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“Folding DNA to create nanoscale shapes and patterns” 1 or “Single-stranded DNA Origami” Paul W. K. Rothemund , Nature, 440, 297 - 302 (2006). Jong-Sun Yi. Molecular self- assembly. Many top down processes create patterns serially and require extreme conditions. (vacuum, temperature, etc.)
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“Folding DNA to create nanoscale shapes and patterns”1or “Single-stranded DNA Origami”Paul W. K. Rothemund, Nature, 440, 297 - 302 (2006) Jong-Sun Yi
Molecular self-assembly • Many top down processes create patterns serially and require extreme conditions. (vacuum, temperature, etc.) • Bottom-up, self-assembly techniques promise of inexpensive, parallel synthesis of nanostructures. From porphyrin- to virus-based systems. But where are the complex structures? Yokoyama et al. Nature, 413 (2001) Mao et al. Science, 303 (2004)
DNA Nanotechnology Single-stranded DNA Origami A simple technique to fold a single, long strand of DNA into a complex, arbitrary two-dimensional scaffold with a spatial resolution of 6 nm. • Exploit specificity of Watson-Crick pairing • Create complex nanostructures • Large number of short oligonucleotidesmakes synthesis highly sensitive to stoichiometry. Zhang & Seeman J. Am. Chem. Soc., 116 (1994) Par et al. AngewandteChemie, 118 (2006) Chen & Seeman. Nature, 350 (1991)
5-step Design • Step 3.4.5. (by computer) • Staple strands designed to create periodic crossovers. • Scaffold crossover twist is calculated and moved to minimize strain. Staples recomputed. • Pairs of staples merged to yield fewer longer staples. • (better specificity and higher binding energy) • Step 2. • Fold a single long scaffold strand in a raster fill pattern. • Scaffold crossovers where it switches from helix to helix. • Odd number of half turns between crossovers. Even number of half turns to switch direction. • Step 1. • Approximate geometric model of DNA in the desired shape. • Periodic crossovers where strands switch to adjacent helix. • Accurate to one turn (3.6 nm) in x-direction ; two helical widths (4 nm) in y-direction.
DNA Origami Yield:
Patterning DNA Origami • Dumbbell hairpins added to 32-mer staples to create a binary pattern. • Original staples ‘0’ (~1.5 nm); Labeled staples ‘1’ (~3 nm) • Yields were similar to those of un-patterned origami. • Most defects were “missing pixels” (~6%) • AFM tip-induced damage
Combining DNA Origami • Controlled combination of shapes by designing ‘extended staples’ • Poor yields (<2% for hexagons) – unlike shapes sensitive to stoichiometry. • Largest man-made molecular complex? • 30.46 mega-Daltons (92,310 nt)
Defects • Stretching (roughly 25% of distinguishable squares): • sequential imaging showed stretching of a square • other designs appeared to slide rather than stretch • Hole defects • Study to better understand folding. AFM (destructive). • Stacking • Many parallel blunt ends of rectangle causes aggregates of ~ 5µm • Causes deformation of single bond linked triangles • Solution: Omit staples on edges (sacrifices pixels) or add 4-T hairpin loops or tails to edge staples.
Discussion • Advantages: • 1) strand invasion, • 2) cooperative effects, • 3) staples do not bind. • Extend to three-dimensional structures. • Application as a “nanobreadboard” • Biological studies (e.g., attach proteins to study spatial organization) • Replace the dumbbell hairpins with biotin or fluorophores • Electronic or plasmonic circuits by attaching nanowires, nanotubes, or gold nanoparticles to scaffold.
