Ultrathin Silica Coating of DNA Origami Nanostructures

Abstract

The DNA origami technique has emerged as one of the most versatile bottom-up nanofabrication methods due to its ability to construct well-defined complex three-dimensional nanostructures and guide assembly of functional nanoscale objects with unprecedented precision, high yields, and controlled stoichiometry. Nonetheless, limited compatibility with biologically relevant fluids and typical solvents utilized in nanofabrication often restricts applications of DNA origami-based assemblies and devices. Here we present an approach for coating DNA origami structures with silica. By careful adjustment of experiment parameters, we achieved reproducible growth of ultrathin silica shell in solution without agglomeration or deformation of DNA origami structures. The silica-coated structures are stable in water and exhibit an increased resistivity to nuclease-mediated degradation. In addition, the coated structures preserve their structural integrity in polar organic solvents. We anticipate that our results will aid further advancement of DNA origami techniques as the nanofabrication method.

Nuclease resistance of DNA nanostructures

“…Simulations of a 2D DNA origami triangle with four or eight staple Peptoid Small protein-like polymer in which the side chains are attached to backbone nitrogen atoms, rather than to the α-carbons, as in peptides. These approaches include a coating formed through the complexation of human serum albumin (HSA) and DNA dendrites 120 (part a); coating nanostructures with dendritic DNA through hybridization to DNA handles 121 (part b); a PEGylated (where PEG is polyethylene glycol) lipid bilayer protective envelope 122 (part c); the charge-based accumulation of a poly ca tionic shell 123 (part d); an oligolysine-PEG coating 124 (part e); a coating formed through glutaraldehyde crosslinking of oligolysines 125 (part f); a bovine serum album (BSA)dendron block copolymer coating 127 (part g); a coating comprising DNA peptoids 128 (part h); and silica-based coatings 130 strands omitted from the structure, each resulting in a metastable assembly, revealed that the accessibility of the enzyme to the structure is dependent on the interconversion between these metastable states. This analysis showed that the reactivity of restriction enzymes is dependent on the steric overlap between the enzyme and the adjacent helices, thus, providing a route to designing nanostructures with higher or lower nuclease resistance.…”

“… Various protective coatings have been developed to increase the nuclease resistance of DNA nanostructures. These approaches include a coating formed through the complexation of human serum albumin (HSA) and DNA dendrites 120 (part a ); coating nanostructures with dendritic DNA through hybridization to DNA handles 121 (part b ); a PEGylated (where PEG is polyethylene glycol) lipid bilayer protective envelope 122 (part c ); the charge-based accumulation of a polycationic shell 123 (part d ); an oligolysine–PEG coating 124 (part e ); a coating formed through glutaraldehyde crosslinking of oligolysines 125 (part f ); a bovine serum album (BSA)–dendron block copolymer coating 127 (part g ); a coating comprising DNA peptoids 128 (part h ); and silica-based coatings 130 (part i ). APTES, (3-aminopropyl)triethoxysilane; DMTO, dimethoxytrityloxy; LPEI, linear polyethyleneimine; Nae, N -(2-aminoethyl)glycine; Nte, N -2-(2-(2-methoxyethoxy)ethoxy)ethylglycine; TEOS, tetraethyl orthosilicate; TMAPS, N -trimethoxysilylpropyl- N , N , N -trimethylammonium chloride.…”

“…To demonstrate the utility in biomedical applications, bovine serum albumin was encapsulated within the DNA octahedra, which protected the encapsulated protein from hydrolysis by trypsin. In another study, a solution-based method was used to coat 24-helix-bundle DNA origami nanostructures with a thin layer of silica 130 (Fig. 6i ).…”

Emission Manipulation by DNA Origami‐Assisted Plasmonic Nanoantennas

“…Nguyen et al recently showed that coating the DNA origami structures with an ultrathin layer of silica prevents the origamis from degradation and aggregation in otherwise lethal ionic solvents. [190,191] However, it was not clear if the structures were functional or modifiable after the coating. Alternatively, Gerling et al showed that at elevated temperatures and in ultrapure water, welding the thymidine groups by ultraviolet light creates additional covalent bonds that enhance the structural stability of origamis.…”

Programmable and Site‐Specific Patterning on DNA Origami Templates with Heterogeneous Condensation of Silver and Silica

“…Tremendous efforts have been done on this end to arrange gold, silver, quantum dots, silica, and carbon nanotubes with the nanoscale precision down to sub 10 nm. [26][27][28][29][30][31][32][33][34][35][36][37] However, there is still plenty room to go toward smaller sizes of materials. The other challenge lies on arranging materials with greater diversity in their chemical composition, which is a necessary step toward the bottom-up fabrication of functional nanodevices.…”