topics in biological physics design and self-assembly of two-dimensional dna crystals benny gil...
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![Page 1: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/1.jpg)
Topics in Biological Physics
Design and self-assembly oftwo-dimensional DNA
crystals
Benny Gil16/12/08
Fig3.a
![Page 2: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/2.jpg)
DNA computation
• Solving computer science problems• Biologically relevant computations• Nanostructures
![Page 3: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/3.jpg)
DNA structure
• Structure• Neighboring Vs Complementary bases• Tm• Nomenclature:
Bases/nucleotides: A,C,T & GStrand/Oligo/ssDNAComplementary, sticky-endMelting/Annealing/ hybridization
![Page 4: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/4.jpg)
• Tiling theory• Motivation to work
with DNA• Seeman & Winfree’s
implementation: Wang tiles
Tiling with DNA
![Page 5: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/5.jpg)
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
![Page 6: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/6.jpg)
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Same molecule –different representation
![Page 7: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/7.jpg)
• A demonstration of striped lattice formation: PAGE analysis
2D structuresRed Grn Blu Yel
![Page 8: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/8.jpg)
DAO-E AB lattice
2D structure images by AFM
![Page 9: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/9.jpg)
DAO-E AB lattice
2D structure images by AFM
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![Page 10: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/10.jpg)
• 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
![Page 11: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/11.jpg)
Further work in this direction
• More complex structures were demonstrated:Seeman’s truncatedoctahedron/cubeRothemund’s smilies
• Computation by self assembly
![Page 12: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/12.jpg)
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)
![Page 13: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/13.jpg)
• 2 states, 2 letters finite automaton implementation (2001)• Shown to interact with biologic molecules (2004)
Biologically relevant computation
![Page 14: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/14.jpg)
Thank you for your attention
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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 theirlength
![Page 16: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/16.jpg)
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Rothemund origami
![Page 18: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/18.jpg)
single-stranded DNA origami
back
![Page 19: Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a](https://reader030.vdocument.in/reader030/viewer/2022032800/56649d485503460f94a22df1/html5/thumbnails/19.jpg)
Cellular automata: counter example