Miniaturized HOXB13 Mimetics Are Sequence-Specific, Methyl-Sensitive DNA Binders

Homeobox protein Hox-B13 (HOXB13) is an oncogenic transcription factor that is associated with prostate cancer risk. Unlike most transcription factors (TFs), HOXB13 is a methyl-plus TF and has been shown to be preferentially recruited to DNA prostate cancer risk loci. Here, we miniaturized HOXB13 to create metal-stapled mimetics that can target its cognate primary DNA-binding site in a sequence-specific, methyl-sensitive manner. Targeted profiling of 5-methylcytosine (5mC) recognition using V269X mimetic mutants revealed that leucine can further enhance both methyl sensitivity and methyl specificity through methyl-methyl contact with 5mC and decreased methyl-pi interactions with cytosine. Collectively, our study revealed novel insights into the molecular interactions of HOXB13 with methylated DNA and new tools that will provide a structural basis for future development of a new class of sequence-specific methylated DNA binders.