In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification

Abstract

Silicification of DNA origami structures increases their stability and provides chemical protection. Yet, it is unclear whether the whole DNA framework is embedded or if silica just forms an outer shell and how silicification affects the origami’s internal structure. Employing in situ small-angle X-ray scattering (SAXS), we show that addition of silica precursors induces substantial condensation of the DNA origami at early reaction times by almost 10 %. Subsequently, the overall size of the silicified DNA origami increases again due to increasing silica deposition. We further identify the SAXS Porod invariant as a reliable, model-free parameter for the evaluation of the amount of silica formation at a given time. Contrast matching of the DNA double helix Lorentzian peak reveals silica growth also inside the origami. The less polar silica forming within the origami structure, replacing more than 40 % of the internal hydration water, causes a hydrophobic effect: condensation. DNA origami objects with flat surfaces show a strong tendency towards aggregation during silicification, presumably driven by the same entropic forces causing condensation. Maximally condensed origami displayed thermal stability up to 60 °C. Our studies provide insights into the silicification reaction allowing for the formulation of optimized reaction protocols.

Full site-specific addressability in DNA origami-templated silica nanostructures

“…Nevertheless, due to the high cost of PNA, we also explored more sustainable options. Inspired by work by Ding and co-workers [8e] , which showed that TMAPS-TEOS precursors accumulated most favorably on double-stranded DNA (dsDNA) compared to the closely packed dsDNA in a DNA origami nanostructure, we hypothesize that ssDNA may show even less accumulation of silica precursors. We assume that ssDNA, possessing comparatively less phosphate groups compared to dsDNA, may consequently attract less TMAPS molecules.…”

“…We recently showed that DNA origami undergo strong condensation during silicification as a result of hydrophobic effects and water depletion forces caused by the influx of silica into the origami structure. [8g] However, even at the maximally condensed state with sub-nm external silica deposition, structures displayed impressive thermal stability. Therefore, we here employed the same structures (24HB and 4LB) as reported in our recent publication and silicified these following our previously published protocol, using a rotator ( Figures S7,8 ).…”

“…Therefore, we here employed the same structures (24HB and 4LB) as reported in our recent publication and silicified these following our previously published protocol, using a rotator ( Figures S7,8 ). [8g] After ~4 h the reaction was stopped, resulting in structures with sub-nm silica deposition that displayed increased stability upon exposure to DNase I (see Figure S9 ). Silicified structures were then incubated with Cy5-labelled T 19 -anti-handles and analyzed by gel electrophoresis.…”

“…We recently also used small angle X-ray scattering (SAXS) to show that even minimal (sub-nm) silica deposition already results in DNA nanostructures that remain stable during prolonged heating. [8g]…”

A DNA origami fiducial for accurate 3D AFM imaging

“…Another research direction would be to go beyond imaging and to use the fiducial as a mechanical stiffness marker to study the compliance of biomolecules to indentation forces 60 , e.g. to probe the effects of silicifaction 61, 62 or other functionalization. We, therefore, anticipate that our fiducial will provide a multi-modal calibration platform for a range of applications.…”