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Molecular State Machines

Molecular State Machines. Masami Hagiya. Finite State Machines. Are the simplest formal computing device Have a finite number of states Change their state autonomously or according to inputs May produce outputs Are the first step towards general-purpose computers

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Molecular State Machines

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  1. Molecular State Machines Masami Hagiya

  2. Finite State Machines • Are the simplest formal computing device • Have a finite number of states • Change their state autonomously or according to inputs • May produce outputs • Are the first step towards general-purpose computers • Have many kinds of applications • Switch • Memory (both holding contents and addressing)

  3. Molecular (DNA) State Machines • Terminal-sequence machines • The terminal sequence encodes the state. • Our whiplash machine • The machine gets longer as it changes the state. • Shapiro’s automaton • The machine gets shorter as it changes the state. • Conformational machines • The state is encoded as a structure. • Yurk’s molecular tweezers • Seeman’s PX-JX2 Switch • Our hairpin-based machine…

  4. : stopper sequence B 2) A B B C B A Whiplash PCR (WPCR) B 1) A C B A

  5. 4) A C B B A C B Whiplash PCR (WPCR) B A 3) B A C B

  6. Polymerization Stop

  7. B A B C B A A B B B A C Back-hybridization B A B A C B Competing Alternative Hairpin Forms

  8. Temperature optimization for WPCR ・8 M urea 8% PAGE Komiya, et al. not 59.8 65.9 74.0 82.1 89.8 incubated 62.2 69.9 78.0 86.1 92.2 (℃) Thermal schedule 94℃ for 1 min. 　 ↓ x ℃ for 5 min. x =59.8 ~ 92.2 in 1X Pfx buffer (the composition unknown) 1 mM MgSO4 0.2 mM dATP, dCTP, dGTP 1.5 units Platinum Pfx DNA polymerase

  9. Successful implementation of transitions ・12％ PAGE Komiya, et al. ( bp ) 155 140 125 110 95 80 65 50

  10. Whiplash Machines • The machine changes its state according to its own transition table. • Various kinds of information can be encoded as a transition table. • Inputs to the machine can be a part of the table. • Multiple-data Multiple-program

  11. Shapiro’s DNA Automaton IIS-type restriction Restriction cite Spacer a’ Rest of input <S,a> <S,a> S,a → S’ Transition molecule a’ Rest of input Rest of input <S’,a’> The input sequence for a’ contains <S’,a’> for each state S’. The transition molecule cuts the input at the right place by the spacer.

  12. Shapiro’s DNA Automaton • Nature 2001 • 2 input symbols, 2 states • FokI a=CTGGCT b=CGCAGC 5’-p…22…GGATGTAC 3’-GGT…22…CCTACATGCCGAp S0,a→S0 5’-p…22…GGATGACGAC 3’-GGT…22…CCTACTGCTGCCGAp S0,a→S1

  13. Yurke: DNA Tweezers

  14. Seeman: PX-JX2 Switch

  15. Multi-state Molecular Machine input1 2 1 …… 3 3 input2 １ 2 input3 …… 3 3 1 Our goals: Successive state change Input order sensitive …… 2

  16. Hairpin-based Machine

  17. シングルヘアピンの状態遷移確認実験 7 20 20 20 Oligomer Hairpin_template (67 bp + 3’ FITC) A B C D E 10 % PAGE A : Hairpin_template B : Hairpin_template + oligomer1 C : Hairpin_template + oligomer2 D : Hairpin_template + oligomer3 E : Hairpin_template + oligomer4 Oligomer1 Oligomer2 Oligomer3 Oligomer4 20 + 20 = 40bp 15 + 20 = 35bp 10 + 20 = 30bp 5 + 20 = 25bp Bではシングルヘアピン構造にオリゴマーが結合し，ヘアピン構造が開いて状態遷移している． そのためヘアピン構造を示すバンドが減少し，新たにヘアピン構造が開いた状態のバンドが現れている． Oliogomer : ヘアピン構造を開くために用いるｓｓDNA

  18. 分子の構造変化経路 自由エネルギー • ΔG1の最小化⇒構造変化の高速化 • 妥当な変化経路の予測が必要 • 局所最適最短経路 • 大域最適最短経路 • 大域最適経路 ΔG1 ΔG2 二次構造

  19. DNAへのアゾベンゼンの導入 DNAに挿入されたアゾベンゼンの状態により，hybridizationの安定度が変化する。(Asanuma et al., 1999)

  20. 300 nm<l<400 nm 400 nm<l trans cis 二重鎖が解離 二重鎖が形成 二重鎖の形成と解離の光制御に成功

  21. Lights as Inputs (still a dream)

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