An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces

Anton V. Persikov, Mona Singh

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


Cys2His2 zinc finger (C2H2-ZF) proteins comprise the largest class of eukaryotic transcription factors. The 'canonical model' for C2H2-ZF protein-DNA interaction consists of only four amino acid-nucleotide contacts per zinc finger domain, and this model has been the basis for several efforts for computationally predicting and experimentally designing protein-DNA interfaces. Here, we perform a systematic analysis of structural and experimental binding data and find that, in addition to the canonical contacts, several other amino acid and base pair combinations frequently play a role in C2H2-ZF protein-DNA binding. We suggest an expansion of the canonical C2H2-ZF model to include one to three additional contacts, and show that computational approaches including these additional contacts improve predictions of DNA targets of zinc finger proteins.

Original languageEnglish (US)
Article number035010
JournalPhysical Biology
Issue number3
StatePublished - Jun 2011

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biophysics
  • Structural Biology
  • Cell Biology


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