**1. Introduction**

Sox2 regulates a remarkable variety of genes differentially; it activates some and represses others [1–3]. This functional diversity is assumed to be mediated by Sox2 heterodimerization with other transcription factors (TFs) such as Oct4, Oct1, Pax6, and Nanog [4,5]. Recent reports, however, suggest that these canonical partners often remain spatiotemporally separated from Sox2 during genome engagement [6–10]. This raises an important question regarding the TF's mechanism of action as to how Sox2 alone can exert differential loci-specific regulatory effects.

Sox2 is a sequence-specific high-mobility group transcription factor (HMG-TF) [11]. These TFs have conserved DNA binding domains [12,13], also known as HMG box. These DNA binding domains are partly disordered and are assumed to undergo binding-induced functional disorder-to-order transitions [14]. HMG-TFs are known to cooperatively form heterodimers on DNA regulatory elements [13,15–17]; each heteromeric TF pair induces characteristic DNA bend and differentially regulates target gene transcription [18–20]. Interestingly, a number of recent studies suggested that Sox2 can also function as homodimers [21–23]. Whether and how such Sox2 assemblies alter DNA conformations remain largely unknown. Here, we utilize the strengths of single-molecule Förster/fluorescence resonance energy transfer (smFRET) measurements along with ensemble methods to understand the effects of Sox2 binding on regulatory DNA structural landscape in the context of the HMG box (Sox2HMG). Our results suggest that Sox2HMG induces stoichiometry-dependent alternate DNA bends and we propose that the resulting alternate DNA conformations may drive different transcriptional outcomes.
