1. Developing DNA nanotechnology for use in nanoelectronics
PLACE NOTES HERE
Paul W.K. Rothemund and Erik Winfree
California Institute of Technology

2. 30

3. The astonishing effectiveness of DNA self-assembly...
nonperiodic crystals with complex patterns at 12 nm
“algorithmic self-assembly”, Rothemund, Papadakis, Winfree, 2004
Shih, 2004
arbitrary patterns 100 nm x 100 nm at 6 nm resolution
200 pixels
shaped
holes
folding “DNA origami” Rothemund, 2006
Mao, 2008
...has allowed us to create arbitrary shapes and patterns, both 2D and 3D at the nanoscale. But...

4. The astonishing effectiveness of DNA self-assembly...
nonperiodic crystals with complex patterns at 12 nm
“algorithmic self-assembly”, Rothemund, Papadakis, Winfree, 2004
Shih, 2004
arbitrary patterns 100 nm x 100 nm at 6 nm resolution
200 pixels
shaped
holes
folding “DNA origami” Rothemund, 2006
Mao, 2008
...has allowed us to create arbitrary shapes and patterns, both 2D and 3D at the nanoscale. But...

5. The astonishing effectiveness of DNA self-assembly...
nonperiodic crystals with complex patterns at 12 nm
“algorithmic self-assembly”, Rothemund, Papadakis, Winfree, 2004
Shih, 2004
arbitrary patterns 100 nm x 100 nm at 6 nm resolution
200 pixels
shaped
holes
folding “DNA origami” Rothemund, 2006
Mao, 2008
...has allowed us to create arbitrary shapes and patterns, both 2D and 3D at the nanoscale. But...

6. The astonishing effectiveness of DNA self-assembly...
nonperiodic crystals with complex patterns at 12 nm
“algorithmic self-assembly”, Rothemund, Papadakis, Winfree, 2004
Shih, 2004
arbitrary patterns 100 nm x 100 nm at 6 nm resolution
200 pixels
shaped
holes
folding “DNA origami” Rothemund, 2006
Mao, 2008
...has allowed us to create arbitrary shapes and patterns, both 2D and 3D at the nanoscale. But...

7. The astonishing effectiveness of DNA self-assembly...
nonperiodic crystals with complex patterns at 12 nm
“algorithmic self-assembly”, Rothemund, Papadakis, Winfree, 2004
Shih, 2004
arbitrary patterns 100 nm x 100 nm at 6 nm resolution
200 pixels
shaped
holes
folding “DNA origami” Rothemund, 2006
Mao, 2008
...has allowed us to create arbitrary shapes and patterns, both 2D and 3D at the nanoscale. But...

8. Kos Galatsis, Mihri Ozkan, Scott Sills
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

9. Kos Galatsis, Mihri Ozkan, Scott Sills
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

10. Kos Galatsis, Mihri Ozkan, Scott Sills
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

11. Kos Galatsis, Mihri Ozkan, Scott Sills
device compatibility
assembly yield
aggregation
defect rates
scaling up to larger
structures
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

12. Kos Galatsis, Mihri Ozkan, Scott Sills
device compatibility
assembly yield
registration
aggregation
defect rates
scaling up to larger
structures
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

13. DNA nanostructures are made in solution....

14. DNA nanostructures are made in solution
DNA nanostructures are made in solution....and deposited randomly on surfaces

15. DNA nanostructures are made in solution
DNA nanostructures are made in solution....and deposited randomly on surfaces
How can we register them so
that they may be “wired up”?

16. Our FENA supported projects
Origami nucleation of ribbons: Robert Barish, Rebecca Schulman and Erik Winfree
Thanks to FENA, NSF
Origami/ribbons/CNT cross-junctions:
Hareem Maune, Siping Han, Marc Bockrath, Bill Goddard, Erik Winfree
Origami placement on technological surfaces with IBM Research Almaden:
Ryan Kershner, Luisa Bozano, Christine Micheel, Albert Hung, Anne Fornoff, Charles Rettner, Marco Bersani, Jennifer Cha, Jane Frommer, Greg Wallraff
thanks to:FENA, NSF
Stacking bonds for larger, more complex structures: Sungwook Woo
thanks to: Microsoft Research, FENA, NSF

17. Our FENA supported projects
Origami nucleation of ribbons: Robert Barish, Rebecca Schulman and Erik Winfree
Thanks to FENA, NSF
Origami/ribbons/CNT cross-junctions:
Hareem Maune, Siping Han, Marc Bockrath, Bill Goddard, Erik Winfree
Origami placement on technological surfaces with IBM Research Almaden:
Ryan Kershner, Luisa Bozano, Christine Micheel, Albert Hung, Anne Fornoff, Charles Rettner, Marco Bersani, Jennifer Cha, Jane Frommer, Greg Wallraff
thanks to:FENA, NSF
Stacking bonds for larger, more complex structures: Sungwook Woo
thanks to: Microsoft Research, FENA, NSF
FENA participation has encouraged us to directly address roadblocks to the use of DNA nanotechnology for nanoelectronics

18. Our FENA supported projects
Origami nucleation of ribbons: Robert Barish, Rebecca Schulman and Erik Winfree
Thanks to FENA, NSF
Origami/ribbons/CNT cross-junctions:
Hareem Maune, Siping Han, Marc Bockrath, Bill Goddard, Erik Winfree
Origami placement on technological surfaces with IBM Research Almaden:
Ryan Kershner, Luisa Bozano, Christine Micheel, Albert Hung, Anne Fornoff, Charles Rettner, Marco Bersani, Jennifer Cha, Jane Frommer, Greg Wallraff
thanks to:FENA, NSF
Stacking bonds for larger, more complex structures: Sungwook Woo
thanks to: Microsoft Research, FENA, NSF
FENA participation has encouraged us to directly address roadblocks to the use of DNA nanotechnology for nanoelectronics
assembly yield
defect rates
device compatibility
registration
aggregation
scaling up to larger
structures

19. Kos Galatsis, Mihri Ozkan, Scott Sills
device compatibility
assembly yield
registration
aggregation
defect rates
scaling up to larger
structures
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

20. Kos Galatsis, Mihri Ozkan, Scott Sills
device compatibility
assembly yield
registration
aggregation
defect rates
scaling up to larger
structures
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

21. Kos Galatsis, Mihri Ozkan, Scott Sills
device compatibility
assembly yield
registration
aggregation
defect rates
scaling up to larger
structures
supported
Kos Galatsis, Mihri Ozkan, Scott Sills

22. Algorithmic self-assembly uses tiles to create large, complex patterns
12 nanometers
sticky ends on monomers encode a pattern in a DNA tile crystal

23. Algorithmic self-assembly uses tiles to create large, complex patterns
12 nanometers
sticky ends on monomers encode a pattern in a DNA tile crystal

24. Algorithmic self-assembly uses tiles to create large, complex patterns
12 nanometers
sticky ends on monomers encode a pattern in a DNA tile crystal
But lack of appropriate nuclei has cause problems...
Yield of self-assembled DNA patterns Previously only 1-2% of material had the desired pattern.
Defect rates (error rates) Previously, within a single pattern a ~2% error rate per “pixel”.

25. Algorithmic self-assembly uses tiles to create large, complex patterns
12 nanometers
sticky ends on monomers encode a pattern in a DNA tile crystal
But lack of appropriate nuclei has cause problems...
Yield of self-assembled DNA patterns Previously only 1-2% of material had the desired pattern.
Defect rates (error rates) Previously, within a single pattern a ~2% error rate per “pixel”.

26. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

27. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

28. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree 1 1 1

29. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree 1 1 1

30. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

31. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

32. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

33. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

34. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

35. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

36. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

37. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

38. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

39. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

40. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

41. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

42. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree

43. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree
DNA ribbon

44. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree
DNA ribbon
Redundant encoding of each bit with two diagonals of tiles gives
error correction.

45. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree
Yield of self-assembled DNA patterns Previously only 1-2% of material had the desired pattern Now >90% appropriately nucleated.
Defect (error) rates Previously, within a single pattern a ~2% error rate per “pixel”. Now .13%, or better.
Self-assembly of larger patterns. Copied ~1 micron DNA origami are limited to about 100 nm in size.

46. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree
Yield of self-assembled DNA patterns Previously only 1-2% of material had the desired pattern Now >90% appropriately nucleated.
Defect (error) rates Previously, within a single pattern a ~2% error rate per “pixel”. Now .13%, or better.
Self-assembly of larger patterns. Copied ~1 micron DNA origami are limited to about 100 nm in size.

47. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree
Yield of self-assembled DNA patterns Previously only 1-2% of material had the desired pattern Now >90% appropriately nucleated.
Defect (error) rates Previously, within a single pattern a ~2% error rate per “pixel”. Now .13%, or better.
Self-assembly of larger patterns. Copied ~1 um. (>5) DNA origami are limited to about 100 nm in size.

48. Origami nucleation improves yield and error rate
Rob Barish, Rebecca Schulman,
Paul Rothemund, Erik Winfree
Other more complex
patterns can be made
using origami nuclei...

49. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami

50. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami

51. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami

52. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add labels

53. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add labels
they bind CNT too

54. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add labels
they bind CNT too
and so many are
unavailable for binding
other DNA-labelled objects

55. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add labels
they bind CNT too
coupling is poor
and so many are
unavailable for binding
other DNA-labelled objects

56. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami

57. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add protection strands

58. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add protection strands
labels remain available

59. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add protection strands
labels remain available

60. Two dimensional organization of carbon nanotubes using DNA origami
Addressing the compatibility of
carbon nanotubes and DNA origami
add protection strands
labels remain available
and coupling yields are higher

61. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree
Where previous exclusively
self-assembled CNT FETs
were “one-dimensional”
origami enables
two-dimensional organization.

62. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

63. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree
protection strands
released if and only if the linker binds an appropriate “hook” on an origami

64. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

65. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

66. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

67. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

68. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

69. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

70. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree

71. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree
Tubes are long enough that
each can bind multiple origami
crosslinking them into networks.
These occur in 3D and have
attached ribbons flopping about.
Tubes can be length sorted but
short tubes are hard to wire to.
Greater incubation times mean more
tubes attach but also more aggregation.

72. Two dimensional organization of carbon nanotubes on DNA origami
Hareem Maune, Si-ping Han, Robert Barish,
Marc Bockrath, Bill Goddard, Paul Rothemund, Erik Winfree
Tedious!
“Hunt &
Peck &
Connect”
Not to mention aggregation!
Unscalable!
Inefficient!
Miserable!

73. DNA nanostructures are made in solution
DNA nanostructures are made in solution....and deposited randomly on surfaces
How can we register them so
that they may be “wired up”?

74. Shape-matching placement and orientation of DNA origami on surfaces
With IBM Research Almaden
Origami are just big enough that their largest feature, their outline matches the smallest feature of top down lithography.
Origami are giant single molecules. To have a handle on them is to have a handle on any single molecule, single device, or atom that we can couple to them.
Ryan Kershner, Luisa Bozano, Christine Micheel, Albert Hung, Anne Fornoff, Charles Rettner, Marco Bersani, Jennifer Cha, Jane Frommer, Greg Wallraff
In principle this solves two problems:
1. aggregation of DNA templates by components
2. allows devices to be easily wired up (no need to find them)
What’s missing to do it is:
1. absolute orientation of shapes
2. the ability to place multiple distinct shapes
Allows us to address “Registration”

75. One solution to placement

76. One solution to placement

77. One solution to placement

78. One solution to placement

79. One solution to placement

80. One solution to placement

81. One solution to placement

82. One solution to placement

83. One solution to placement

84. One solution to placement

85. One solution to placement

86. One solution to placement

87. One solution to placement

88. One solution to placement

89. One solution to placement

92. Largely single triangles (95%) Largely well-aligned (+/- 10%)
TMS on
silicon dioxide
DLC on
DLC

93. On control features triangles have random orientations +/- 33 degrees

94. An AFM movie of triangle binding

95. Combining placement (registration) with positioning of devices
In principle this solves two problems:
1. aggregation of DNA templates by components
2. allows devices to be easily wired up (no need to find them)
What’s missing to do it is:
1. absolute orientation of shapes
2. the ability to place multiple distinct shapes

96. Combining placement (registration) with positioning of devices
In principle this solves two problems:
1. aggregation of DNA templates by components
2. allows devices to be easily wired up (no need to find them)
What’s missing to do it is:
1. absolute orientation of shapes
2. the ability to place multiple distinct shapes

97. Combining placement (registration) with positioning of devices
In principle this solves two problems:
1. aggregation of DNA templates by components
2. allows devices to be easily wired up (no need to find them)
What’s missing to do it is:
1. absolute orientation of shapes
2. the ability to place multiple distinct shapes

98. Future of shape matching, placement and orientation
Absolute orientation of an asymmetric shape
Multiple shapes with specific binding
New template materials for easy fabrication
Standard wafers (a kit) offering multiple shapes at a variety of spacings, perhaps using nanoimprint lithograpy.

99. How can origami be combined into larger structures?
See Sungwook Woo’s poster
How can the length of DNA nanotubes
be controlled?
See Rizal Hariadi’s poster

100. Much progress in the control of DNA nanotechnology
Origami nucleation provides better yield and error rates
Origami provide a 2D template for CNT alignment
Protecting strands increase available label, decreases CNT-CNT aggregation, (but not DNA-CNT-DNA component-mediated aggregation.)
Lithography can provide registration (placement + orientation); may avoid aggregation based on components.
Stacking provides another (reversible) method for organizing DNA origami into higher order structures; perhaps it can be combined with placement.
We’ve got a long way to go....