A new strategy to determine the target DNA sequence of a short peptide.

The design of molecules that target desired DNA sequences has been one of the major challenges in the field of molecular recognition. We report here a general strategy for defining the sequence-preference of DNA-binding short peptide by using its heterodimer. Our method successfully identified specific sequences of short peptides derived from native DNA-binding proteins. The usefulness of this approach has been demonstrated by identifying preferred DNA targets for a peptide composed only of D-amino acids.