NSF-ITR: EIA-0086015:
Structural DNA Nanotechnology
Nadrian C. Seeman, Subcontractor
Department of Chemistry
New York University
New York, NY 10003, USA
ned.seeman@nyu.edu
February 17, 2003
~20 Å
D N A BASE PAIRS
A
T
H
3.4 Å
H
C
N
N
C
N
3
C
C
C
C
CH
O
H
N
H
C
N
H
R
N
C
C
H
N
R
O
G
C
H
H
C
C
N
H
O
N
C
C
C
N
H
H
C
C
C
N
H
C
N
R
N
H
N
O
N
R
H
Reciprocal Exchange:
A Theoretical Tool To Generate
New DNA Motifs
Reciprocal Exchange in a
Double Helical Context
a
Reciprocal
Exchange
+
Resolve
b
Reciprocal
Exchange
+
Resolve
Biological Reciprocal Exchange:
The Holliday Junction
1
A•T
T•A
G•C
T•A
C•G
CGA
• • •
GC T
I
1
4
A•T
T•A
G•C
T•A
C•G
A•T
G•C
C•G
2
3
T•A
A•T
C•G
A•T
G•C
T•A
C•G
G•C
1
A•T
T•A
G•C
T•A
CGA C
• • • •
G CTG
2
2
4
4
TCG
• • •
AG C
G•C
A•T
C•G
A•T
T•A
3
G TC G
• • • •
CAGC
A•T
C•G
A•T
T•A
3
II
1
A•T
T•A
G•C
CGA C T
• • • • •
GC TG A
2
4
A G TC G
• • • • •
T CAG C
C•G
A•T
T•A
3
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
II
G C A
• • •
C G T
T G A T A C C G
• • • • • • • •
A C T A T G G C
C G A G T
• • • • •
G C T C A
IV
C • G
2
C• G
3
G• C
A • T
A • T
T • A
G • C
C • G
III
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
Sticky-Ended Cohesion: Affinity
AT GGCT A GT T GCA T GA T G CTCA CG
• • • • •• • • • • • • • • • • • • • •
T A C C GA T C A A C G T A C T A C G A
+
GCGT T A GGT GA T A CCGT A C
• • • •• • • •• • • • • • • •• • •
GT GC C G CA A T C CA C T A T G G C A T G
HYDROGEN BON DI N G
AT GGCT A GT T GCA T GA T G CT CAC GGC GT T A GGT GA T A CCGT A C
• • • • •• • • • • • • • • • • • • • • • • • • • • • •• • • •• • • • • • • •• • •
T A C C GA T C A A C G T A C T A C G A G TG C C G CA A T C CA C T A T G G C A T G
LI GA TI ON
AT GGCT A GT T GCA T GA T G CT CAC GGC GT T A GGT GA T A CCGT A C
• • • • •• • • • • • • • • • • • • • • • • • • • • • •• • • •• • • • • • • •• • •
T A C C GA T C A A C G T A C T A C G A G T G C C G CA A T C CA C T A T G G C A T G
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. Theor.Biol. 99, 237-247.
OBJECTIVES & APPLICATIONS
[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
P
REP ORTER S TRA N DS
L IGA TI O N
L I G A TI O N
LIGATION
LI G A T I ON
LIGA T ION
L IGA TI O N
L A RGE R L I NE A RS
A PP LY DI RECT LY
LIGA T ION
L A RGE R CYCL ICS
E XO N U C L EA S E F I R S T
CYCL I C
MOL E CU LE S
L IN E A R
A ND
CYCL IC
MOL E CU L ES
DEN A TU RI N G GEL
A U TORA DI OGRA M
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
a
2 Reciprocal
Exchanges
+
Resolve
Twice
2 Reciprocal
Exchanges
Resolve
Twice
b
2 Reciprocal
Exchanges
+
Resolve
Twice
2 Reciprocal
Exchanges
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
DX
HP
DX+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
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
AB Array
ABC'D Array
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
Jens Birktoft
Yariv Pinto
Hao Yan
Tong Wang
Bob Sweet
Pam Constantinou
Chengde Mao
Phil Lukeman
Jens Kopatsch
Bill Sherman
Mike Becker
A 3D TX Lattice
A
B
C
C'
D
D'
AB Array
QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.
ABC'D' Array
Furong Liu
Jens Birktoft
Yariv Pinto
Hao Yan
Bob Sweet
Pam Constantinou
Phil Lukeman
Chengde Mao
Bill Sherman
Mike Becker
A 3D Trigonal DX Lattice
Chengde Mao
Jens Birktoft
Yariv Pinto
Hao Yan
Bob Sweet
Pam Constantinou
Phil Lukeman
Furong Liu
Bill Sherman
Mike Becker
Algorithmic Assembly
Chengde Mao
Thom LaBean
John Reif
The XOR Operation
A
B A XOR B
0
0
1
1
0
1
0
1
0
1
1
0
A
B
A XOR B
Cumulative XOR
A
B
A XOR B
C
(A XOR B) XOR 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
Mao, C., LaBean, T.H., Reif, J.H. &
Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation: Assembly
Y4
Y3
Y2
Y1
C2
1
0
1
C1
0
0
1
1
0
X4
X3
X2
X1
Mao, C., LaBean, T.H., Reif, J.H. &
Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation:
Extracting the Answer
Y2
Y1
X2
C1
X1
C2
Mao, C., LaBean, T.H., Reif, J.H. &
Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation: Data
Calculation 1
M
2,000
1,500
800
600
500
400
Calculation 2
1
C 1 0 /
0
1
C 1 0 /
0
X4
X3
X2
X1
C2
=
=
=
=
0
1
1
1
X4
X3
X2
X1
=0
=1
=0
=1
C2
M
2,000
1,500
800
600
500
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
<----------------7.3 Microns---------------->
Fred Mathieu
Shiping Liao
Chengde Mao
DNA
Nanomechanical
Devices
B-Z Device
Chengde Mao
Right-Handed and Left-Handed DNA
[-] NODE
RIGHT-HANDED
B-DNA
[-] NODES
[+] NODE
LEFT-HANDED
Z-DNA
[+] NODES
A Device Based on the B<-->Z Transition
- Co(NH 3)6+++
+ 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
Percent Energy Transfer
Percent Energy Transfer
25
20
15
10
5
20
15
10
5
0
0
B
Z
B
Z
B
Z
B
Solution Conditions
Proto-Z
Z
Solution Conditions
Control
Mao, C., Sun, W., Shen, Z. & Seeman, N.C. (1999), Nature 397, 144-146.
Sequence-Dependent
Device
Hao Yan
Derivation of PX DNA
Seeman, N.C. (2001) NanoLetters 1, 22-26.
PX DNA
Seeman, N.C. (2001) NanoLetters 1, 22-26.
PX
JX2
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
PX
JX2
A
B
A
B
C
D
D
C
Machine Cycle of the PX-JX2 Device
A
B
I
II
PX
A
C
JX2
B
C
D
A
B
D
IV
III
D
C
A
B
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
A
~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
AB Array
ABC'D Array
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
PX Conformation
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
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 lay er
first lay er
template
(c)
(d)
Control Region & Sticky Ends on the Same Strand
PX Conformation
JX2 Conformation
Mix & Split Synthesis -- Central
Levulinyl Protected Branch Point
3'
B ox 1
B ox 2
5'
Perform C onventional 3'-->5' Synthes is
from End of B ox 1 to Start of B ox 2.
1.
3'
B ox 1
B ox 2
5'
Split Grow ing Strands into A, T, C , G
C ompartments; A dd B ase t o B ox 2.
2.
3'
B ox 1
B ox 2
5'
3'
B ox 1
B ox 2
5'
3'
B ox 1
B ox 2
5'
3'
B ox 1
B ox 2
5'
A dd Same B ase [ or F(B ase)] with Levulinyl
Protection and5' Phosphoramidite to B ox 1.
3.
3'
B ox 1
B ox 2
5'
3'
B ox 1
B ox 2
5'
3'
B ox 1
B ox 2
5'
3'
B ox 1
B ox 2
5'
C ombine Grow ing Strand Supports;
R epeat St eps 2 and 3 until Boxes are f illed.
4.
3'
5'
3'
5'
3'
5'
3'
5'
C omplete C onventional Synthesis of the
Strands
5.
3'
5'
3'
5'
3'
5'
3'
5'
Mix & Split Synthesis -- Ends
Levulinyl Protected Branch Point
3'
B ox 1
B ox 2
5'
Perform C onventional 3'-->5' Synthes is
from End of B ox 1 to Start of B ox 2.
1.
3'
B ox 1
B ox 2
5'
R everse Polarity of Strand G rowing
at Branch; A dd D irectionality Segment.
2.
5'
B ox 1
B ox 2
5'
Split Grow ing Strands into A, T, C , G
C ompartments; A dd B ase t o B ox 2.
3.
5'
B ox 1
B ox 2
5'
5'
B ox 1
B ox 2
5'
5'
B ox 1
B ox 2
5'
5'
B ox 1
B ox 2
5'
A dd Same B ase [ or F(B ase)] with Levulinyl
Protection and5' Phosphoramidite to B ox 1.
4.
5'
B ox 1
B ox 2
5'
5'
B ox 1
B ox 2
5'
5'
B ox 1
B ox 2
5'
5'
B ox 1
B ox 2
5'
C ombine Grow ing Strand Supports;
R epeat St eps 3 and 4 until Boxes are f illed.
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
[1 ]
T O EXT EN D 2 -D RESU LT S T O 3 -D W IT H HIGH ORD ER - Cr y s ta ll o g r a p h y .
[2 ]
T O IN CORP ORAT E D N A D EV ICES IN 2 -D A N D 3 -D A RRA YS
-- N a n o r o b o ti c s .
[3 ]
T O IN CORPORA TE H ET EROLO GOU S GU EST S IN LA T T ICES
-- 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 .
[4 ]
T O EXT EN D A LG OR IT H M I C A S SEM B LY T O
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 .
[5 ]
T O A C H I EV E A S S EM B LI E S W I T H
CHA RA CT ER -- Co m p l e x M a t e ri a l s .
[6 ]
T O ACHIEV E FU N CT ION A L AS W ELL A S ST RU CT U RA L
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 .
[7 ]
T O IN T ERFA CE W IT H T OP- D OW N MET HOD S A N D T H E
M ACROSCOP IC W ORLD -- N a n o e l e c tr o n i c Re a l i ty .
[8 ]
T O IN CORPORA TE COM BIN A T ORIAL AP PROA CHES IN T ILE
D ESIGN -- D i v e rs i t y ; Pr o g r a m m a b i l it y .
[9 ]
T O PROD U CE SYST EM S CA P ABLE OF SELF-REP LICA TIO N - Ec o n o m y ; Ev o l v a b i l i t y .
[1 0 ]
H IG HER
H IERA RCH I CA L
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
BIOM IMET IC SYST EM S -- Ch e m ic a l Co n t r o l .
TO