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

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)

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)

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

© 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)

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)

© 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)

© 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)

© 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)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 1 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 2 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 3 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 4 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 5 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 6 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 7 © 2004 SNU CBIT (Center for Bioinformation Technology)

© 2004 SNU CBIT (Center for Bioinformation Technology) Step 8 © 2004 SNU CBIT (Center for Bioinformation Technology)

Overview of the operation © 2004 SNU CBIT (Center for Bioinformation Technology)