DNA Computing and Robotics:Engineering (Science?), Fun, and Applications

Milan N. StojanovicNSF Center for Molecular Cybernetics

Department of MedicineColumbia University

Suppose we have a set of primitives:

Sensor primitives: Computing primitives: Moving primitives:

? ? ?

??

?

Recipe for Computing Primitives:

ACAA

TGGA

CACAT

TGA

CTCT

AGA

Beacons (Tyagi and Kramer)

1. Take Recognition Regions,

2. Take Nucleic acid catalysts,

+ +

Phosphodiesterase (Joyce)

E S

Ligase (Szostak)

+ +E S1

S2

+

0 1

3. And combine (for computing elements, at least) them in:

Cf. modular design (e.g. Breaker…)

0 1

I1

Stojanovic et al., ChemBioChem 2001Stojanovic et al., J. Am. Chem. Soc. 2002

0

50000

100000

150000

200000

250000

0 100 200 300 400t (min)

FU

Logic Gates: YES (Detector or Sensor Gate)

Joyce 1995, Breaker 1999, Tyagi, Kramer 1996

ACAA

TGGA

CACAT

TGA

TA C A C T FTrA

CTCTTC

TAGTGA

C

A

CG

G

GC

A GC

TC

GAA

T

AGAAG

G G

GA

CC

A

CG

G

GC

A GC

TC

GAA

T

AGAAG

CA TT AT AG CG CT

AGC

TA

TA

AT

ATC

G

TATA

TA

CACT

F

TrAG

AG

AGAG

R A*S*IA

TAT

ATGCTAGCAT

GA TA TG CA TG C

rAG

F

R

+

Cleavage

Inactive Form

Active Form

YES IA

A GG

AGG

IA

A

OF

SIA

0 10 0

I2

I1I1

I20

I2

1

Switching Primitives (Logic Gates):

ANDNOT

0 00 01

I3 I3 I3

0

I3

00

I3

I2I2I1I1 I1

I2I1I2

Three-input Gates

c3

1

2

T

c2

1

3T

c1

2

3T

c1

3

2T

i1 i2 i3

SUM

i1ANDi2ANDi3

i1ANDNOTi2ANDNOTi3

i2ANDNOTi1ANDNOTi3

i3ANDNOTi2ANDNOTi1

i1ANDi2

1

2

F

1

3

Fi1ANDi3

3

2

Fi3ANDi2

i1 i2 i3

CARRY

Some demonstrations of molecular computing:A. Full adder (Lederman et. al, Biochem. 2006) B. Maya-II (Macdonald et al. Nano Lett. 2006)

11 × 01 = 11 × 10 = 11 × 11 =

(3×1=3) (3×2=6) (3×3=9)

01 × 01 =

(1×1=1)

01 × 10 =

(1×2=2)

C. DNA Calculator (Macdonald) D. AND Hub with Beads (Rudchenko)(Yashin et al. JACS ~2007)

10A

7AND9 D10

7AND9 D10

6D7

3 41 25

3AND4A->D5

1D3 2D45A

Implementation of Naughts-and-Crosses Playing Algorithm with Deoxiribozymes: Molecular Array of YES and ANDANDNOT Gates (MAYA)

Stojanovic, Stefanovic, Nat. Biotech. 2003

9

7

4

7

8

4

4

6

9

1

2

6

1

7

6

1

6

4

9

6

7

2

7

9

18

9

1

2

6

7

9

2

1

4

2

94

3

9

4

7

9

4

8

9

1

3

6

1

8

6

1

9

6

6

8

7

6

9

7

1

4

F

X

Mg2+

-1

0

1

2

3

4

1 2 3 4 5 6 7 8 9

Wells

F

9

7

4

7

8

4

4

6

9

1

2

6

1

7

6

1

6

4

9

6

7

2

7

9

18

9

1

2

6

7

9

2

1

4

2

9

4

3

9

4

7

9

4

8

9

1

3

6

1

8

6

1

9

6

6

8

7

6

9

7

1

4

F

F

i4 i4 i4

i4i4i4

i4 i4 i4

XXOi4

-1

0

1

2

3

4

1 2 3 4 5 6 7 8 9

Wells

F

9

7

4

7

8

4

4

6

9

1

2

6

1

7

6

6

7

2

7

9

18

9

1

2

6

7

9

2

1

4

2

9

4

3

9

4

7

9

4

8

9

1

3

6

1

8

6

1

9

6

6

8

7

6

9

7

1

4

F

F

i4 i4 i4

i4i4i4

i4 i4 i4

i9 i9i9

i9 i9

i9 i9i9

4

9F

i9

XXO

O

X

-1

0

1

2

3

4

1 2 3 4 5 6 7 8 9

Wells

F

i9 XXO

O

X

X

O

9

7

4

7

8

4

4

6

9

1

2

6

1

7

6

6

7

2

7

9

18

9

1

4

2

9

4

3

9

4

7

9

4

8

9

1

3

6

1

8

6

1

9

6

1

4

F

F

i4 i4 i4

i4i4i4

i4 i4 i4

i9 i9i9

i9 i9

i9 i9i9

4

9F

i9

9

2

1

i2 i2 i2

i2 i2 i2

i2i2 i2

F

-1

0

1

2

3

4

1 2 3 4 5 6 7 8 9

Wells

F

i2

MAYA vs. Milan: Losing Game

Zn2+

The Simplest Moving Primitive:

Zn2+

But, what about multivalent design?

Pei et. al JACS, 2006

AFM Images of Spider at Starting Point

Kyle Lund, Hao Yan, video now: with Nadine Dabby, Erik Winfree

AFM images of Spider on Lanes of Substrates

Kyle Lund, Hao YanVideo with: Nadine Dabby, Erik Winfree

START

END

Center for Molecular Cybernetics Phase II?

A

B

C

D

START

START

END

A

B

END

Center Members & Friends• Erik Winfree (CS)• Hao Yan (CHE)• Niles Pierce (ApM)• Paul Krapivsky (Phys)• Sergei Rudchenko (BPh)• Nils Walter (CHE)• Milan Mrksich (CHE)• Darko Stefanovic (CS/EE)• Milan Stojanovic (MEDSci)• Nadrian Seeman (CHE)

• Henry Hess (CHE/MATS)• William Shih (CHE)• Srboljub Mijailovich (ME)• Natasha Yonoska (MATH)• Satoshi Murata (CS/ME)• Friedrich Simmel (P-CHE)• Vojislav Stojkovic (CS)• Qiao Lin (ME)• Paul Rothemund (CHE/CS)

CHE

0533096

CHE

0533096

Chemical Bonding Center NSF (CHE-0533096)

• Postdocs: Steven Taylor, Renjun Pei, Dmitry Kolpashchikov, Joanne Macdonald• Tech’s: Stanka Semova, Erik Green, Payal Pallavi, Ma Li• High Shool Program: Harvey Lederman, Yang Lee, Marko Sutovic, Kiran Pendri,

Wengho Lu, Kirill Lebedov, Srikanth Damera, George Lederman, Kaitlin Kyi. • Tiffany Elizabeth Mitchell• Collaborators:• Sergei Rudchenko (HSS), Ruslan Yashin• Darko Stefanovic (UNM), Mark Olah• Nils Walter (UM, Ann Arbor), Tony Manzo, Chamaree De Silva• Vincent Butler (Columbia)• Milan Mrksich (Chicago), Haim Tsubery• Erik Winfree (Caltech), Georg Seelig, Nadine Dabby• Hao Yan (ASU), Kyle Lund

Current funding NSF (ITR, 3xEMT, and CBC), JDRF, NIH (NCI-R21)Lymphoma and Leukemia Society Scholarship

Previously: NASA, NSF QuBIC, NSF Biophotonics, NIH (NIBIB), Searle

Acknowledgments:

M1

M2

Cell Type I

AND CellDeath

M1

Cell Type II

AND Spare Cell

B.A.M1

M2

Cell Type III

ANDC.

M3NOT

Spare Cell

NOT NOT

Glucose

GGGG

+ Insulin

Negative Feedback

1. Cell-death by Boolean Calculations:

2. Glucose-triggered movement of catalytic nanoassemblies:

Potential practical applications: