Minor groove contacts are essential for an interaction of the human cytomegalovirus IE2 protein with its DNA target

The 86 kDa immediate early-2 protein (IE2, IE86) of human cytomegalovirus (HCMV) is a multifunctional polypeptide that can regulate gene expression both positively and negatively. In particular, it represses its own mRNA synthesis by binding directly to a sequence element, termed cis repression signal (CRS), that is located between the TATA box and the transcriptional start site of the major IE enhancer/promoter of HCMV. Here, we provide evidence that IE86, unlike most sequence-specific DNA-binding proteins, interacts primarily within the minor groove of the DNA helix. This was shown by hydroxyl radical and methylation interference assays. In addition, binding studies with inosine-substituted oligonucleotides which have an altered major groove morphology without changing the surface of the minor groove, confirmed the results obtained in interference analyses. This establishes IE86 as a member of a small group of DNA binding proteins that interact with A - T rich sequences within the minor groove and which also includes the TATA-box binding protein TBP. Remarkably, IE86 and TBP are able to bind simultaneously in an immediate vicinity at the major IE enhancer/promoter of HCMV. As minor groove binding proteins are known to bend DNA heavily this could contribute to the observed negative regulation of transcription by IE86.