We have designed and synthesized a set of peptides-based amphiphiles that are capable of dynamic folding and self-assembly for the selective separation and quantification of charged macromolecules. Our approach is to rationally design peptides that are dependent on configurational fluctuations and binding to form a well-ordered state. This process has been coined fishing because the fluctuating linear chain is facilitating the capture and separation of target molecules. The dynamic nature of our designed peptides contradicts 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 is often used to define the thermodynamics and kinetics of biological processes, but the model underestimates nature's versatility. Our goal is to capitalize on structural transitions to develop bio-mimetic molecules that can actively respond to the environment. The engineering of natively disordered proteins is accomplished by judiciously manipulating the topography of the folding energy landscape to control nanostructure. Peptide design is directed towards charged systems such as DNA, where careful design can influence nucleotide sequence specificity and promote interfacial separation.