Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures

Abstract

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with unique DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer-long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of structures through multiple routes: one-pot assembly, formation of dimers and trimers and an alternating copolymer of two different origami structures, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

Coarse-grained nucleic acid–protein model for hybrid nanotechnology

“…We model the two bioconjugate linkers, LC-SPDP and DBCO-triazole, (Fig. 5), that are typically used in protein-DNA hybrid nanotechnology 54,55 using a spring potential as defined in eqn ( 7) with parameters k and r 0 parameterized to mimic the end-to-end average distance and standard deviation of each linker at temperature 300 K. LC-SPDP links the thiol group of a modified cysteine residue to an amine-modified nucleotide. DBCO-trizaole is the product of a copper-free click reaction involving a DBCO-modified residue to link to an azide-modified nucleotide.…”

Multivalency Pattern Recognition to Sort Colloidal Assemblies

“…[ 15 ] Recently, we introduced host/guest complexation to 3D DNA origami NPs as non‐DNA interaction for higher level SA, making use of strong multivalency effects, [ 16 ] and others have reported the use of coiled‐coil peptide motifs. [ 17 ]…”

Reversible Control of Gelatin Hydrogel Stiffness by Using DNA Crosslinkers**

“…This handle would in turn allow for dynamic control of a model ligand (in this case the fluorophore Cy3) tethered to the complementary strand (Figure 4). Following hydrogel formation as described previously, we appended a second handle to the GelMA by functionalizing free amine residues with azides (via an NHS‐PEG4‐azide linker) and then coupling them to dibenzocyclooctyne (DBCO)‐DNA strand via copper‐free click chemistry (Figure 4A, B) [41] . Gels with both DNA strands and fluorophores showed both red and green fluorescence (Figure 4C, sample (a) ).…”

“…Following hydrogel formation as described previously, we appended a second handle to the GelMA by functionalizing free amine residues with azides (via an NHS-PEG4-azide linker) and then coupling them to dibenzocyclooctyne (DBCO)-DNA strand via copper-free click chemistry (Figure 4A, B). [41] Gels with both DNA strands and fluorophores showed both red and green fluorescence (Figure 4C, sample (a)). Adding a displacement strand for the Cy3 ligand effectively removed the red fluorophore, while leaving the green one intact (Figure 4C, sample (b)).…”