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DNA Nanotechnology The science of assembly

DNA Nanotechnology The science of assembly. Nathaniel Bryans CS9981 Presentation. A proximity-based programmable DNA nanoscale assembly line. [ Hongzhou Gu , Jie Chao, Shou -Jun Xiao & Nadrian C. Seeman . Nature, Vol 465, 13 May 2010 ]. Overview. What is DNA? How it Works

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DNA Nanotechnology The science of assembly

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  1. DNA NanotechnologyThe science of assembly Nathaniel Bryans CS9981 Presentation

  2. A proximity-based programmable DNA nanoscale assembly line [ HongzhouGu, Jie Chao, Shou-Jun Xiao & Nadrian C. Seeman. Nature, Vol 465, 13 May 2010 ]

  3. Overview • What is DNA? • How it Works • Necessary Structures • A Two-State DNA Machine • DNA Origami • DNA Walker • Procedures and Results • Applications and Works Cited

  4. What is DNA? How it Works

  5. Deoxyribonucleic Acid • Nucleotides • Sugar, Phosphate Backbone. Nitrogenous Base • 4 Bases • Complementarity • Adenine – Thymine Cytosine - Guanine

  6. Deoxyribonucleic Acid • ssDNA versus dsDNA • Backbones Antiparallel • 5’ to 3’ • Denaturation & Reannealing • Through heating and cooling

  7. What is DNA? Necessary Structures

  8. DNA Crossover • Reciprocal Exchange • Natural Mode of Genetic Recombination

  9. PX DNA[Seeman, Nano Letters 2001] • Paranemic Crossover (PX) DNA • Well behaved in solution (unlike DX) • An extreme topology

  10. A Two-State DNA Machine

  11. JX2 DNA[Yan et al., Nature, 2002] • Paranemic Crossover with Two Juxtaposed Sites • Results in a 180o Twist • (Relative to PX DNA)

  12. Fuel & Removal (Set & Unset) • Set Strands • Bind two strands of ssDNA together • Usually leave single stranded overhang • Unset Strands • Complementary to Fuel strands • Bind to a single stranded overhang • Systematically remove the entire strand

  13. Example

  14. PX - JX2 Conversion[Yan et al., Nature, 2002] • Utilizes DNA Fuel • ‘set’ and ‘unset’ strands • Rotary Device

  15. One Step Further, the PX-JX2 Device[Ding & Seeman, Science, 2006] • Added Features • Reporter Hairpin (arm?) • Cassette

  16. DNA Origami

  17. DNA Origami[Rothemund, Nature, 2006] • Describes a technique called ‘scaffolded DNA origami’ • Shapes are roughly: • 100 nm • 6 nm spatial resolution 100nm

  18. DNA Origami Construction – 5 steps[Rothemund, Nature, 2006] • Build a geometric model that approximates the desired shape • Fold a single long scaffold strand (single-strand DNA) back in forth to make the general pattern. It will comprise one of the two strands in every helix - M13mp18 virus

  19. DNA Origami Construction – 5 steps[Rothemund, Nature, 2006] • Computer design of staple strands • Twist of the scaffold crossovers is calculated Staples sequences are recomputed to minimize strain.

  20. DNA Origami Construction – 5 steps[Rothemund, Nature, 2006] • The staples are given larger binding domains with the scaffold by merging pairs of adjacent staples. Staples to be altered to cross the seam and strengthen the overall structure

  21. DNA Origami (in the assembly line)[Gu et al, Nature Nanotechnology, 2009] • DNA origami with slots in it • Non-symmetrical to gauge orientation • Single strands on cassette bind to single strands in the slot

  22. DNA Walkers

  23. DNA Biped Walking Device[Sherman & Seeman, Nano Letters, 2004] • Prior to this only intramolecular motion • Sherman and Seeman show motion relative to an external substrate (intermolecular)

  24. 2 Main Components[Sherman & Seeman, Nano Letters, 2004] 1. Biped region 2. TX ‘footpath’ • 2 double helical domains • 3 flexible, 9nt linker strands • Triple Crossover Molecule • Each domain has a single stranded region called a ‘foothold’

  25. Movement of the Biped[Sherman & Seeman, Nano Letters, 2004] Set strands Unset strands Linker strands Inchworm like movement

  26. Practical Concerns[Sherman & Seeman, Nano Letters, 2004] • Linker Strands • Long enough to reach foothold • Short enough to minimize enthropic barrier of setting down foot (no wandering)

  27. A Foot-Passing Walker[Shin & Pierce, JACS, 2004]

  28. Kinesin Protein Source: KK Müller-Nedebock Homepage http://www.physics.sun.ac.za/~kkmn/research.php

  29. Tensegrity(tensional integrity) • Rigid struts and flexible tendons • Struts push outwards • Tendons pull inwards • Their balance leads to stable, rigid structures Needle Tower by Kenneth Snelson (1968)

  30. Tensegrity-Triangle Walker • DNA tensegrity-triangles first constructed by D. Liu et al. (2003) • Walker in assembly line constructed with these

  31. Movement of Triangular Walker[Guet al., Nature, 2010] • 3 Hands • 120o turn with every step • 4 Feet • Three in corners • One in centre

  32. Procedures and Results A Proximity-based programmable DNA nanoscale assembly line [Gu et al., Nature, 2010]

  33. Summary • A DNA origami track/foundation • 3 two-state DNA machines • A triangular walker

  34. DNA Origami Tile • 3 Slots • 9 footholds • Non-symmetrical

  35. 2-State DNA Machines • PX – JX2 devices • 3 substrates • (5nm, 5nm/5nm, 10nm gold particles) • JX2 Off(no donation), PX On(donation)

  36. Operation of the Assembly Line

  37. Operation cont. – Particle Transfer

  38. A Complete Pass

  39. Evidence of Operation • Atomic Force Microscopy • Only gold particles & origami visualized

  40. Evidence of Operation – cont. • Transmission Electron Microscope • Only gold particles show

  41. Average Yields

  42. Applications and Works Cited

  43. Applications • Atom-by-Atom assembly • Cost effective • Minimal waste products • New chemicals and products

  44. Works Cited • Ding, B., & Seeman, N. C. (2006). Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate. Science, 314, 1583-1585. • Drexler, K. E. (2001, September). Machine-Phase Nanotechnology. Nano Visions , 74-75. • Gu, H., Chao, J., Xiao, S.-J., & Seeman, N. C. (2010). A proximity-based programmable DNA nanoscale assembly line. Nature, 465, 202-205. • Gu, H., Chao, J., Xiao, S.-J., & Seeman, N. C. (2009, February). Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nature Nanotechnology , 245-248. • Liu, D., Wang, M., Deng, Z., Walulu, R., & Mao, C. (2004). Tensegrity: Construction of Rigid DNA Triangles with Flexible Four-Arm DNA Junctions. J. Am. Chem. Soc., 126, 2324-2325. • Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440, 297-302. • Seeman, N. C. (2001). DNA Nicks and Nodes and Nanotechnology. Nano Letters, 1 (1), 22-26. • Shen, Z. (1999). DNA Polycrossover Molecules and their Application in Homology Recognition. New York Univ. • Sherman, W. B., & Seeman, N. C. (2004). A Precisely Controlled DNA Biped Walking Device. Nano Letters, 4 (7), 1203-1207. • Shin, J.-S., & Pierce, N. A. (2004). A Synthetic DNA Walker for Molecular Transport. J. Am. Chem. Soc., 126, 10834-10835. • Yan, H., Zhang, X., Shen, Z., & Seeman, N. C. (2002). A robust DNA mechanical device controlled by hybridization topology. Nature, 415, 62-65.

  45. Thank You Questions?

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