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Finding a Hamiltonian path on a folded DNA shape. Hanny Seaman Advisors: Dr. Ido Bachelet Prof. Ron Unger 2013. The Mina and Everard Goodman Faculty of Life Sciences , Bar- Ilan University Ramat- Gan. Hamiltonian path. 1 3245. 1 472365. NP-complete problem!. - PowerPoint PPT Presentation
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Finding a Hamiltonian path on a folded DNA shape
The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University Ramat-Gan
Hanny Seaman
Advisors:Dr. Ido BacheletProf. Ron Unger
2013
Hamiltonian path
147236513245
NP-complete problem!
DNA strands represent vertices and paths of a 7-node graph
Mix in tube – self complementarity Filtration
Adleman’s solution
Folding of DNA to create nanoscale shapes
Terminology:◦ Scaffold◦ Staples
caDNAno
Origami DNA
Representing the graph Example: 4 vertices0
Representing the graph Example: 4 vertices0
1
Representing the graph Example: 4 vertices0
1
2
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Representing the graph Example: 4 vertices0
1
23
Example: 4 vertices
Start End Sequence Length Color
0[45] 0[26] GGGCGAAAAACCGTCTATCA 20#aaaa00
0[64] 0[46] CGTGGACTCCAACGTCAAA 19#cc0000
1[26] 1[45] TGTTGTTCCAGTTTGGAACA 20#f74308
1[46] 1[64] AGAGTCCACTATTAAAGAA 19#03b6a2
2[45] 2[26] TAGCCCGAGATAGGGTTGAG 20#03b6a2
2[64] 2[46] CCCTTATAAATCAAAAGAA 19#aaaa00
3[26] 3[45] GAAAATCCTGTTTGATGGTG 20#f7931e
3[46] 3[64] GTTCCGAAATCGGCAAAAT 19#007200
Example: 4 vertices
Edges details
Example: 4 vertices
Scaffold details
7 vertices – planning the graph
Calculate the edges and verticessequences
7 vertices – planning the graph
1 2
7
6
5
4
3
Experiments
7 vertices – increase number of vertices
Experiment 1- increase number of vertices
7 vertices – increase number of vertices
1
Experiment 1- increase number of vertices
7 vertices – increase number of vertices
1 2
Experiment 1- increase number of vertices
7 vertices – increase number of vertices
1 2
3
Experiment 1- increase number of vertices
Experiment 1- increase number of vertices
7 vertices – increase number of vertices
1 2
7
6
5
4
3
Experiment 1- increase number of vertices
7 vertices – increase number of vertices
Unfolded segments
Partial fold
Max fold
Experiment 2- Stepwise assembly
1
Experiment 2- Stepwise assembly
1
Experiment 2- Stepwise assembly
1 2
Experiment 2- Stepwise assembly
1 2
5
4
3
Experiment 2- Stepwise assembly
1 2
7
6
5
4
3
Experiment 3- 7 vertices - FACS
1 2
7
65
4
3
Experiment 3- 7 vertices - FACS
(1)Beads
(2)Beads
Ver1-marked
(3)Beads
Ver7-marked
(4)BeadsVer1
unmarked Vers 2-6
Ver7-markedAll staples
(5)Beads
Ver1-marked Vers 2-6
Ver7-markedAll staples
FL4-H
Cou
nt
102 103 104 105 106 1070
682
1364
2046
2728
Cou
nt
0
1364
2728
1364
2728
Cou
nt
1364
2728
Cou
nt
1364
2728
Cou
nt
102 103 104 105 106 107
FL4-H
1364
2728
Cou
nt
Experiment 3- 7 vertices - FACS
Results - Red
(5)(4)(3)(2)(1)
FL1-H
Cou
nt
102 103 104 105 106 1070
656
1311
1967
2622
Cou
nt
0
1311
2622
1311
2622
Cou
nt
1311
2622
Cou
nt
1311
2622
Cou
nt
102 103 104 105 106 107
FL1-H
1311
2622
Cou
nt
Experiment 3- 7 vertices - FACS
Results - Green(5)(4)(3)(2)(1)
Representing graph using origami DNA
Find if exists a Hamiltonian Path
Summary
Watching folded DNA using AFM Experiments with:
◦ edges including polyT◦ Large number of vertices◦ Graph with several paths – not only Hamiltonian
What’s next?
' והליווי" ההנחייה על אונגר רון ולפרופ בצלת עידו ר לד. הפרוייקט כל לאורך
. העזרה על המעבדה חברי לכל
! ההקשבה על תודה
תודות