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

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Cellular automata: counter example