Genomic i-Motifs Display Diverse Binding Preferences Towards Small Molecules, Transcription Factors, and Antibodies

In this study, we have designed custom DNA microarray slides containing 10,976 distinct iM-forming sequences found in human promoters, centromeres, and telomeres, with varied lengths of cytosine repeats from two to ten bases and loops ranging from one to ten bases. We screen this array against a relevant small molecule, an antibody, and four endogenous transcription factors to elucidate differences in iM binding and recognition in the genome. Four identical custom Agilent 8X60K DNA i-motif arrays were screened against increasing concentrations of mitoxantrone, Cy5-labelled iMab monoclonal antibody, or GST-tagged hnRNP K. Additionally, we screened leftover blocks on the microarrays against GST-tagged hnRNP LL, hnRNP A1, and ASF/SF2 protein. Please note that, as Each array has 8 sectors/blocks (i.e. 8 samples hybridized on a single array), the raw outputs (directly from innoscan) have been modified as per sector/block corresponding to each sample.