Protein Engineering, Vol. 14, No. 8, 591-599,
August 2001
© 2001 Oxford University Press
Modular construction of extended DNA recognition surfaces: mutant DNA-binding domains of the 434 repressor as building blocks
1 Present address: Institute of Botany, Chinese Academy of Sciences, Xiang Shan, Hai Dian Qu, Bejing 100093, China 2 Present address: Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano 99, I-34012 Trieste, Italy
Single-chain derivatives of the 434 repressor containing one wild-type and one mutant DNA-binding domain recognize the general operator ACAA–6 base pairs–NNNN, where the ACAA operator subsite is contacted by the wild-type and the NNNN tetramer by the mutant domain. The DNA-binding specificities of several single-chain mutants were studied in detail and the optimal subsites of the mutant domains were determined. The characterized mutant domains were used as building units to obtain homo- and heterodimeric single-chain derivatives. The DNA-binding properties of these domain-shuffled derivatives were tested with a series of designed operators of NNNN–6 base pairs–NNNN type. It was found that the binding specificities of the mutant domains were generally maintained in the new environments and the binding affinities for the optimal DNA ligands were high (with Kd values in the range of 10–11–10–10 M). Considering that only certain sequence motifs in place of the six base pair spacer can support optimal contacts between the mutant domains and their subsites, the single-chain 434 repressor mutants are highly specific for a limited subset of 14 base pair long DNA targets.