Fluorous-Directed Assembly of DNA Origami Nanostructures

Abstract

An orthogonal, noncovalent approach to direct the assembly of higher-order DNA origami nanostructures is described. By incorporating perfluorinated tags into the edges of DNA origami tiles we control their hierarchical assembly via fluorous-directed recognition. When we combine this approach with Watson-Crick base-pairing we form discrete dimeric constructs in significantly higher yield (8x) than when either molecular recognition method is used in isolation. This integrated "catch-and-latch" approach, which combines the strength and mobility of the fluorous effect with the specificity of base-pairing, provides an additional toolset for DNA nanotechnology, one that enables increased assembly efficiency while requiring significantly fewer DNA sequences. As a result, our integration of fluorous-directed assembly into origami systems represents a cheap, atom-efficient means to produce discrete superstructures.

Keywords: DNA nanotechnology; DNA origami; DNA origami dimerization; fluorous; fluorous DNA; molecular recognition; self-assembly.

Figure 1

Schematics showing (a) a typical origami structure with configurable edge modifications, folded into shape using a circular DNA scaffold (black line) and DNA staples (colored lines). (b) Assembly of DNA origami dimers using edge modifications: (i) previously known DNA-based methods; (ii) the fluorous effect as a tool for hierarchical origami assembly.

Figure 2

(a)i. Schematic illustration of an origami tile modified at 14 positions along one edge using either an alkyl (hydrophobic, nonfluorous control), R_F4, R_F6, R_F8, (R_F8)₂, or (R_F8)₄ tag. (a)ii. Schematic showing dimerization via fluorous-modified DNA hybridized to the edge staples of the origami. (b) AFM images and (c) AGE images showing origami assemblies resulting from (a). (d) Schematic illustration of origami tiles modified at 2–14 postions along one edge using (R_F8)₂ tags. (e) AFM images and (f) AGE images showing origami assemblies resulting from (d).

Figure 3

Origami assembly using integrated R_F staples; comparison of assembly via sticky ends and fluorous (R_F8)₂ tags. (a) Schematic showing dimerization via fluorous-modified staples. (b) AFM data analysis showing origami dimerization rates for (i) (R_F8)₂ staples and (ii) DNA sticky ends. (c) AFM images of origami with 14 (R_F8)₂ staples, from (b), showing the existence of dimers, trimers, tetramers, and pentamers. (d) AGE analysis of assembly using 2–14 overhangs of either (i) (R_F8)₂ staples or (ii) DNA sticky ends.

Figure 4

(a) Schematic representation of the two monomer designs. The rectangular origami is shorter than the origami used previously and only has 12 staple strands available for edge modification. (b) Individual monomer motifs are folded before being mixed together. (c) AFM analysis of the observed homodimer, heterodimer, and multimer yields of origami after the two designs are mixed.

Figure 5

(a) Schematics highlighting the relative position of the fluorous core and flanking sticky-end recognition elements. The central fluorous core contains four (RF₈)₂ tags, with sticky-end overhangs placed on either side of this fluorous region. (b) AGE data showing heterodimerization driven by a combination of the fluorous effect and sticky-end association. (c) Representative AFM images used for heterodimer analysis showing the origami dimerization driven by sticky ends only (top) and the impact of combining sticky ends with fluorous recognition (bottom). (d) AFM analysis of observed assembly yields formed with origami containing sticky ends and those containing both fluorous and sticky ends.