DNA as a Molecular Ruler: Interrogation of a Tandem SH2 Domain with Self-Assembled, Bivalent DNA-Peptide Complexes

摘要

The recognition properties of DNA enable the sequence-programmed construction of defined DNA architectures by self-assembly. Chemically modified DNA molecules have been used to precisely control the spatial arrangement of chromophores, metals, nanoparticles, and proteins. The vast majority of studies have been concerned with the design of materials properties. Comparatively few studies have investigated the DNA-scaffolded arrangement of bioactive ligands for use in the life sciences. Among the notable examples are DNA-assembled glycoclusters and encoded self-assembled libraries. The aim was to mimic biological ligand display and/or to facilitate the drug-discovery process. Herein we present a new approach. We prepared self-assembled DNA-peptide complexes and explored whether the DNA-con-trolled presentation of peptides can be used to probe the structural properties of the cognate target protein. Specifically, we studied a protein-binding domain of the Syk kinase, a protein kinase that is involved in the regulation of lymphocyte activation. We demonstrate that important structural parameters, such as the preferred arrangement of protein-binding pockets and the flexibility of the connecting interdomain, can be assessed by using a set of DNA complexes. It is shown that the combination of single-stranded and double-stranded segments in self-assembled ternary complexes provides a convenient means to systematically vary the distance constraint as well as the flexibility of the ligand display.