Full Site‐Specific Addressability in DNA Origami‐Templated Silica Nanostructures

Abstract

DNA nanotechnology allows for the fabrication of nanometer‐sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site‐specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA‐PAINT super‐resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site‐specifically addressable silica nanostructure with complete control over size and shape.

Controlling Silicification on DNA Origami with Polynucleotide Brushes

“…Compared to room temperature, silicification on 6HB at a higher temperature of 35 °C led to more aggregation after two-day incubation (AFM images in Supporting Information Figure S5). This result is consistent with what was reported in previous work, 36 suggesting higher temperature significantly increases kinetics of silicification on DNA origami and thus elevates aggregation. When silicification was extended to 4 days, we observed a clear height difference between the two samples.…”

“…While there may have been a small degree of silica growth also on the double-stranded brushes, it was not detectable in the AFM images. In previous work, 36 it was observed that silica preferetially grew at locations where short DNA duplexes were attached. Our AFM images showed the silicification primarily takes place on or very close to the 6HB DNA origmai surface, when using long, double-stranded DNA brushes.…”

“…Additionally, there is a significant difference in the surface charge distribution between double-stranded DNA and single-stranded DNA, and some studies have shown that silicification occurs preferentially on DNA duplexes rather than on single-stranded DNA. 36,37 We thus hypothesized that, in addition to providing steric repulsion, the polyT brushes on 6HB are much less likely to interact with TMAPS and thus effectively reduce 6HB cross-linking during silicification.…”

“…It was recently reported that short DNA duplexes on DNA origami surfaces promote silicification. 36 Therefore, we sought to investigate the effect of long, double-stranded (DS) DNA brushes on the silicification process as compared to the singlestranded polyT brushes we used above. To convert singlestranded polyT brushes to double-stranded brushes, we added an excess of DNA strands that contained a hairpin with a complementary, 15-adenine single-stranded domain, to the reaction mixture (Figure 5A).…”

“…To achieve this, we harnessed TdT-catalyzed enzymatic polymerization (TcEP), a surface-initiated, enzymatic polymerization reaction we developed previously. ,, Unlike double-stranded DNA, which has a well-defined, rod-like conformation, single-stranded DNA is conformationally much more flexible. Additionally, there is a significant difference in the surface charge distribution between double-stranded DNA and single-stranded DNA, and some studies have shown that silicification occurs preferentially on DNA duplexes rather than on single-stranded DNA. , We thus hypothesized that, in addition to providing steric repulsion, the polyT brushes on 6HB are much less likely to interact with TMAPS and thus effectively reduce 6HB cross-linking during silicification.…”