Protein−DNA binding in the absence of specific base-pair recognition

Significance Understanding molecular mechanisms of how regulatory proteins, called transcription factors (TFs), recognize their specific binding sites encoded into genomic DNA represents one of the central, long-standing problems of molecular biophysics. Strikingly, our experiments demonstrate that DNA context characterized by certain repeat symmetries surrounding specific TF binding sites significantly influences binding specificity. We expect that our results will significantly impact the understanding of molecular, biophysical principles of transcriptional regulation, and significantly improve our ability to predict how variations in DNA sequences, i.e., mutations or polymorphisms, and protein concentrations influence gene expression programs in living cells. Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)−DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF−DNA binding preferences. We used high-throughput protein−DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying repeat symmetries. Based on statistical mechanics modeling, we identify a new protein−DNA binding mechanism induced by DNA sequence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed governs protein−DNA binding preferences.