Our goal is to develop a novel technology for robust and sequence specific DNA separation. The approach is based on the formation of a self-assembly composed of de novo designed amphiphilic peptides, where the specific binding results in secondary structure enhancement and self-assembled phase transformations. Peptides can be rationally designed with native configurational fluctuations, and this entropically favored state is only broken on binding to form a well-ordered state. This process has been coined fishing because the fluctuating linear chain is facilitating the capture and catalysis of target molecules. A common misconception that is prominent in our teaching of molecular biology is the paradigm that protein sequence (primary structure) defines a uniquely folded protein structure (tertiary structure) that, in turn, directly relates to the presentation of an active binding site. This paradigm has been frequently used to define the thermodynamics and kinetics of biological processes. Yet the model underestimates nature's versatility. This work describes the development of peptide-motifs where peptides can actively respond to specific sequences of DNA, resulting in enhanced amphiphilicity and self-assembly. The engineering of these natively disordered proteins is accomplished by judiciously manipulating the topography of the folding energy landscape to control actively assembly as a function of binding.