Nature 349, 175 - 178 (10 January 1991); doi:10.1038/349175a0

Base sequence discrimination by zinc-finger DNA-binding domains

Jeannette Nardelli^*, Toby J. Gibson^†, Christine Vesque^* & Patrick Charnay^*

^*Laboratoire de Génétique Moléculaire, CNRS D 1302, École Normale Supérieure, 46, rue d'Ulm, F-75230 Paris Cedex 05, France
^†European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 10-2209, D-6900 Heidelberg, Germany

ZINC fingers^1,2 constitute important eukaryotic DNA-binding domains, being present in many transcription factors^3–5. The Cys₂/His₂zinc-finger class has conserved motifs of 28–30 amino acids which are usually present as tandem repeats^1,2. The structure of a Cys₂/His₂ zinc finger has been determined by nuclear magnetic resonance⁶, but details of its interaction with DNA were not established. Here we identify amino acids governing DNA-binding specificity using in vitro directed mutagenesis guided by similarities between the zinc fingers of transcription factors Spl (ref. 7) and Krox-20 (ref. 8). Krox-20 is a serum-inducible transcription activator^8,9 which is possibly involved in the regulation of hindbrain development¹⁰; it contains three zinc fingers similar to those of Spl (refs 7, 8, 11) and binds to a 9-base-pair target sequence which is related to that of Spl (ref. 9). Our results show that each finger spans three nucleotides and indicate two positions in Krox-20 zinc fingers that are important for base-pair selectivity. Modelling with molecular graphics suggests that these residues could bind directly with the bases and that other amino acid–base contacts are also possible.

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