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Phys Biol. 2011 Jun;8(3):035010. doi: 10.1088/1478-3975/8/3/035010. Epub 2011 May 13.

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

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Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ, USA.


Cys(2)His(2) 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.

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