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

Three Essential Ingredients 1.algorithms 2.DNAs 3.self-assembly 4/4/2013General Introduction2

4/4/20133 [ 2007] Example of Self-Assembly Self-Assembly by Magnetic Forces General Introduction

4/4/20134 [Campbell et al., 2007] Example of Self-Assembly LEGO Bricks + Water + Capillary Forces General Introduction

4/4/20135 [ proteins and molecules on cell membrane Example of Self-Assembly Self-Assembly by Hydrophilic and Hydrophobic Interactions General Introduction

4/4/20136 [ Zhang, 2001] Example of Self-Assembly Crystal Formation General Introduction

4/4/20137 [Tuci et al., 2006] Example of Self-Assembly Robot Self-Assembly via Cellular Automata A 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

4/4/20138 [ 2007] Example of Self-Assembly Insulation around Copper Wiring This 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 4/4/2013General Introduction9

4/4/ Algorithmic DNA Self-Assembly 1.Nano Technology Using computation to build nanostructures 2.Computational Technology Using nanostructures to perform computation General Introduction

4/4/ 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-assembly some progress recently General Introduction

4/4/ TILE G C A T C G C G T A G C DNA Tiles -- Basic Unit of 2D Self-Assembly General Introduction

4/4/ Algorithmic DNA Self-Assembly Program = Tiles + Lab StepsOutput = Shape + Pattern General Introduction

4/4/ 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

4/4/ 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

4/4/ 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

4/4/ Examples of DNA Tiles aaa a [Holliday, 1964] exchange of genetic information in yeast General Introduction

4/4/ TILE Examples of DNA Tiles aaa a General Introduction

4/4/ Examples of DNA Tiles [Reif’s Group, Duke University] A C G C T G C G General Introduction

4/4/ [Park, Pistol, Ahn, Reif, Lebeck, Dwyer, and LaBean, 2006] Examples of DNA Tiles General Introduction

4/4/ Examples of DNA Tiles [Winfree ’ s Group, Cal Tech] General Introduction

4/4/ Examples of DNA Tiles [Sierpinski Triangle, Rothemund, Papadakis, Winfree, 2004] General Introduction

4/4/ Self-Assembly for Binary Counters [Winfree, 2000] General Introduction

4/4/ D Self-Assembly for Turing Machines [Winfree, Yang, and Seeman, 1998] General Introduction

4/4/ Self-Assembly for Circuit Patterns [Cook, Rothemund, and Winfree, 2003] General Introduction

4/4/ Example of 3D Self-Assembly [Shaw, University of Southern California] General Introduction

4/4/ D DNA Cube [Seeman, New York University] General Introduction

4/4/ D DNA Truncated Octahedron [Seeman, New York University] General Introduction

4/4/ 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: Published by AAAS

4/4/ Linear Self-Assembly for Regular Languages [Winfree, Yang, and Seeman, 1998] General Introduction

4/4/ Tree Self-Assembly for Context-Free Languages [Winfree, Yang, and Seeman, 1998] General Introduction

4/4/ 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

4/4/ Typical Examples Used in This Discussion N x N Squares k x N rectangles Counters General Introduction

4/4/ 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 [Rothemund and Winfree, STOC 2000] General Introduction

4/4/ 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 Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 S Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 Sa Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 c Sa Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 d c Sa Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 d c Sab Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 d cx Sab Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 d cxx Sab Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 dx cxx Sab Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ Example: Build a Square temperature t = 2 dxx cxx Sab Sa xc b d T = G(, ) = 2 G(, ) = 1 General Introduction

4/4/ The End General Introduction