Molecular State Machines Masami Hagiya
Jan 18, 2016
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-JX2 Switch
– Our hairpin-based machine…
B AC
B
: stopper sequence
1)B
B AC
B
A2) B
A
Whiplash PCR (WPCR)
Whiplash PCR (WPCR)
B A C B
3)
B A
C
B A C B
4)B
A
Polymerization Stop
B A C B
B A
Back-hybridization
B A C B
B
A
B A C
BB A
Competing Alternative Hairpin Forms
・ 8 M urea 8% PAGE
Temperature optimization for WPCR
incubated 62.2 69.9 78.0 86.1 92.2 (℃)not 59.8 65.9 74.0 82.1 89.8
in 1X Pfx buffer (the composition unknown) 1 mM MgSO4
0.2 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
65
80
95110125140
50
155
( 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 AutomatonIIS-type restrictionRestriction cite Spacer
<S,a><S,a>
a’ Rest of input
Rest of input
a’ Rest of input
<S’,a’>
S,a → S’Transition molecule
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.
Shapiro’s DNA Automaton
• Nature 2001
• 2 input symbols, 2 states
• FokI
a=CTGGCT b=CGCAGC
5’-p…22…GGATGTAC3’-GGT…22…CCTACATGCCGAp
5’-p…22…GGATGACGAC3’-GGT…22…CCTACTGCTGCCGAp
S0,a→S0
S0,a→S1
Yurke: DNA Tweezers
Seeman: PX-JX2 Switch
Multi-state Molecular Machine
input1
input2
input3
2
1
2
3
1
3
3 3
1
2
……
……
……Our goals:Successive state changeInput order sensitive
Hairpin-based Machine
Hairpin_template Oligomer
20
7
2020
(67 bp + 3’ FITC)
Oligomer1Oligomer2Oligomer3Oligomer4
20 + 20 = 40bp15 + 20 = 35bp10 + 20 = 30bp 5 + 20 = 25bp
Oliogomer : ヘアピン構造を開くために用いるss DNA
A B C D E10 % PAGEA : Hairpin_templateB : Hairpin_template + oligomer1C : Hairpin_template + oligomer2D : Hairpin_template + oligomer3E : 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
ΔG1
ΔG2
二次構造
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
自由エネルギー
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)