Tramtrack protein-DNA interactions - A cross-linking study

Interaction of the Tramtrack protein from Drosophila melanogaster with DNA was analyzed by a cross-linking method. Tramtrack, residues cross-linkable to the partially, depurinated DNA were identified by direct sequencing. The N-terminal alpha -amino group of the protein DNA-binding domain was found to be the major product of cross-linking. The location of the N terminus on the DNA was determined by identification of the DNA bases that were cross-linked to the protein cy-amino group. We conclude that accessory N-terminal peptide preceding the first zinc finger of Tramtrack directly interacts with DNA, both in specific and nonspecific DNA-protein complexes. Our finding explains the role in the protein binding of the DNA bases outside of the direct interaction with the zinc fingers.