Design Strategies for DNA Nanostructures Part I: Problem Formulation

1. Design Strategies for DNA Nanostructures Part I: Problem Formulation Presented By:Jacob Girard and Mary Spuches, Saint Michael’s College With collaboration from: Thomas Dickerson, Andrew Gilbert, Brian Goodhue, Daniel Koch, Daniel Lewis, and Andrew Parent

2. 2 Outline Background DNA and Nanostructures Terminology Octet Truss Our Geometric model Schlegel Diagram Constructions Coming Attractions Acknowledgments Source: MS Office Clip Art

3. Structure of DNA 3 • Sugar, phosphate, nitrogenous base. • Complementary base pairing • Chemical composition determines structure

4. 4 The Chemists Job • Build DNA nanostructures • Topoisomerases • Cut and mend specific sequences of DNA • Ligation • The final binding process

5. 5 The Basics • Branched Junction Molecule • Series of double stranded ends extending from the central vertex • Sticky end (cohesive end) • A double stranded DNA sequence with a single strand extending longer than the other

6. 6 Practical Applications • Biochip technology • Self assembling DNA nanocapsules for drug delivery • Nanoelectronics www.sciencedaily.com/.../ 05/080513130424.htm

7. 7 What is a tile? • A tile represents a branched junction molecule with specific half edge orientation and type. A tile Branched-Junction Molecule

8. 8 Complementary bases adhere c ĉ. ATTCG TAAGCCCATTG GGTAACATTCG TAAGC c ĉ. • Denoted by hatted and un-hatted letter labels • Each edge needs a complimenting edge • Chemically this is this different bases pairing

9. 9 Sticky ends ATTCG TAAGCCCATTG GGTAACATTCG TAAGC D. Luo, “The road from biology to materials,” Materials Today, 6 (2003), 38-43

10. 10 What are some self-assembled DNA nanostructues? • A self-assembled DNA cube and Octahedron http://seemanlab4.chem.nyu.edu/nanotech.html

11. a â a â ŝ s s ŝ t1 t2 t3 t4 ĉ ĉ c c c a t1 t3 t1 t2 t2 ŝ 11 A pot of tiles Both complete complexes (1) and incomplete complexes (2) can be constructed by the following pot type P with 4 tiles

12. 12 Octahedron Construction

13. 13 Geometric Constraints • Arms are straight and rigid • The positions of the arms are fixed • Arms are of unit length • The arms do not bend or twist in order to bond • No molecule has more than 12 arms or less than 2 arms • Final DNA structures must be complete • No design may allow structures smaller than the target structure to form

14. 14 Why the Octet Truss? Source: Wikimedia Commons Distributed under GNU Free Documentation license.

15. Problem Statement 15 The goal is to build self assembling DNA Nanostructures within the octet truss using a minimal number of tile types.

16. 16 Identifying arms at a vertex Geometric Configuration Only four possible angles • π/3 radians • π/2 radians • (2π)/3 radians • π radians

17. 17 Schlegel Diagram of Cuboctahedron • Naming Tiles • This diagram is easier to draw than the actual geometric arrangement • Vertices in the Schlegel diagram correspond to arms

18. 18 Orientation is important Tile B Tile A c ĉ. • The problem of orientation • What are equivalent tiles? Tile C Tile D c ĉ.

19. 19 Tetrahedron Source: Wikimedia Commons Distributed under GNU Free Documentation license.

20. 20 Truncated Tetrahedron Source: Wikimedia Commons Distributed under GNU Free Documentation license.

21. 21 Octahedron Source: Wikimedia Commons Distributed under GNU Free Documentation license.

22. 22 Truncated Octahedron Source: Wikimedia Commons Distributed under GNU Free Documentation license.

23. 23 Cuboctahedron Source: Wikimedia Commons Distributed under GNU Free Documentation license.

24. 24 Coming attractions • Determine the graphs within the octet truss that can be self assembled using one or two tile types • Determine all possible geometric configurations of n-armed tiles for n from 2 to 12 • Then determine all possible sticky end assignments for those tiles • From these possibilities determine the complete complexes that can self assemble

25. 25 Questions?

26. 26 Acknowledgements

27. 27 References