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 Nomenclature: Bases/nucleotides: A,C,T & G Strand/Oligo/ssDNA Complementary, sticky-end Melting/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 tile with sticky ends Wang’s colors are represented in these sticky ends Self assembly is controllable and predictable

A A A A A A A A A A A A A A A AA A A Same molecule – different representation

A demonstration of striped lattice formation: PAGE analysis 2D structures RedGrnBluYel

DAO-E AB lattice 2D structure images by AFM

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

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 truncated octahedron/cube Rothemund’s smilies 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

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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 their length

A A A A A A

Rothemund origami

single-stranded DNA origami back

Cellular automata: counter example