4/4/20131 eecs 395/495 algorithmic dna self-assembly general introduction thursday, 4/4/2013...
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4/4/2013 1
EECS 395/495Algorithmic DNA Self-Assembly
General Introduction
Thursday, 4/4/2013
Ming-Yang Kao
General Introduction
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Three Essential Ingredients
1. algorithms
2. DNAs
3. self-assembly
4/4/2013 General Introduction 2
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4/4/2013 3
[http://www.math.udel.edu/MECLAB, 2007]
Example of Self-Assembly
Self-Assembly by Magnetic Forces
General Introduction
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[Campbell et al., 2007]
Example of Self-Assembly
LEGO Bricks + Water + Capillary Forces
General Introduction
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[http://staff.jccc.net/pdecell/chemistry/selfassem.html]
proteins and molecules on cell membrane
Example of Self-Assembly
Self-Assembly by Hydrophilic and Hydrophobic InteractionsGeneral Introduction
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[http://web.mit.edu/lms/www, Zhang, 2001]
Example of Self-Assembly
Crystal Formation
General Introduction
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[Tuci et al., 2006]Example of Self-Assembly
Robot Self-Assembly via Cellular AutomataA group of robots physically connected to each other that (a) moves on rough terrain and (b) passes over a gap during an experiment in a close arena with a flat terrain.
General Introduction
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[http://www.technologyreview.com/Biztech, 2007]
Example of Self-Assembly
Insulation around Copper WiringThis microprocessor cross section shows empty space in between the chip’s copper wiring. Wires are usually insulated with a glasslike material, but IBM has used self-assembly techniques, which can be employed in chip-making facilities, to create air gaps that insulate the wires. Credit: IBM
General Introduction
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DNA-based Self-Assembly + Algorithms
1. DNA – four bases A, C, G, T
2. paring of A/T and C/G self-assembly
3. two pairs two bits 0 and 1 encoding of programs and data algorithms
4. self-assembly executing algorithms guiding self-assembly
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Algorithmic DNA Self-Assembly
1. Nano Technology
Using computation to build nanostructures
2. Computational Technology
Using nanostructures to perform computation
General Introduction
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Algorithmic DNA Self-Assembly
Nano Technology +
Computational Technology
• 1 dimensional self-assembly e.g., 1990s’ DNA computing
• 2 dimensional self-assembly this course’s focus
• 3 dimensional self-assemblysome progress recently
General Introduction
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TILE
G C A T C G
C G T A G C
DNA Tiles -- Basic Unit of 2D Self-Assembly
General Introduction
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Algorithmic DNA Self-Assembly
Program = Tiles + Lab Steps Output = Shape + Pattern
General Introduction
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Algorithmic DNA Self-Assembly
Input: the description of a shape (or pattern)
Output: a set of tiles and a sequence of lab steps to produce the shape (or pattern)
Computational Objectives:• minimize the # of different tiles (i.e., tile types)• minimize the range of temperatures• minimize the # different temperatures used• minimize the # of lab steps• minimize the complicatedness of steps• minimize the assembly time• minimize errors• others
General Introduction
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Outline of This Discussion
1. Examples of DNA Tiles
2. Examples of DNA Self-Assemblies
3. Examples of DNA Nano Structures
4. A Basic Model
General Introduction
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Outline of This Discussion
1. Examples of DNA Tiles
2. Examples of DNA Self-Assemblies
3. Examples of DNA Nano Structures
4. A Basic Model
General Introduction
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Examples of DNA Tiles
aaaa
[Holliday, 1964]exchange of genetic information in yeast
General Introduction
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TILE
Examples of DNA Tiles
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General Introduction
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Examples of DNA Tiles
A T A G CT A T C G
T G A T C G G AA C T A G C C T
A C T A G C C TA C T A G C C T
C T A G C C G TG A T C G G C A
G C T T G A C CC G A A C T G G
A G A
T C G
A C
T C T
A G C
T G
T A C
C G
C A
TA T
G G
C G
T A
T G A
A T A
G C
A C T
T A T
C G
A C T
A G C
C T
A C T
A G C
C T
A T A G CT A T C G
A T A G CT A T C G
G T A C AC A T G T
A T A
G C
T A T
C G
A T A
G C
T A T
C G
A T A
G C
T A T
C G
A T A
G C
T A T
C G
C G G T C
T T C C A
G A C
A G
T T A
G T
[Reif’s Group, Duke University]
A C
G C
T G C G
General Introduction
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[Park, Pistol, Ahn, Reif, Lebeck, Dwyer, and LaBean, 2006]
Examples of DNA Tiles
General Introduction
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Examples of DNA Tiles
[Winfree’s Group, Cal Tech]
General Introduction
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Examples of DNA Tiles
[Sierpinski Triangle, Rothemund, Papadakis, Winfree, 2004]
General Introduction
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Self-Assembly for Binary Counters
[Winfree, 2000]
General Introduction
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2D Self-Assembly for Turing Machines
[Winfree, Yang, and Seeman, 1998]
General Introduction
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Self-Assembly for Circuit Patterns
[Cook, Rothemund, and Winfree, 2003]
General Introduction
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Example of 3D Self-Assembly[Shaw, University of Southern California]
General Introduction
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3D DNA Cube
[Seeman, New York University]
General Introduction
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3D DNA Truncated Octahedron
[Seeman, New York University]
General Introduction
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Clonable DNA Octahedron
[Shih, Quispe, Joyce, 2004]
one 1,669-mer + five 40-mers
General Introduction
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Fig. 1 Design of DNA brick structures analogous to structures built of LEGO® bricks.
Y Ke et al. Science 2012;338:1177-1183
Published by AAAS
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Linear Self-Assembly for Regular Languages
[Winfree, Yang, and Seeman, 1998]
General Introduction
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Tree Self-Assembly for Context-Free Languages
[Winfree, Yang, and Seeman, 1998]
General Introduction
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Outline of This Discussion
1. Examples of DNA Tiles
2. Examples of DNA Self-Assemblies
3. Examples of DNA Nano Structures
4. A Basic Model – the Abstract Tile Assembly Model
General Introduction
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Typical Examples Used in This Discussion
• N x N Squares
• k x N rectangles
• Counters
General Introduction
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Standard Tile Model of DNA Self-Assembly
tile system: (T, s, G, t)
T: tile set
s: seed tile
G: glue function
t : temperature, positive integer
t}..., 1, {0,:G
, , ... { }r
r
w
g
p
y yb
r
b
r
b,
[Rothemund and Winfree, STOC 2000]
General Introduction
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Example: Build a Square
temperature t = 2
1. positive strength between same glues
2. zero strength between distinct glues
3. start with the seed tile
4. add one tile at a time
5. bind if total strength is at least t
6. order must not affect final shape and pattern
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2
S
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2
S a
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2
c
S a
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2d
c
S a
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2d
c
S a b
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2d
c x
S a b
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2d
c x x
S a b
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2d x
c x x
S a b
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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Example: Build a Square
temperature t = 2d x x
c x x
S a b
S a
x c
b
d
T =
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 2
G( , ) = 1
G( , ) = 1
G( , ) = 1
General Introduction
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The End
General Introduction