Distinct Phosphate Backbone Contacts Revealed by Some Mutant Peptides of Zinc Finger Protein Sp1: Effect of Protein-Induced Bending on DNA Recognition

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Abstract
By using some mutant peptides of transcription factor Sp1, phosphate backbone contacts with the DNA binding protein containing three zinc fingers have been investigated by alkylation interference, circular permutation, DNase I footprinting, and methylation protection methods. The ethylation interference analyses of Sp1(R565S) and Sp1(K595S) mutants demonstrate that arginine at 565 position and lysine at 595 position interact with the phosphate between G(3) and G(4) and with the phosphate between G(9) and G(10) in GC-box DNA, respectively. On the basis of the experimental results for Sp1(K535G), Sp1(537−623), and Sp1(530−623), lysine and glutamine at 535 and 536 positions have been clarified to be in contacts with phosphate between G(7) and G(8) and with phosphate outside GC-box, respectively. In particular, glutamine at the N-terminal side of zinc finger 1 is a key amino acid residue to induce DNA bending and also participates in total base specificity of Sp1. The present study strongly indicates that (1) each zinc finger is not independent for the DNA interaction with Sp1 and (2) DNA base recognition of the zinc finger protein is influenced by local conformational change of DNA induced by the protein binding.