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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 - PowerPoint PPT Presentation
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Topics in Biological Physics
Design and self-assembly oftwo-dimensional DNA
crystals
Benny Gil16/12/08
Fig3.a
DNA computation
• Solving computer science problems• Biologically relevant computations• Nanostructures
DNA structure
• Structure• Neighboring Vs Complementary bases• Tm• Nomenclature:
Bases/nucleotides: A,C,T & GStrand/Oligo/ssDNAComplementary, sticky-endMelting/Annealing/ hybridization
• Tiling theory• Motivation to work
with DNA• Seeman & Winfree’s
implementation: Wang tiles
Tiling with DNA
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
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Same molecule –different representation
• A demonstration of striped lattice formation: PAGE analysis
2D structuresRed Grn Blu Yel
DAO-E AB lattice
2D structure images by AFM
DAO-E AB lattice
2D structure images by AFM
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• 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
Further work in this direction
• More complex structures were demonstrated:Seeman’s truncatedoctahedron/cubeRothemund’s smilies
• Computation by self assembly
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)
• 2 states, 2 letters finite automaton implementation (2001)• Shown to interact with biologic molecules (2004)
Biologically relevant computation
Thank you for your attention
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 theirlength
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Rothemund origami
single-stranded DNA origami
back
Cellular automata: counter example