Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion

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Dec 1, 2013 (3 years and 10 months ago)

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Autonomous DNA Nanomechanical Device Capable of
Universal Computation and Universal Translational Motion


Peng Yin*, Andrew J. Turberfield

, Sudheer Sahu*, John H. Reif*


* Department of Computer Science, Duke University


Department of Physics, Clarendon Laboratory, University of Oxford




1

Motivation

2

DNA cellular computing devices


Finite state automata


Turing machine


Cellular automata


Intelligent DNA lattice


Intelligent robots,


arbitrarily complex motion


Parallel, universal


computing device

DNA nanorobotics

DNA lattices

(
Benenson
et al

03
)

DNA nanocomputation

Autonomous unidirectional DNA walker


Abstract

3

Intelligent

nanomechanical

devices

that

operate

in

an

autonomous

fashion

are

of

great

theoretical

and

practical

interest
.

Recent

successes

in

building

large

scale

DNA

nano
-
structures,

in

constructing

DNA

mechanical

devices,

and

in

DNA

computing

provide

a

solid

foundation

for

the

next

step

forward
:

designing

autonomous

DNA

mechanical

devices

capable

of

arbitrarily

complex

behavior
.

One

prototype

system

towards

this

goal

can

be

a

DNA

mechanical

device

that

is

capable

of

universal

computation,

by

mimicking

the

operation

of

a

universal

Turing

machine
.

Building

on

our

prior

theoretical

designs

and

a

prototype

experimental

construction

of

autonomous

unidirectional

DNA

walking

devices

that

move

along

linear

tracks,

we

present

in

this

paper

the

design

of

a

nanomechanical

DNA

device

that

autonomously

mimics

the

operation

of

a

2
-
state

5
-
color

universal

Turing

machine
.

Our

autonomous

nanomechanical

device,

which

we

call

an

Autonomous

DNA

Turing

Machine
,

is

thus

capable

of

universal

computation

and

hence

complex

translational

motion

which

we

define

as

universal

translational

motion
.

Prior work

4



Self

assembly

of

DNA

lattices
:



DX,

rhombus,

TX,

4
x
4
,

and

barcode

lattices





DNA

nano
-
robotics

devices
:



An

autonomous

DNA

unidirectional

walking

device

(Reif’s

group)




DNA

nano
-
computation
:



Design

of

a

non
-
autonomous

universal

DNA

Turing

machine

driven

by

enzymes

(Rothemund)




Autonomous

DNA

Finite

State

Automata

(Shapiro’s

group)

Comp 101: Turing Machine

5

Turing Machine

Tape

Read/write head

Transition rule



A Turing machine is a theoretical computational device.



DNA Turing Machine: Structure

6

Transitional rules:
Rule molecules

Turing head:
Head molecules

Data tape:
Symbol molecules

Molecular structure

Operational overview

7

Autonomous universal DNA Turing machine: 2 states, 5 colors

DNA Biochemistry 101:

8

Recognition site

cleavage site

Complementary
sticky ends

Restriction enzymes:

9

Operation: Step 1

10


In

Step
1
,

the

active

Head

Molecule

(
H
)

is

ligated

to

the

Symbol

Molecule

(
S
)

directly

below

it,

creating

an

endonuclease

recognition

site

in

the

ligation

product
.

The

ligation

product

is

subsequently

cleaved

into

two

molecules

by

an

endonuclease
.

The

sticky

end

of

each

of

the

two

newly

generated

molecules

encodes

the

current

state

(
q
)

and

the

current

color

(
c
)
.


Operation: Step 2

11

In

Step

2
,

the

Symbol

Molecule

is

ligated

to

floating

Rule

Molecule,

which

possesses

complementary

sticky

end

to

it

and

corresponds

to

one

entry

in

the

Turing

machine

Transitional

table
.

The

ligation

product

is

subsequently

cleaved,

generating

a

new

Symbol

Molecule

dictated

by

the

current

state

(
q
)

and

color

(
c
)

as

well

as

the

transitional

rule
.

The

new

Symbol

Molecule

encodes

the

new

color

(
c’
)

in

its

sticky

end
.


Operation: Step 3

12

In

Step

3
,

the

newly

generated

Symbol

Molecule

(
S
)

is

further

modified

by

an

Assisting

Molecule

(
E
)

so

that

it

encodes

the

new

color

(
c’
)

in

its

duplex

portion

(rather

than

sticky

end)

and

possess

a

default

sticky

end

([
s
])
.

Operation: Step 4

13

In

Step

4
,

the

Head

Molecule

is

ligated

to

a

floating

Rule

Molecule,

which

possesses

a

complementary

sticky

end

to

it

and

corresponds

to

one

entry

in

the

Turing

machine

Transitional

Table
.

The

ligation

product

is

in

subsequently

cleaved,

generating

a

new

Head

Molecule

whose

duplex

portion

encodes

information

of

Turing

machine's

next

state

(
q’
)

and

whose

sticky

end

encodes

the

moving

direction

of

the

head

(
p’
)
.

Operation: Step 5

14

In

Step

5
,

the

sticky

end

of

the

Head

Molecule

(
H
)

dictates

it

to

hybridize

with

either

the

Head

Molecule

to

its

left

or

to

its

right

(
H’
),

depending

on

which

of

its

neighbors

possesses

a

complementary

sticky

end
.

Next,

the

ligation

product

between

these

two

Head

Molecules

is

cleaved,

generating

sticky

ends

encoding

the

position

information

for

the

head

molecules

(
p,

p’
)

and

the

new

state

(
q’
)
.

Operation: Step 6

15

In

Step

6
,

the

Head

Molecule,

H’
,

is

modified

by

a

floating

Assisting

Molecule

(
T
)

and

becomes

active
:

it

encodes

the

state

information

in

its

duplex

part

and

possesses

an

active

sticky

end

([
s
])

and

thus

becomes

active,

ready

to

interact

with

the

Symbol

Molecule

located

directly

below

it
.


Operation: Step 7

16

In

Steps

7

and

8
,

the

Head

Molecule

H

is

modified

by

floating

Assisting

Molecules

and

is

restored

to

its

inactive

configuration

(with

a

default

sticky

end)
.



Operation: Step 8

17

Reaction flow chart

18

Technical challenges: encoding space: overlaid molecules

19



Challenge
:

use

limited

encoding

space

dictated

by

the

four

(six)

letter

vocabulary

of

DNA

bases

and

by

the

sizes

of

the

recognition,

restriction,

and

spacing

regions

of

endonucleases
.




Technique
:

use

overlaid

molecules

and

carefully

select

the

sticky

ends

to

avoid

undesirable

reactions
.



Overlaid molecules

Unique 3
-
base sticky ends

Technical challenges: Futile reactions

20



Many

futile

reactions

happen

in

the

background

during

the

operation

of

the

DNA

Turing

machine
.





A

key

feature

of

these

futile

reactions

is

that

they

are

fully

reversible
.

This

is

critical

in

ensuring

the

autonomous

operation
:

we

initially

supply

the

system

with

sufficiently

high

concentrations

of

Rule

Molecules

and

Assisting

Molecules

as

well

as

all

the

byproducts

generated

in

the

futile

reactions
.

As

such,

the

futile

reactions

will

reach

a

dynamic

balance

and

the

active

component

will

not

be

depleted

by

the

futile

reactions
.


Conclusion & Future work

21



The

design

of

a

DNA

Autonomous

Universal

Turing

machine




Universal

translational

motion




Computer

simulation
:

http
:
//www
.
cs
.
duke
.
edu/~py/paper/dnaUTM/simulation




Autonomous

DNA

cellular

computing

devices
:



DNA

Finite

state

automata



DNA

Turing

machine



DNA

Cellular

automata

Turing machine

Finite state automata

Cellular automata

Experimental construction

Computer simulation

Design

Computer simulation