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Enzymatic capture of an extrahelical thymine in the search for uracil in DNA

Author

Listed:
  • Jared B. Parker

    (Departments of Pharmacology and Molecular Sciences and,)

  • Mario A. Bianchet

    (Biophysics and Biophysical Chemistry of the Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA)

  • Daniel J. Krosky

    (Departments of Pharmacology and Molecular Sciences and,)

  • Joshua I. Friedman

    (Departments of Pharmacology and Molecular Sciences and,)

  • L. Mario Amzel

    (Biophysics and Biophysical Chemistry of the Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA)

  • James T. Stivers

    (Departments of Pharmacology and Molecular Sciences and,)

Abstract

The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U•A pairs arising from incorporation of dUTP in DNA, and for increasing immunoglobulin gene diversity during the acquired immune response. A central event in all of these UNG-mediated processes is the singling out of rare U•A or U•G base pairs in a background of approximately 109 T•A or C•G base pairs in the human genome. Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T•A and U•A base pairs and not by active participation of the enzyme. Thus, base-pair dynamics has a critical role in the genome-wide search for uracil, and may be involved in initial damage recognition by other DNA repair glycosylases.

Suggested Citation

  • Jared B. Parker & Mario A. Bianchet & Daniel J. Krosky & Joshua I. Friedman & L. Mario Amzel & James T. Stivers, 2007. "Enzymatic capture of an extrahelical thymine in the search for uracil in DNA," Nature, Nature, vol. 449(7161), pages 433-437, September.
    • Handle: RePEc:nat:nature:v:449:y:2007:i:7161:d:10.1038_nature06131
    DOI: 10.1038/nature06131
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    Cited by:

    1. Zoe M. Wright & Kevin John Butay & Juno M. Krahn & Isha M. Wilson & Scott A. Gabel & Eugene F. DeRose & Israa S. Hissein & Jason G. Williams & Mario J. Borgnia & Meredith N. Frazier & Geoffrey A. Muel, 2025. "Spontaneous base flipping helps drive Nsp15’s preferences in double stranded RNA substrates," Nature Communications, Nature, vol. 16(1), pages 1-14, December.

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