Direct Observation of Polynucleotide Brush Growth Using Video-Rate Atomic Force Microscopy

Abstract

Recent research demonstrates spatiotemporal control over the enzymatic polymeriza-tion brushes from initiators patterned on a DNA origami surface. Potential applications of this technique to drug delivery, actuation of DNA nanostructures, and supramolecu- lar self-assembly would benefit from the ability to resolve changes in the topography of DNA nanostructures and brush conformations over time. However, current experimental techniques demonstrate tradeoffs between temporal and spatial resolution. This research at- tempted high spatiotemporal observation of polymer brush growth using high-speed atomic force microscopy. Terminal deoxynucleotidyl transferase was used to extend polynucleotide brushes from gold substrates patterned with oligonucleotide initiators. Ellipsometric mea- surements revealed dry brush thicknesses exceeding 100nm, while atomic force measure- ments of brushes in good solvent showed thicknesses of about 10nm. While brush growth was observed, the atomic force microscopy frame rates achieved in this study were too low to decouple the spatial and temporal features of brush growth. Moreover, the discrepancy be- tween atomic force microscopy and ellipsometric measurements of brush thickness indicates probe-sample interactions lead to a significant underestimate of brush thickness. These results indicate refining this imaging process, by reducing the stiffness and length of the cantilver, is needed for high-speed monitoring of origami-brush composite nanostructures.