Design Strategies for DNA Nanostructures

1. Design Strategies for DNA Nanostructures Presented By:Jacob Girard & Keith Randall With collaboration from: Andrew Gilbert, Daniel Lewis, & Brian Goodhue

2. Outline Introduction & Problem Statement Differentiating the Molecular Building Blocks Categorization Graphing Octet Truss Orientation Cohesive Ends Approach Constructions Tetrahedron Truncated Octahedron Truncated Tetrahedron Cuboctahedron Octahedron Conclusions Extensions Future Problem Statement Questions or Answers Acknowledgements References Source: MS Office Clip Art

3. Introduction • DNA and Math? • Chemical composition determines structure Source: MS Office Clip Art

4. What is a tile? A tile Branched-Junction Molecule

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

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

7. Cohesive Ends c ĉ. ATTCG TAAGCCCATTG GGTAACATTCG TAAGC c ĉ. • Depicted by hatted (prime) and un-hatted letter labels • Each edge needs a complimenting edge. • Chemically this is this different bases pairing.

8. Terminology and Definitions • A tile is a branched junction molecule with specific half edge orientation and type.

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

10. The Octet Truss • Why is the Octet Truss a good construct? • What else is it used for? • Why do we use it? Source: Wikimedia Commons Distributed under GNU Free Documentation license.

11. Differentiating the Molecular Building Blocks Categorizations Only four possible angles • π/3 radians • π/2 radians • (2π)/3 radians • π radians

12. Graphing • Naming Tiles • Schlegel diagrams • It is very helpful to be able to picture these molecules as one dimensional and 3D dimensional.

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

14. Constraints • Arms are straight and rigid • The positions of the arms are fixed • 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.

15. Approach • What exists within the octet truss for possible arm configurations? • What can we build by just looking at the octet truss? • What do we think we can build? • What about the Platonic & Archimedean Solids? • How can we do this in as few different tile types as possible?

16. Constructions • Platonic Solids • Tetrahedron • Octahedron • Archimedean Solids • Cuboctahedron • Truncated Tetrahedron • Truncated Octahedron

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

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

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

20. Octahedron Construction

21. Octahedron Construction

22. Octahedron Construction

23. Octahedron Construction

24. Octahedron Construction

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

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

27. Conclusions • Development of the Tile Model • Constructs • Categorization • Cohesive Ends • Orientation • Determined Platonic and Archimedean Solids do fit in Octet Truss. • Proof by Tile Model

28. Extensions • Looking for a better way to talk about orientations of tiles and arms. • Model is limited in some respects. • Arms are not entirely rigid in reality and this does affect the problem statement.

29. Future Problem Statement • What we know: • We have all the 2 and 3 arm configurations • We possibly have all the 4 configurations • Need to find all the structures that can be made from • one tile type with an even number of arms, and • two tile types with an odd number of arms. • Hopefully we will be able to find some pattern and be able to create a generalization of rule, but we will need data and examples first.

30. Questions or Answers?

31. Acknowledgements

32. References