jong-sun yi

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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

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Molecular self-assemblyMany 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)

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DNA NanotechnologyExploit specificity of Watson-Crick pairingCreate complex nanostructuresLarge number of short oligonucleotides makes synthesis

highly sensitive to stoichiometry.

Zhang & Seeman J. Am. Chem. Soc., 116 (1994)Par et al. Angewandte Chemie, 118 (2006)

Chen & Seeman. Nature, 350 (1991)

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.

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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 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 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.

5-step Design

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DNA Origami

linear scaffold asymmetric non-raster fill2.5-turn spacing

13% (25/25%)

90% 11%63% 70% < 1% 88% (63%)

1 µm 100 nm 100 nm 100 nm 100 nm

Yield:

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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

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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)

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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.

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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.

Thank you.