Binding properties of the artificial zinc fingers coding gene Sint1

On the basis of the recognition "code" that suggests specific rules between zinc finger's primary structure and the finger's potential DNA binding sit es, we have constructed a new three-zinc finger coding gene to target the n ine base pair DNA sequence: 5'-TGG-ATG-GAC-3'. This artificial gene named " Sint1" belongs to the Cys(2)-His(2) zinc finger type. The amino acid positi ons, crucial for DNA binding, have been specifically chosen on the basis of the amino acid/base contacts more frequently represented in the available list of the proposed recognition "code". Here we demonstrate that Sint1 pro tein binds specifically the double strand "code" DNA target, with a dissoci ation constant (Kd) comparable to the Kd of the well known Zif268 protein. Sint1 "code" deduced and the "experimental" selected DNA binding sites shar e five nucleotide positions. Interestingly, Sint1 shows both high affinity and specificity toward the single strand "code" DNA binding site, with a Kd comparable to the corresponding double strand DNA target. Moreover, we pro ve that Sint1 is able to bind RNA similarly to several natural zinc finger proteins. (C) 1998 Academic Press.