NSF-ITR: EIA-0086015:

Structural DNA Nanotechnology

Nadrian C. Seeman, Subcontractor

Department of Chemistry
New York University
New York, NY 10003, USA
[Link]@[Link]
February 17, 2003
 ~20 Å

DNABASEPAIRS
A T H
3.4 Å H O CH
N N H 3
C
C C C C
N C N H N C H
R
N C C N
10-10.5 H O R
Pairs/Turn

G C
H

H O H N H
N
C
C C C C
N C N C H
N H
R
N C C N

N H O R

H
 Reciprocal Exchange:
A Theoretical Tool To Generate
New DNA Motifs

Reciprocal
Exchange

Resolve
Reciprocal Exchange in a
Double Helical Context
a

Reciprocal

Exchange

+
Resolve

Reciprocal

Exchange

+
Resolve
 Biological Reciprocal Exchange:
The Holliday Junction
A•T
T•A
G•C
T•A
1 C•G 4
CGA TCG
• • • • • •
GC T AG C
2 G•C 3
I
A•T
1 4 2 3 A•T C•G
T•A A•T
A•T T•A
T•A A•T G•C T•A
1 T•A 4
G•C C•G
T•A A•T CGA C G TC G
• • • • • • • •
C•G G•C G CTG CAGC
A•T T•A 2 A•T 3
G•C C•G C•G
C•G G•C A•T
T•A A•T
T•A
II 1 4
G•C
CGA C T A G TC G
• • • • • • • • • •
GC TG A T CAG C
2 C•G 3
A•T
T•A
Design of Immobile Branched Junctions:
Minimize Sequence Symmetry
I
C•G
G• C
C•G
A• T
A• T
T •A
1 C•G 4
C• G
G C A C GA G T T GA T A C C G
II • • • • • • • • • • • • • • • • IV
C G T G C T C A A C T A T G GC
C• G
2 C• G 3
G• C
A• T
A• T
T• A
G• C
C• G

III Seeman, N.C. (1982), J. [Link]. 99, 237-247.

Sticky-Ended Cohesion: Affinity
A
•T
•G
•G
•C
•T
•A
•G
•T
•T
•G
•C
•A
•T
•G
•A
•T
•G
•C
•T
• CACG
TACCGATCAACGTACTACGA + G
•C
•G
•T
•T
•A
•G
•G
•T
•G
•A
•T
•A
•C
•C
•G
•T
•A
•C
•
GTGCCGCAATCCACTATGGCATG

HYDROGEN BONDING

ATGGCTAGTTGCATGATGCTCACGGCGTTAGGTGATACCGTAC
• • • • •• • • • • • • • • • • • • • • • • • • • • • •• • • •• • • • • • • •• • •
TACCGATCAACGTACTACGAGTGCCGCAATCCACTATGGCATG

LIGATION

A
•T
•G
•G
•C
•T
•A
•G
•T
•T
•G
•C
•A
•T
•G
•A
•T
•G
•C
•T
•C
•A
•C
•G
•G
•C
•G
•T
•T
•A
•G
•G
•T
•G
•A
•T
•A
•C
•C
•G
•T
•A
•C
•
TACCGATCAACGTACTACGAGTGCCGCAATCCACTATGGCATG
Sticky-Ended Cohesion: Structure

Qiu, H., Dewan, J.C. & Seeman, N.C. (1997) J. Mol. Biol. 267, 881-898.
 The Central Concept:
Combine Branched DNA with Sticky Ends to
Make Objects, Lattices and Devices

B' B'

A
B' A'

A
A'

B A
A'

B B

Seeman, N.C. (1982), J. [Link]. 99, 237-247.

O B J E C T I V E S & A P P L IC A T I O N S

[1] Architectural Control

DESIGN MOLECULES TO ASSEMBLE INTO ORDERED ARRAYS.
[A] SCAFFOLD MACROMOLECULAR CRYSTALLIZATION (PERIODIC).
[B] SCAFFOLD NANOELECTRONICS ASSEMBLY (PERIODIC).
[C] GENERATE ALGORITHMIC PATTERNS (APERIODIC).

[2] Nanomechanical Devices

[A] NANOROBOTICS.
[B] NANOFABRICATION.
[C] MOLECULAR PEGBOARDS.

[3] Self-Replicating Systems

A Method for Organizing Nano-Electronic Components

Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, 295-300..

A Suggestion for a Molecular Memory Device
Organized by DNA (Shown in Stereo)

Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, 295-300.

 WHY D N A?

PRED ICT ABLE IN T ERM OLECU LA R IN T ERA CT IO N S

CON VEN IEN T A U T OMA T ED CHEM IS TRY

CON VEN IEN T M OD IFYIN G EN ZYMES

LOCALLY ST IFF PO LYMER

EXTERN A LLY READ A BLE CO D E

HIGH FU N CT ION A L GRO U P D EN SITY

PRO T OT YPE FOR MA N Y D ERIV AT IVES

A Method to Establish DNA Motif Flexibility
32
P REPORTER STRANDS
P

LIGA TI ON

LIGA TI ON
LIGATION

LIGATION
LIGATION
LIGA TI ON
LIGATION
LA RGER LI NEA RS LA RGER CYCLICS

A PPLY DI RECTLY EXONUCLEA SE FIRST

CYCLI C
MOLECULES
LINEAR
A ND
CYCLIC
MOLECULES

DENATURI NG GEL
AUTORADI OGRAM
Geometrical Constructions
(Regular Graphs)

Cube: Junghuei Chen

Truncated Octahedron: Yuwen Zhang

Cube ..

Chen, J. & Seeman. N.C. (1991), Nature 350, 631-633..

Truncated
Octahedron
Zhang, Y. & Seeman, N.C. (1994),
J. Am. Chem. Soc. 116, 1661-1669.
Construction
of
Crystalline
Arrays
 REQU IREMEN TS FOR LATTICE
D ESIGN COMPON EN TS

PRED ICT ABLE IN T ERA CTION S

PRED ICT ABLE LOCA L PROD U CT ST RU CT U RES

ST RU CT U RA L IN T EGRIT Y
 Derivation of DX and TX Molecules
DS + DS DX TX

2 Reciprocal
Exchanges

+ 2 Reciprocal
Resolve Exchanges
Twice

Resolve
Twice

2 Reciprocal
Exchanges

+ 2 Reciprocal
Resolve Exchanges
Twice

Resolve
Twice

Seeman, N.C. (2001) NanoLetters 1, 22-26.

2D DX Arrays

Erik Winfree (Caltech)

Furong Liu
Lisa Wenzler
 Derivation of DX+J Molecules

D X H P D X + J

Reciprocal

Exchange

Resolve

Seeman, N.C. (2001) NanoLetters 1, 22-26.

Schematic of a Lattice Containing
1 DX Tile and 1 DX+J Tile

A B*
AFM of a Lattice Containing
1 DX Tile and 1 DX+J Tile

Winfree, E., Liu, F., Wenzler, L.A. & Seeman, N.C. (1998), Nature 394, 539-544.
Schematic of a Lattice Containing
3 DX Tiles and 1 DX+J Tile
A B C D*
AFM of a Lattice Containing
3 DX Tiles and 1 DX+J Tile

Winfree, E., Liu, F., Wenzler, L.A. & Seeman, N.C. (1998), Nature 394, 539-544.
 Holliday Junction
Parallelogram Arrays

Chengde Mao
Holliday Junction Parallelogram Arrays
I I
II I

1 4 1 4
II IV II IV
2 3 2 3

III IV
III III

Y Z
X X
B' D'

A' C'
D B
C A

SELF
ASSEMBLY

Mao, C., Sun, W & Seeman, N.C. (1999), J. Am. Chem. Soc. 121, 5437-5443.
Holliday Junction Parallelogram Arrays

Mao, C., Sun, W & Seeman, N.C. (1999), J. Am. Chem. Soc. 121, 5437-5443.
 Triple Crossover
Molecules

Furong Liu, Jens Kopatsch, Hao Yan

Thom LaBean, John Reif
Triple Crossover Molecules
 TX+J Array

A B*

LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H.
& Seeman, N.C (2000), J. Am. Chem. Soc. 122, 1848-1860.
 TX Array With Rotated Components

A B C C' D

ABArray

ABC'DArray

LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H.
& Seeman, N.C (2000), J. Am. Chem. Soc. 122, 1848-1860.
 Progress
Toward
Three-Dimensional
Arrays
Furong Liu Pam Constantinou
Jens Birktoft Chengde Mao
Yariv Pinto Phil Lukeman
Hao Yan Jens Kopatsch
Tong Wang Bill Sherman
Bob Sweet Mike Becker
 A 3D TX Lattice

A B C C' D D'

ABArray

QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.

ABC'D'Array

Furong Liu Pam Constantinou

Jens Birktoft Phil Lukeman
Yariv Pinto Chengde Mao
Hao Yan Bill Sherman
Bob Sweet Mike Becker
A 3D Trigonal DX Lattice

Chengde Mao Pam Constantinou

Jens Birktoft Phil Lukeman
Yariv Pinto Furong Liu
Hao Yan Bill Sherman
Bob Sweet Mike Becker
Algorithmic Assembly

Chengde Mao
Thom LaBean
John Reif
 The XOR Operation

A B A XOR B
0 0 0
0 1 1 A
A XOR B
1 0 1 B
1 1 0
 Cumulative XOR

A
A XOR B
B (A XOR B) XOR C
C
A Cumulative XOR Calculation: Tiles

Mao, C., LaBean, T.H., Reif, J.H. &

Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation: System

xi = 0 xi = 1
xi = 0 Si xi = 1 Si yi = 0 Pair to C1 S0

0 1 C1 C2
Si-1 Si-1 Pair to C2

yi = 0 yi = 0 yi = 1 yi = 1
xi = 0 xi = 1 xi = 0 xi = 1
yi-1 = 0 yi-1 = 1 yi-1 = 1 yi-1 = 0
yi = 0 yi = 0 yi = 1 yi = 1

0 0 1 1
yi-1 = 0 xi = 0 yi-1 = 1 xi = 1 yi-1 = 1 xi = 0 yi-1 = 0 xi = 1

Mao, C., LaBean, T.H., Reif, J.H. &

Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation: Assembly
Y4
Y3 0

Y2 0 0

Y1 1 1 X4
1 0 X3 Y4
C1 1 X2 Y3 1
C2 X1 Y2 1 0

Y1 0 1 X4
1 1 X3
C1 1 X2
C2 X1
Mao, C., LaBean, T.H., Reif, J.H. &
Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation:
Extracting the Answer

Y 2

Y 1

X 2

C 1 X 1

C 2

Mao, C., LaBean, T.H., Reif, J.H. &

Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation: Data
Calculation 1 Calculation 2

1 1
M C 1 0 / C 1 0 / M
0 0
2,000 2,000
1,500 X4 = 0 X4 =0 1,500
800 X3 = 1 X3 =1 800
600 X2 = 1 X2 =0 600
500 X1 = 1 X1 =1 500
400 C2 C2 400

300 300

Y1 = 1 Y1 = 1
200 200

Y2 = 0 Y2 = 1

100 100
Y3 = 1
Y3 = 0

Y4 = 1 Y4 = 0

Mao, C., LaBean, T.H., Reif, J.H. &

Seeman, N.C. (2000), Nature 407, 493-496.
N-Colorability of Graphs

Natasha Jonoska
Phiset Sa-Ardyen
 A 3-Colorable Graph and its Prototype for Computation

• A graph is 3-colorable if it is possible to assign one color to each vertex such that no two adjacent vertices are
colored with the same color. In this example, one 2-armed branched molecule, four 3-armed branched molecules and
one 4-armed branched molecule are needed.
• (b) The same graph was chosen for the construction. Since the vertex V5 in (a) has degree 2, for the experiment a
double helical DNA is used to represent the vertex V5 and the edges connecting V5 with V1 and V4. The target
graph to be made consists of 5 vertices and 8 edges. (c) The target graph in DNA representation.
 Results
• An irregular DNA graph whose edges correspond to DNA helix axes has
been constructed and isolated based on its closed cyclic character.
• The molecule may contain multiple topoisomers, although this has no
impact on the characterization of the product.
• The graph assembles with the correct edges between vertices, as
demonstrated by restriction analysis
Six-Helix Bundle

Fred Mathieu
Chengde Mao
Six-Helix DNA Bundle

Fred Mathieu
<----------------7.3 Microns----------------> Shiping Liao
Chengde Mao
 DNA
Nanomechanical
Devices
 B-Z Device

Chengde Mao
Right-Handed and Left-Handed DNA

[-] NODE [+] NODE

RIGHT-HANDED LEFT-HANDED
B-DNA Z-DNA
[-] NODES [+] NODES
A Device Based on the B<-->Z Transition

- Co(NH 3)6+++ Z-B B-Z + Co(NH 3)6+++

Mao, C., Sun, W., Shen, Z. & Seeman,N.C. (1999), Nature 397, 144-146.
 FRET Evidence for Motion Induced
by the B→ Z Transition
Donor Energy Transfer Acceptor Energy Transfer
25 25

20 20

15 15
Percent Energy Transfer Percent Energy Transfer
10 10

5 5

0 0
B Z B Z B Z B Z
Solution Conditions Solution Conditions

Proto-Z Control

Mao, C., Sun, W., Shen, Z. & Seeman, N.C. (1999), Nature 397, 144-146.
Sequence-Dependent
Device

Hao Yan
Derivation of PX DNA
PX
a

Reciprocal
Exchange
Everywhere
+
Resolve
Everywhere

Reciprocal
Exchange
Everywhere
+
Resolve
Everywhere

Seeman, N.C. (2001) NanoLetters 1, 22-26.

PX DNA

Seeman, N.C. (2001) NanoLetters 1, 22-26.

 P X J X 2

A B A B

C D D C

Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65..
Switchable Versions of PX and JX2
P X J X 2

A B A B

C D D C
Machine Cycle of the PX-JX2 Device
A B

I II

PX JX2
A B A B

C D

A B

C D D C

IV III

D C
The PX-JX2 System is Robust

Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.
System to Test the PX-JX2 Device

PX PX PX

JX2

JX2 JX2
AFM Evidence for Operation
of the PX-JX2 Device

Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.
 New
Cohesive Motifs
Paranemic Cohesion

Xiaoping Zhang
Paranemic Cohesion with the PX Motif

Left: Ubiquitous Reciprocal Exchange Creates a PX Molecule.

Center Right: The Strand Connectivity of a PX Molecule.
Far Right: The Blue and Red Dumbbell Molecules are Paranemic.
PX Cohesion of DNA Triangles: Theory

+
PX Cohesion of DNA Triangles: Experiment

Zhang, X. Yan, H.,Shen, Z. & Seeman, N.C. (2002) J Am. Chem. Soc.124, 12940-12941 (2002)
Edge-Sharing

Hao Yan
One-Dimensional Arrays of Edge-Sharing Triangles
(Short Direction)

A'
A

~20 nm

Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.

One-Dimensional Arrays of Edge-Sharing Triangles
(Long Direction)

B
B'

~30 nm

Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.

 One-Dimensional Arrays of
Double Edge-Sharing Triangles

~20 nm

A'

~30 nm

Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.

 A Cassette for the
Insertion of a PX-JX2
Device into a 2D TX
Array
Baoquan Ding
 TX Array With Rotated Components

A B C C' D

ABArray

ABC'DArray

LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H.
& Seeman, N.C (2000), J. Am. Chem. Soc. 122, 1848-1860.
Cassette to Insert the PX-JX2 Device
~Perpendicularly Into a TX Lattice
P1

4B

1
P2
3

4A
2B

5
PX Conformation
2A

J1
2B

3
J2
1

4A
4B

5 2A JX2 Conformation
Molecular Models of the 2 states of the Sequence-Driven DNA Devices
Application of the PX-JX2 Device
in a 1D Molecular Pegboard
PX JX

PX JX JX JX PX JX PX PX

1 2 3 4 5 6 7 8

PX + MARKER ---> MARKED PX JX INERT

+ --->

PX JX JX JX PX JX PX PX

1 2 3 4 5 6 7 8
Towards 2D Circuits

Alessandra Carbone (IHES)

Circuits and triangular patterns
2 layers assembly
 Tiles

inputs

operation

TX Molecule
outputs
Molecular Programming: programmed board

4 different states
 Possible Components: Programmable Pawns
PX PX JX JX

PX JX JX PX

Possible Components: TX Middle Domains

Possible Arrangement
PX PX JX JX JX PX PX JX
(a) (b)
second layer
first layer
template

(c) (d)
Control Region & Sticky Ends on the Same Strand

PX Conformation

JX2 Conformation
Mix & Split Synthesis -- Central
Levulinyl Protected Branch Point
3' Box 1 Box 2 5'
1. Perform
from EndConventional 3'-->5'
of Box 1 to Start Synthesis
of Box 2.
3' Box 1 Box 2 5'
2. Split Growing Strands
Compartments; intotoA,Box
Add Base T, C,
2. G
3' Box 1 Box 2 5'
3' Box 1 Box 2 5'
3' Box 1 Box 2 5'
3' Box 1 Box 2 5'
Add Same Base [or F(Base)] with Levulinyl
3. Protection and5' Phosphoramidite to Box 1.
3' Box 1 Box 2 5'
3' Box 1 Box 2 5'
3' Box 1 Box 2 5'
3' Box 1 Box 2 5'
Combine Growing
Repeat Steps 2 andStrand
3 until Supports;
Boxes are filled.
4.
3' 5'
3' 5'
3' 5'
3' 5'
5. Complete
Strands Conventional Synthesis of the
3' 5'
3' 5'
3' 5'
3' 5'
Mix & Split Synthesis -- Ends
Levulinyl Protected Branch Point
3' Box 1 Box 2 5'
Perform Conventional 3'-->5' Synthesis
1. from End of Box 1 to Start of Box 2.
3' Box 1 Box 2 5'
2. Reverse Polarity of Strand Growing
at Branch; Add Directionality Segment.
5' Box 1 Box 2 5'
Split Growing Strands into A, T, C, G
3. Compartments; Add Base to Box 2.
5' Box 1 Box 2 5'
5' Box 1 Box 2 5'
5' Box 1 Box 2 5'
5' Box 1 Box 2 5'
4. Add Same Base
Protection and5'[or F(Base)] with Levulinyl
Phosphoramidite to Box 1.
5' Box 1 Box 2 5'
5' Box 1 Box 2 5'
5' Box 1 Box 2 5'
5' Box 1 Box 2 5'
Combine Growing
Repeat Steps 3 andStrand
4 until Supports;
Boxes are filled.
5.
5' 5'
5' 5'
5' 5'
5' 5'
Triple Crossover Molecules
An Algorithmic Arrangement Based on Mix & Split Synthesis
 Summary of Results (1)
• Reciprocal exchange generates new DNA
motifs, and sequence-symmetry
minimization provides an effective way to
generate sequences for them.
• Sticky ends, PX cohesion and edge-sharing
are can hold DNA motifs together in a
sequence-specific fashion.
 Summary of Results (2)
• 2D lattices with tunable features have been
built from DX, TX and DNA parallelogram
motifs. Preliminary evidence for 3D
assembly has been obtained.
• DNA nanomechanical devices have been
produced using both the B-Z transition and
PX-JX2 conversion through sequence
control.
 Summary of Results (3)
• An algorithmic 4-bit cumulative XOR
calculation has been performed.
• An irregular graph has been synthesized in
solution, establishing the principle of using
this type of assembly for calculations.
• New motifs include a 6-helix bundle and a
cassette for inserting a PX-JX2 device into a
TX array.
 CHALLEN GES FOR STRU CTU RA L
D N A N AN OTECH N OLOGY

T O EXT EN D 2 -D RESU LT S T O 3 -D W IT H HIGH ORD ER - -

[1 ] Cr y s ta ll o g r a p h y .

T O IN CORP ORAT E D N A D EV ICES IN 2 -D A N D 3 -D A RRA YS

[2 ] -- N a n o r o b o ti c s .

T O IN CORPORA TE H ET EROLO GOU S GU EST S IN LA T T ICES

[3 ] -- N a n o e l e c t ro n i c s ; Cr y s ta ll o g ra p h y .

T O EXT EN D A LG OR IT H M I C A S SEM B LY T O H IG HER

[4 ] D IM EN SION S -- Sm a r t Ma te r i a l s ; Co m p u t a t io n .

T O A C H I EV E A S S EM B LI E S W I T H H IERA RCHI CA L
[5 ] CHA RA CT ER -- Co m p l e x M a t e ri a l s .

T O ACHIEV E FU N CT ION A L AS W ELL A S ST RU CT U RA L

[6 ] SYST EM S -- A c t i v e M a t e ri a l s ; Se n s o r Sy s te m s .

T O IN T ERFA CE W IT H T OP- D OW N MET HOD S A N D T H E

[7 ] M ACROSCOP IC W ORLD -- N a n o e l e c t r o n i c Re a l i ty .

T O IN CORPORA TE COM BIN A T ORIAL AP PROA CHES IN T ILE

[8 ] D ESIGN -- D i v e rs i t y ; Pr o g r a m m a b i l it y .

T O PROD U CE SYST EM S CA P ABLE OF SELF-REP LICA TIO N - -

[9 ] Ec o n o m y ; Ev o l v a b i l i t y .

T O A D V A N C E F R O M B I O K LE P T I C S Y S T E M S TO
[1 0 ] BIOM IMET IC SYST EM S -- Ch e m ic a l Co n t r o l .