Figure 1.

(A) Hairpin Py-Im polyamide recognition of the DNA minor groove. Aromatic amino acid ring pairs recognize distinct DNA base pairs. Complete structures for each hairpin polyamide-biotin conjugate used can be found in Supporting Information. (B) Scheme for Bind-n-Seq analysis of DNA binding polyamides. Double-stranded DNA containing a degenerate, 21-bp segment is enriched, purified, and analyzed via high-throughput sequencing. Commonly bound DNA consensus sequences are identified via motif searching.