Binding of the herpes simplex virus major regulatory protein to viral DNA

Infected-cell protein 4 (ICP4), the major regulatory protein specified by herpes simplex virus 1 in infected cells, binds to homologs of the sequence ATCGTCnnnnYCGRC (A sites, where n is any nucleotide, Y is a pyrimidine, and R is a purine) and to unrelated sequences for which no consensus sequence has been derived (B sites). We have examined the binding of ICP4 to each of two A and two B binding sites by using Fab fragments of a monoclonal antibody that is reactive with an epitope located at the N terminus of ICP4 and that decreases the mobility of ICP4-DNA complexes in non-denaturing gels. The results indicate that each type of site binds two monomers of ICP4. Methylation-interference studies on the type B sites mapped the guanines whose methylation interfered with the binding of ICP4. The methylation-interference pattern obtained with one of the B sites was similar to that obtained on an A site but differed from that of the other B site. The ability of ICP4 to bind to DNA fragments containing the binding site appears to be dependent on length and on the proximity of the binding site to the fragment end. Short DNA fragments did not form stable complexes with ICP4 even though they contained all of the purines whose methylation interfered with the binding of the regulatory protein.