Topics in Biological Physics

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

• Solving computer science problems
• Biologically relevant computations
• Nanostructures

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DNA structure

• Structure
• Neighboring Vs Complementary bases
• Tm
• NomenclatureBases/nucleotides A,C,T
  GStrand/Oligo/ssDNAComplementary,
  sticky-endMelting/Annealing/ hybridization

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Tiling with DNA

• Tiling theory
• Motivation to work with DNA
• Seeman Winfrees implementation Wang tiles

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Tiling implementation

• Basic building blockDNA strands are entwined to
  form a Rigid tilewith sticky ends
• Wangs colors are represented in these sticky
  ends
• Self assembly is controllable and predictable

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Same molecule different representation
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2D structures

• A demonstration of striped lattice formation
  PAGE analysis

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2D structure images by AFM

• DAO-E AB lattice

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2D structure images by AFM
ˆ

• DAO-E AB lattice

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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

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Further work in this direction

• More complex structures were demonstratedSeeman
  s truncatedoctahedron/cubeRothemunds smilies
• Computation by self assembly

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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 solveHPP,
  SAT, math calculations (including copying and
  counting)

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Biologically relevant computation

• 2 states, 2 letters finite automaton
  implementation (2001)
• Shown to interact with biologic molecules (2004)

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Thank you for your attention
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PAGE

• Poly Acrylamide Gel Electrophoresis
• DNA (negatively charged) migrate according to
  its 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

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Rothemund origami
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single-stranded DNA origami
back
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Cellular automata counter example