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Design and Self-Assembly of 2D DNA Crystals in Biological Physics

Explore the design and self-assembly of two-dimensional DNA crystals, including DNA computation, structure, tiling theory, and applications. Discover how DNA can be utilized for biologically relevant computations and complex structures. Learn about the controllable and predictable self-assembly process and its implications in biological physics.

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Design and Self-Assembly of 2D DNA Crystals 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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