Structure of Aart, a Designed Six-finger Zinc Finger Peptide, Bound to DNA

David J. Segal, Justin W. Crotty, Mital S. Bhakta, Carlos F. Barbas, Nancy C. Horton

Research output: Contribution to journalArticlepeer-review

81 Scopus citations


Cys2-His2 zinc fingers are one of the most common types of DNA-binding domains. Modifications to zinc-finger binding specificity have recently enabled custom DNA-binding proteins to be designed to a wide array of target sequences. We present here a 1.96 Å structure of Aart, a designed six-zinc finger protein, bound to a consensus DNA target site. This is the first structure of a designed protein with six fingers, and was intended to provide insights into the unusual affinity and specificity characteristics of this protein. Most protein-DNA contacts were found to be consistent with expectations, while others were unanticipated or insufficient to explain specificity. Several were unexpectedly mediated by glycerol, water molecules or amino acid-base stacking interactions. These results challenge some conventional concepts of recognition, particularly the finding that triplets containing 5′A, C, or T are typically not specified by direct interaction with the amino acid in position 6 of the recognition helix.

Original languageEnglish (US)
Pages (from-to)405-421
Number of pages17
JournalJournal of Molecular Biology
Issue number2
StatePublished - Oct 20 2006


  • Aart
  • peptide
  • structure
  • zinc finger

ASJC Scopus subject areas

  • Molecular Biology
  • Biophysics
  • Structural Biology


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