Protein-nucleic acid interactions are essential in a multitude of biological processes. Protein interactions with single-stranded DNA are particularly important in DNA replication, repair, and telomere regulation. Previously, our laboratory had designed a β-hairpin dimer, (WKWK)2 which binds ssDNA with a Kd of 3 μM and dsDNA with a Kd of 5 μM. These results later led to the redesign of a β-sheet peptide from a native protein which displayed 10-fold selectivity for dsDNA but overall lower affinity for ssDNA at a Kd of 20 μM. In this work, with the insight gained from these studies, a third de novo β-sheet was designed, S123. This new system was found to bind ssDNA with a dissociation constant of 170 nM. Several derivatives were investigated to determine the origins of the marked improvement in binding affinity. It was found that high β-sheet structure was necessary to achieve the observed nanomolar affinity of S123 to ssDNA. In another study, the use of the copper(I)-assisted azide-alkyne cycloaddition as a method of β-hairpin stabilization was investigated at several different positions. It was determined that the CuAAC reaction was a suitable method for locking in β-hairpin structure in peptides possessing the type I' turn, VNGO and the type II' turn, VpGO. All cyclic variants exhibited improved thermal stability and resistance to proteolysis as compared to the non-cyclic peptides. Additionally, the function of the CuAAC cyclized peptides was not altered as exhibited by similar binding affinities for ATP as the WKWK peptide. These studies provided a comprehensive method for CuAAC cyclization of β-hairpin peptides, which could further be utilized in the inhibition of protein-protein interactions.Doctor of Philosoph
