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Letter
Nature Structural Biology  5, 104 - 109 (1998)
doi:10.1038/nsb0298-104

Structural basis for Gfilled circleC recognition in the DNA minor groove

Clara L. Kielkopf1, Eldon E. Baird2, Peter B. Dervan2, 4 & Douglas C. Rees2, 3

  1Division of Biology, California Institute of Technology.

  2Division of Chemistry and Chemical Engineering, California Institute of Technology.

  3The Howard Hughes Medical Institute, Pasadena, California 91125, USA. email: rees@dtray.caltech.edu

  4email: dervan@cco.caltech.edu

Small molecules that target specific DNA sequences offer a potentially general approach for the regulation of gene expression. Pyrrole−imidazole polyamides represent the only class of synthetic small molecules that can bind predetermined DNA sequences with affinities and specificities comparable to DNA binding proteins. Antiparallel side-by-side pairings of two aromatic amino acids, imidazole (Im) and pyrrole (Py), distinguish GC from CG, and both from AT/TA base pairs. A high resolution X-ray crystal structure of a four-ring pyrrole−imidazole polyamide specifically bound as a dimer to a six-base pair predetermined DNA site reveals a structural framework of hydrogen bonds and interactions with the walls of the minor groove that underlies the pairing rules for DNA recognition.


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Nature Structural & Molecular Biology
ISSN: 1545-9993
EISSN: 1545-9985
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