The Autographa californica nucleopolyhedrovirus IE-1 protein complex has two modes of specific DNA binding.

Missing contact footprinting with formic acid as a modifying reagent was used to examine specific IE-1 binding contacts to double-stranded oligonucleotides that contained either a consensus hr repeat sequence or a sequence from the pe38 promoter, which is down regulated by IE-1. The hr repeat sequences contain two consensus IE-1 binding motifs (IBMs) flanking a central EcoRI site that are oriented in opposite directions with respect to each other. IE-1 was found to contact regions including both IBMs. The bases footprinted in the top strand included the left IBM (IBM-A), whereas bases in the bottom strand were footprinted in a region that included IBM-B and part of IBM-A. When substitution mutations were introduced into either IBM, bases on both strands of the remaining IBM were strongly footprinted. As with the hr IBM-mutant constructs, bases footprinted in the pe38 promoter construct included both strands of the single IBM.