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Topics in Biological Physics

Topics in Biological Physics. Design and self-assembly of two-dimensional DNA crystals. Benny Gil 16/12/08. Fig3.a. DNA computation. Solving computer science problems Biologically relevant computations Nanostructures. DNA structure. Structure Neighboring Vs Complementary bases Tm

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Topics in Biological Physics

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  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 & GStrand/Oligo/ssDNAComplementary, sticky-endMelting/Annealing/ hybridization

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

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

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

  7. Red Grn Blu Yel 2D structures • A demonstration of striped lattice formation: PAGE analysis

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

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

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

  11. Further work in this direction • More complex structures were demonstrated:Seeman’s truncatedoctahedron/cubeRothemund’s smilies • Computation by self assembly

  12. Computation by self assembly • 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. Biologically relevant computation • 2 states, 2 letters finite automaton implementation (2001) • Shown to interact with biologic molecules (2004)

  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 scanwill reveal labeled DNA location • Denaturating gel should separate ssDNA molecules according to theirlength

  16. A A A A A A

  17. Rothemund origami

  18. single-stranded DNA origami back

  19. Cellular automata: counter example

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