Folding DNA to create nanoscale shapes and patterns
Summary (2 min read)
Design of scaffolded DNA origami
- The design of a DNA origami is performed in five steps, the first two by hand and the last three aided by computer (details in Supplementary Note S1).
- Thus for the scaffold to raster progressively from one helix to another and onto a third, the distance between successive scaffold crossovers must be an odd number of half turns.
- Once the geometric model and a folding path are designed, they are represented as lists of DNA lengths and offsets in units of halfturns.
- Staples reverse direction at these crossovers; thus crossovers are antiparallel, a stable configuration well characterized in DNA nanostructures 16 .
- The pattern of merges is not unique; different choices yield different final patterns of nicks and staples.
Folding M13mp18 genomic DNA into shapes
- To test the method, circular genomic DNA from the virus M13mp18 was chosen as the scaffold.
- Six different folds were explored; Fig. 2 gives their folding paths and their predicted and experimentally observed DNA structures.
- By AFM, 13% of structures were well-formed squares (out of S ¼ 45 observed structures) with aspect ratios from 1.00 to 1.07 and bore the expected pattern of crossovers (Fig. 2a , upper AFM image).
- A range of aspect ratios implied a gap size from 0.9 to 1.2 nm; later designs assume 1 nm.
- Even when bridging staples at the vertices were not used, a large number of sharp triangles were well-formed (55%, S ¼ 22).
Patterning and combining DNA origami
- In addition to binding the DNA scaffold and holding it in shape, staple strands provide a means for decorating shapes with arbitrary patterns of binary pixels.
- Patterns are created by mixing appropriate subsets of these strands.
- Whether missing pixels represent real defects or artefacts of imaging is unknown; sequential AFM images occasionally showed '1' pixels that later converted irreversibly to '0' pixels, suggesting tip-induced damage.
- Controlled combination of shapes was achieved by designing 'extended staples' that connected shapes along their edges.
Discussion
- The scaffolded self-assembly of DNA strands has been used to create linear structures 17, 18 and proposed as a method for creating arbitrary patterns 18, 19 .
- M13mp18 is essentially a natural sequence that has a predicted secondary structure which is more stable (lower in energy) than similar random sequences (Supplementary Note S8).
- Further, each correct addition of a staple organizes the scaffold for subsequent binding of adjacent staples and precludes a large set of undesired secondary structures.
- In addition, each structure required about one week to design and one week to synthesize ; the mixing and annealing of strands required a few hours.
- These ideas suggest that scaffolded DNA origami could find use in fields as diverse as molecular biology and device physics.
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Cites background from "Folding DNA to create nanoscale sha..."
...Since then, DNA origami technology [44] has enabled the construction of significantly longer tracks with more complex geometry [50, 96] leading to correspondingly longer processive walks and integration of multiple different kinds of DNA nanomotors....
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...Several recent advances in structural DNA selfassembly have been based on the DNA origami technology [44], which uses short oligonucleotide “staple” strands to fold a long single-stranded “scaffold” (typically the m13 viral genome) into two- and threedimensional shape of interest [9]....
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References
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"Folding DNA to create nanoscale sha..." refers background in this paper
...These are (1) strand invasion, (2) an excess of staples, (3) cooperative effects and (4) design that intentionally does not rely on binding between staples....
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...But the widespread use of scaffolded self-assembly, and in particular the use of long DNA scaffolds in combination with hundreds of short strands, has been inhibited by several misconceptions: it was assumed that (1) sequencesmust be optimized(20) to avoid secondary structure or undesired binding interactions, (2) strands must be highly purified, and (3) strand concentrations must be precisely equimolar....
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