1. Peng Yin… Presented by Sung-kyu Kim
Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translation Motion
Peng Yin…
Presented by Sung-kyu Kim

2. Universal Turing Machine
Read-write head : head has internal state q
Linear tape of cell : each cell has a color c
Color of the cell and the state of the head together determines a transition
Smallest Turing machine capable of universal computation is 2-state 5-color Turing machine
A universal Turing machine with 2-state 5-colors
© 2004 SNU CBIT (Center for Bioinformation Technology)

3. Structural overview (1/2)
H: Head-molecules
S: Symbol-molecules
q: state {QA = LONG, QB = SHORT}
c: color {CA, CB, CC, CD, CE}
p: position {PA, PB, PC}, position type of Head-molecules
An information encoding scheme : Xa[y]b
X: duplex portion of DNA strand
[y]: sticky end portion
a, b are state/color/position encoded in X, [y] respectively
is complementary sticky end of [y]
© 2004 SNU CBIT (Center for Bioinformation Technology)

4. Structural overview (2/2)
© 2004 SNU CBIT (Center for Bioinformation Technology)

5. © 2004 SNU CBIT (Center for Bioinformation Technology)
4 endonucleases
The recognition site of an enzyme is bounded by a box and the cleavage site indicated with a pair of bold arrows
The symbol ‘-’ can be anything of ATGC
© 2004 SNU CBIT (Center for Bioinformation Technology)

6. Operational overview - terms
H: Head-molecule
S: Symbol-molecule
R: Rule-molecule
A: Assisting-molecule
[s]: active sticky end -> active Head-molecule
- R & A are floating.
© 2004 SNU CBIT (Center for Bioinformation Technology)

7. © 2004 SNU CBIT (Center for Bioinformation Technology)
Operational overview
Stage 1
Active Head-molecule interacts with Symbol molecule below it
Stage 2
New S and H are ligated to floating Rs. (2), (4)
Stage 3
S is modified by an A.
H hybridize with either side of H (left or right)
Stage 4
First H is restored to its inactive configuration
Second H becomes active H
© 2004 SNU CBIT (Center for Bioinformation Technology)

8. © 2004 SNU CBIT (Center for Bioinformation Technology)
Active Head-molecule
Operational overview
(1)
(5)
(3)
(4)
(6)
(7,8)
(2)
© 2004 SNU CBIT (Center for Bioinformation Technology)

9. © 2004 SNU CBIT (Center for Bioinformation Technology)
Implementation step
Each step consists of ligation and cleavage events
Configuration of the Head-molecules array along the Head-track is
^ denotes active configuration
Symbol molecules array along the Symbol-track
© 2004 SNU CBIT (Center for Bioinformation Technology)

10. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 1
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11. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 2
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12. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 3
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13. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 4
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14. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 5
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15. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 6
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16. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 7
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17. © 2004 SNU CBIT (Center for Bioinformation Technology)
Step 8
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18. Overview of the operation
© 2004 SNU CBIT (Center for Bioinformation Technology)