Transcription factors (TFs) have a remarkable role in the homeostasis of the organisms and there is a growing interest in how they recognize and interact with specific DNA sequences. TFs recognize
DNA using a variety of structural motifs. Among those, the ribbon-helix-helix (RHH)
proteins, exemplified by the MetJ and
ARC repressors, form dimers that insert antiparallel β-sheets into the major groove of
DNA. A great chemical challenge consists of using the principles of
DNA recognition by TFs to design minimized
peptides that maintain the
DNA affinity and specificity characteristics of the natural counterparts. In this context, a
peptide mimic of an antiparallel β-sheet is very attractive since it can be obtained by a single
peptide chain folding in a β-hairpin structure and can be as short as 14
amino acids or less. Herein, we designed eight linear and two cyclic dodeca-
peptides endowed with β-hairpins. Their
DNA binding properties have been investigated using fluorescence spectroscopy together with the conformational analysis through circular dichroism and
solution NMR. We found that one of our
peptides,
peptide 6, is able to bind
DNA, albeit without sequence selectivity. Notably, it shows a topological selectivity for the major groove of the
DNA which is the interaction site of
ARC and many other
DNA-binding proteins. Moreover, we found that a type I' β-hairpin folding pattern is a favorite
peptide structure for interaction with the
B-DNA major groove.
Peptide 6 is a valuable lead compound for the development of novel analogs with sequence selectivity.