1. Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a

2. DNA computation Solving computer science problems Biologically relevant computations Nanostructures

3. DNA structure Structure Neighboring Vs Complementary bases Tm Nomenclature: Bases/nucleotides: A,C,T & G Strand/Oligo/ssDNA Complementary, sticky-end Melting/Annealing/ hybridization

4. Tiling theory Motivation to work with DNA Seeman & Winfree’s implementation: Wang tiles Tiling with DNA

5. Tiling implementation Basic building block: DNA strands are entwined to form a Rigid tile with sticky ends Wang’s colors are represented in these sticky ends Self assembly is controllable and predictable

6. A A A A A A A A A A A A A A A AA A A Same molecule – different representation

7. A demonstration of striped lattice formation: PAGE analysis 2D structures RedGrnBluYel

8. DAO-E AB lattice 2D structure images by AFM

9. DAO-E AB lattice 2D structure images by AFM ˆ

10. DNA was demonstrated to be able to tile nano-scale surfaces by self assembly Structures architectures are predictable and robust Decoration could facilitate applications Work conclusion

11. Further work in this direction More complex structures were demonstrated: Seeman’s truncated octahedron/cube Rothemund’s smilies Computation by self assembly

12. Wang developed a method by which a tiling problem reduces the halting problem (1963), i.e. tiling is theoretically as powerful as general purpose computers Cellular automata can be simulated by a self assembly process Theoretical schemes were developed to solve: HPP, SAT, math calculations (including copying and counting)

13. 2 states, 2 letters finite automaton implementation (2001) Shown to interact with biologic molecules (2004) Biologically relevant computation

14. Thank you for your attention

15. PAGE Poly Acrylamide Gel Electrophoresis DNA (negatively charged) migrate according to it’s weight (=length) The smaller the molecule – the faster it will migrate Autoradiogram or fluorescence scan will reveal labeled DNA location Denaturating gel should separate ssDNA molecules according to their length

16. A A A A A A

17. Rothemund origami

18. single-stranded DNA origami back

19. Cellular automata: counter example