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 Have many kinds of applications –Switch –Memory (both holding contents and addressing)

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-JX 2 Switch –Our hairpin-based machine…

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

BACB 3) BA C BACB 4) B A

Polymerization Stop

BACB B A Back-hybridization BAC B B A BA C B B A Competing Alternative Hairpin Forms

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

・ 12 ％ PAGE ( bp ) Successful implementation of transitions Komiya, et al.

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

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

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

Yurke: DNA Tweezers

Seeman: PX-JX 2 Switch

Multi-state Molecular Machine input1 input2 input １ 2 …… Our goals: Successive state change Input order sensitive

Hairpin-based Machine

Hairpin_template Oligomer 20 7 (67 bp + 3’ FITC) Oligomer1 Oligomer2 Oligomer3 Oligomer = 40bp = 35bp = 30bp = 25bp Oliogomer : ヘアピン構造を開くために用いるｓｓ DNA 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 シングルヘアピンの状態遷移確認実験 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．

分子の構造変化経路 ΔG 1 ΔG 2 二次構造 ΔG 1 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

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)

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

Lights as Inputs (still a dream)