G-quadruplex and i-motif DNA structures form in the promoter of the key innate immune adaptor MYD88.

Innate immune responses rely on a critical adaptor protein, MYD88, to bridge extracellular inflammatory signals and transcription factor networks inside the cell. Dysregulation of MYD88 is associated with immunodeficiencies, autoimmunity, and cancer. Here, we identify a stretch of guanine/cytosine-rich DNA in the MYD88 promoter capable of adopting stable G-quadruplex and i-Motif structures. Molecular characterization of the i-motif reveals a unique folding pattern with asymmetric lateral loop sizes, a transition pH in line with previously documented i-motifs, and in vitro recognition by the chromatin insulator/transcription factor (CTCF). In exploring the transcriptional role and therapeutic potential of the MYD88 structures, we show the known G-quadruplex ligand, TMPyP4, destabilizes the i-motif, stabilizes the G-quadruplex, and promotes MYD88 expression. A ligand, 33353, from the National Cancer Institute (NCI) Diversity Set, also differentially interacts with the two structures yet represses MYD88. This work discovers DNA structures in MYD88 that can be pharmacologically leveraged for their ability to control gene expression.