed in the complex. Thus, the alpha-anomeric lesion directly facilitates recognition by its repair enzyme.
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