DNA complexes obtained with the integron integrase Intl1 at the attl1 site

Integrons are genetic elements that are able to capture genes by a site-specific recombination mechanism. Integrons contain a gene coding for a lambda -like integrase that carries out site-specific recombination by interacting with two different target sites; the attl site and the palindromic sequence attC (59 base element). Cassette integrations usually involve the attl site, while cassette excisions use attC. Therefore, the integrase should bind both sites to cleave DNA and perform site-specific recombination reactions. We have used purified maltose-binding protein fused with the integrase (MBP-Intl1) and native Intl1 protein and gel retardation assays with fragments containing the complete and partial attl1 site to show formation of four complexes in this region. Chemical modification of specific nucleotides within the attl1 site was used to investigate their interference with binding of the integrase protein. We attribute Intl1 specific binding to four regions in the attl1 site and a GTTA consensus sequence is found in three of the four regions. Interference by modified guanine and thymine residues in the DNA major groove and adenine residues in the minor groove were observed, indicating that the integrase interacts with both sides of the helix. Binding of Intl1 to attC is also discussed.