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Algorithmic self-assembly for nano-scale
fabrication
Erik Winfree Computer Science
Computation & Neural Systemsand
The DNA Group @ Caltech
DARPA NSF NASA
Constructing Complex Molecular Objects(Development/Morphogenesis)
Information specifies a process that creates organization
Creating OrderBlueprints,Template
-------------Arbitrary structure.
Larger object requires
larger template.
Periodiccrystals
-------------Few components,
large homogeneousobject.
Algorithmicgrowth
-------------Few components,
large intelligently-organized
object.
Nadrian Seeman &
DNA nanotechnology
Chemical structure of DNA
G
A
A
G
T
C
C
T
DNA
single-stranded double-stranded
AGTCTTCGAATGCTAATTGCGCT
AGCGCAATTAGCATTCGAAGACT
Designing DNA molecular complexes
Nadrian Seeman, 1980’s
GATTACA
CTAATGTTAGGCAG
ATCCGTC
AC
TG
GT
G
TG
AC
CA
C
GATTACA
CTAATGT
ATCCGTC
TG
AC
CA
C
AC
TG
GT
G
TAGGCAG
Chen and Seeman, Nature 350, 631 (1991).
Periodic 2-tile crystal (DAO-E lattice)
TCACT
AGTGA
CATAC
GTATG
TCTTG
AGAAC ATCTC
TAGAG
Winfree, Liu, Wenzler, Seeman, Nature 394: 539-544 (1998)
1 24 3
3 42 1
Self-Assembly of DNA
High resolution AFM imaging
Hole = lattice defect Conformation of helix and sticky ends?
Rizal Hariadi, Winfree groupcrystal growth movie
Some variations
Mao, Sun, Seeman, JACS 1999
Winfree, Liu, Wenzler, Seeman, Nature, 1998
LaBean et al, JACS, 2000
More variations
1D ribbons
1D tubes
(Schulman, Winfree, 06)
Zigzag ribbon 2D periodic
lattices
Nano-track
3-helix bundle
TX-tube
6-helix bundle
4x4 tube
DX tube
DX lattice
TX lattice
4x4 lattices
triangle lattice
hexagonal lattice
3 point-star lattices
symmetry lattice
single-strand DX-like tubes …
Rhombus ribbon
…
(Mao, Sun & Seeman, 1999)
Rhombus lattice
(Mao, Sun & Seeman 99)
(Winfree, Liu, Wenzler & Seeman 98)
(LaBean, Yan, Kopatsch, Liu, Winfree, Reif, & Seeman 00)
(Liu, Park, Reif & LaBean 04)
(Liu, Wang, Deng, Walulu & Mao 04) (He, Tian, Chen, Deng,
Ribbe & Mao 05)
(He, Chen, Liu,Ribbe & Mao 05)
(He, Chen, Liu,Ribbe & Mao 05)
(Park, Yin, Liu, Reif LaBean & Yan 05)
(Park, Barish, Li, Reif,Finkelstein,Yan & LaBean 05)
(Rothemund, Ekani-Nkodo, Papadakis, Kumar,
Fygenson & Winfree 04)
… (Mathieu, Liao,
Kopatsch, Wang, Mao & Seeman
05)
Chiral DX tube
(Mitchell, Harris, Malo, Bath &Turberfield 04)
HJ lattice
(Malo, Mitchell, Venien-Bryan, Harris,Wille,Sherratt &
Turberfield 05)
(Reishus, Shaw, Brun,Chelyapov & Adleman 05)
DDX lattice
(Chelyapov, Brun, Gopalkrishnan, Reishus, Shaw & Adleman 04)
(Yan, Park, Finkelstein,Reif & LaBean 03)
(Yan, Park, Finkelstein,Reif & LaBean 03)
TX ribbon
(Li, Park, Reif, LaBean, Yan 03)
(Rothemund 05)
SAO lattice
DNA computing
Adleman, Science (1994)
Len Adleman:DNA self-assembly is programmable
The Sierpinski Triangle(aka Pascal’s Triangle mod 2)
0 0 0 0 0 0 0 1 0 0 0 0 0 0 00 0 0 0 0 0 1 1 0 0 0 0 0 0
0 0 0 0 0 0 1 0 1 0 0 0 0 00 0 0 0 0 1 1 1 1 0 0 0 0 0
0 0 0 0 0 1 0 0 0 1 0 0 0 00 0 0 0 1 1 0 0 1 1 0 0 0 0
0 0 0 0 1 0 1 0 1 0 1 0 0 0
0 0 0 0 0 0 1 1 0 0 0 0 0 0
each new number is the sum of the two below it
Paul Rothemund, Nick Papadakis, Erik Winfree, PLoS Biology 2:e424, 2004
The Sierpinski Triangle(aka Pascal’s Triangle mod 2)
Paul Rothemund, Nick Papadakis, Erik Winfree, PLoS Biology 2:e424, 2004
The Sierpinski Triangle
(aka Pascal’s Triangle mod 2)
Paul Rothemund, Nick Papadakis, Erik Winfree, PLoS Biology 2:e424, 2004
DAO-E Sierpinski Tile Set
decorrelation movie powers of two movie
Making the boundary (the input string)
750
nm
}
25 nm
DAO-E Sierpinski experiments
Algorithmic crystals
1.6 um scan
deco
rrel
atio
n m
ovie
scaffold strand
algorithmic growth
errors during assembly
DAO-E Sierpinski triangle experiments
Paul Rothemund, Nick Papadakis, Erik Winfree, PLoS Biology 2: e424 (2004)
340nm
Scaffolded DNA origami
Folding long single-stranded DNA
The sequence of DNA provides unique addresses for each location.
“Staple strands” bind locations together according to the design.
Folding long single-stranded DNA
The sequence of DNA provides unique addresses for each location.
“Staple strands” bind locations together according to the design.
Folding long single-stranded DNA
The sequence of DNA provides unique addresses for each location.
“Staple strands” bind locations together according to the design.
Scaffolded DNA origami
Scaffolded DNA origami
Scaffolded DNA origami
Creating OrderBlueprints,Template
-------------Arbitrary structure.
Larger object requires
larger template.
Periodiccrystals
-------------Few components,
large homogeneousobject.
Algorithmicgrowth
-------------Few components,
large intelligently-organized
object.
