Abstract
In nature, co-assembly of polypeptides, nucleic acids, and polysaccharides is used to create functional supramolecular structures. Here, we show that DNA nanostructures can be used to template interactions between peptides and to enable the quantification of multivalent interactions that would otherwise not be observable. Our functional building blocks are peptide–oligonucleotide conjugates comprising de novo designed dimeric coiled-coil peptides covalently linked to oligonucleotide tags. These conjugates are incorporated in megadalton DNA origami nanostructures and direct nanostructure association through peptide–peptide interactions. Free and bound nanostructures can be counted directly from electron micrographs, allowing estimation of the dissociation constants of the peptides linking them. Results for a single peptide–peptide interaction are consistent with the measured solution-phase free energy; DNA nanostructures displaying multiple peptides allow the effects of polyvalency to be probed. This use of DNA nanostructures as identifiers allows the binding strengths of homo- and heterodimeric peptide combinations to be measured in a single experiment and gives access to dissociation constants that are too low to be quantified by conventional techniques. The work also demonstrates that hybrid biomolecules can be programmed to achieve spatial organization of complex synthetic biomolecular assemblies.
Highlights
N atural biological molecules lipids, nucleic acids, peptides, proteins, and polysaccharides fold, assemble, and co-assemble to form a stunning variety of functional three-dimensional structures and complexes
The simplest previously reported coiled-coil heterodimers have glutamic acid (Glu) at all “e” and “g” sites in one peptide and lysine (Lys) at these sites in the complementary peptide.[35−37,41] we confirmed that the basic peptide binds nonspecifically and tightly to DNA, consistent with strong electrostatic interactions, making it unsuitable for use in composite peptide−DNA nanostructures
We have shown that DNA origami nanostructures can be used to template and quantify the assembly of de novo designed peptides
Summary
N atural biological molecules lipids, nucleic acids, peptides, proteins, and polysaccharides fold, assemble, and co-assemble to form a stunning variety of functional three-dimensional structures and complexes. With the peptides linked via the same ends that is, both C-termini, consistent with parallel helix formation the resulting conjugate was highly helical, thermally stable, and monomeric (SI Figures S2 and S3, Tables S2 and S3).
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