4/4/20131 EECS 395/495 Algorithmic DNA Self-Assembly General Introduction Thursday, 4/4/2013 Ming-Yang Kao General Introduction.

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EECS 395/495Algorithmic DNA Self-Assembly

General Introduction

Thursday, 4/4/2013

Ming-Yang Kao

General Introduction

Three Essential Ingredients

1. algorithms

2. DNAs

3. self-assembly

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[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

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

aaaa

aaaa

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

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