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Explore the breakthrough method of Single-stranded DNA Origami to fold intricate nanostructures with high precision, leveraging Watson-Crick pairing for complex designs. Learn step-by-step processes for scaffold folding, crossover design, and yield optimization. Discover the potential applications, such as biological studies and nanocircuitry. Unravel the challenges and innovative solutions for defect management and shape control in DNA origami. Dive into the fascinating world of molecular self-assembly and nanotechnology with this comprehensive guide.
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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.
