DNA binding of peptides derived from natural products or proteins and bending of DNA double strands

Two different DNA binding peptides were investigated with the intention to obtain new and selective molecules for DNA recognition. The first class of peptides is derived from the natural product and DNA bisintercalator triostin A. Two quinoxaline chromophores are well preorganized for bisintercalation by a rigid bicyclic depsipeptide backbone. Within this study the chromophores and the backbone were modified in order to provide possible major groove binders or a diagnostic tool for abasic sites next to bisintercalation. The second peptide construct was derived from an IHF-protein/DNA co-crystal structure with a 180 degrees bent of the double stranded DNA. A lysine dendrimer (non specific charge interaction) was linked via a glycine oligomer to a cyclopeptide (specific minor groove recognition) in order to mimic the function of IHF. Specific binding to double stranded DNA was indicated and also slight bending seems likely.