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NSF-ITR: EIA-0086015:Structural DNA Nanotechnology
Nadrian C. Seeman, SubcontractorDepartment of Chemistry
New York UniversityNew York, NY 10003, USA
ned.seeman@nyu.edu
February 17, 2003
DNA BASE PAIRS
C C
N
C
C
O
NH
O R
H
CH3
T
H
CC
NC
N C
N
N N
H
HC
H
R
A
O
C C
N
N
C
C
R
H
HN
H
H
CC
NC
C
N
N
C
OC
H
NR
H
N H
H
G
3.4 Å
~20 Å
10-10.5Pairs/Turn
ReciprocalExchange
Resolve
Reciprocal Exchange:A Theoretical Tool To Generate
New DNA Motifs
b
a
+Resolve
Reciprocal
Exchange
Resolve
Reciprocal
Exchange
+
Reciprocal Exchange in aDouble Helical Context
Biological Reciprocal Exchange:The Holliday Junction
1 4
2 3
1 4
2 3
1 24 3
1 4
2 3
I
I I
A•T
G•C
C•G
C•G
G•C
T•A
A•TT•AG•CT•AC•G
T•AA•TC•GA•TG•C
A•TT•AG•C
T•AA•TC•G
C•G
A•T
G•C
C•G
C•G
G•C
T•A
G•C
A•T
T•A
A•TT•AG•CT•AC•GA•TG•CC•G
T•AA•TC•GA•TG•CT•AC•GG•C
A•TT•AG•CT•A
T•AA•TC•GA•T
C•G
A•T
G•C
C•G
C•G
G•C
T•A
G•C
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
Design of Immobile Branched Junctions:Minimize Sequence Symmetry
IIACTCGTGC
TGAGCACG••••••••
A
T
C
G A
T A
T A
T
C
G
C
G C
G• • • • • • • •
3322
11 44
C G
C G
CG
A T
A T
AT
CG
C G
•
•
•
•
•
•
•
•
IV
I
III
C GCG
C G
A T
A TAT
C G
••
•
••
•
•
C G•
C•GG•CC•GTA•TA•AT•C•GC•GTA•C•GAT•TA•
G•CG•CA
T•
C•GTA•AT•G•C
GTGCC•GT
A•A
T•
C•GC•GG•CTA•AT• T
A•TA•C•GG•CAT•TA•C•GAT•TA•C•GG•CTA•CACG
LIGATION
+HYDROGEN BONDING
C•GT
A•A
T•
C•GC•GG•CTA•AT• T
A•TA•C•GG•CAT•TA•C•GAT•TA•C•GG•CTA•G•CAT•G•CC•GC•GG•CC•GTA•TA•AT•C•GC•GTA•C•GAT•TA•
G•CG•CA
T•
C•GTA•AT•G•C
••••C•GT
A•A
T•
C•GC•GG•CTA•AT• T
A•TA•C•GG•CAT•TA•C•GAT•TA•C•GG•CTA•GTGCC
•GG•CC•GTA•TA•AT•C•GC•GTA•C•GAT•TA•
G•CG•CA
T•
C•GTA•AT•G•CCACG
Sticky-Ended Cohesion: Affinity
Qiu, H., Dewan, J.C. & Seeman, N.C. (1997) J. Mol. Biol. 267, 881-898.
Sticky-Ended Cohesion: Structure
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
The Central Concept:Combine Branched DNA with Sticky Ends to
Make Objects, Lattices and Devices
AB'
B
A'A
B' B'
B
A
A'
A'
B
O B J E C T IV E S & A P P L IC A T IO N S
DESIGN MOLECULES TO ASSEMBLE INTO ORDERED ARRAYS.
[A] SCAFFOLD MACROMOLECULAR CRYSTALLIZATION (PERIODIC).
[C] GENERATE ALGORITHMIC PATTERNS (APERIODIC).[B] SCAFFOLD NANOELECTRONICS ASSEMBLY (PERIODIC).
Architectural Control[1]
[3] Self-Replicating Systems
[A] NANOROBOTICS.[B] NANOFABRICATION.[C] MOLECULAR PEGBOARDS.
[2] Nanomechanical Devices
Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, 295-300..
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 DeviceOrganized by DNA (Shown in Stereo)
WHY DNA?
PREDICTABLE INTERMOLECULAR INTERACTIONS
CONVENIENT AUTOMATED CHEMISTRY
CONVENIENT MODIFYING ENZYMES
HIGH FUNCTIONAL GROUP DENSITY
EXTERNALLY READABLE CODE
LOCALLY STIFF POLYMER
PROTOTYPE FOR MANY DERIVATIVES
DENATURING GELAUTORADIOGRAM
CYCLICMOLECULES
LINEARAND
CYCLICMOLECULES
APPLY DIRECTLY EXONUCLEASE FIRST
LIGATION
LIGATION
LIGATION
LIGATION
LIGATION
LIGATION
LIGATION
PP32 REPORTER STRANDS
LA RGER LINEA RS LA RGER CYCLICS
A Method to Establish DNA Motif Flexibility
Geometrical Constructions(Regular Graphs)
Cube: Junghuei Chen
Truncated Octahedron: Yuwen Zhang
Chen, J. & Seeman. N.C. (1991), Nature 350, 631-633..
Cube..
Zhang, Y. & Seeman, N.C. (1994), J. Am. Chem. Soc. 116, 1661-1669.
TruncatedOctahedron
Constructionof
CrystallineArrays
REQUIREMENTS FOR LATTICEDESIGN COMPONENTS
PREDICTABLE INTERACTIONS
PREDICTABLE LOCAL PRODUCT STRUCTURES
STRUCTURAL INTEGRITY
Seeman, N.C. (2001) NanoLetters 1, 22-26.
+
b
Resolve
Twice
2 Reciprocal
Exchanges
a
+Resolve
Twice
2 Reciprocal
Exchanges
Resolve
Twice
2 Reciprocal
Exchanges
Resolve
Twice
2 Reciprocal
Exchanges
DS + DS DX TX
Derivation of DX and TX Molecules
Erik Winfree (Caltech)Furong Liu
Lisa Wenzler
2D DX Arrays
D X + JD X
+
H P
Resolve
Reciprocal
Exchange
Seeman, N.C. (2001) NanoLetters 1, 22-26.
Derivation of DX+J Molecules
A B*
Schematic of a Lattice Containing1 DX Tile and 1 DX+J Tile
Winfree, E., Liu, F., Wenzler, L.A. & Seeman, N.C. (1998), Nature 394, 539-544.
AFM of a Lattice Containing1 DX Tile and 1 DX+J Tile
D*D*A CB
Schematic 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.
AFM of a Lattice Containing3 DX Tiles and 1 DX+J Tile
Chengde Mao
Holliday JunctionParallelogram Arrays
Holliday Junction Parallelogram Arrays
Mao, C., Sun, W & Seeman, N.C. (1999), J. Am. Chem. Soc. 121, 5437-5443.
II
IVIII
II
III
II IV4
32
1
I
III
II IV4
32
1
D
A'
C
B'
C'
A
D'
B
YX
Z
X
SELFASSEMBLY
Mao, C., Sun, W & Seeman, N.C. (1999), J. Am. Chem. Soc. 121, 5437-5443.
Holliday Junction Parallelogram Arrays
Triple Crossover Molecules
Furong Liu, Jens Kopatsch, Hao YanThom LaBean, John Reif
Triple Crossover Molecules
B*A
TX+J 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.
BA C C' D
AB Array
ABC'D Array
TX Array With Rotated Components
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.
ProgressToward
Three-DimensionalArrays
Furong LiuJens BirktoftYariv PintoHao YanTong WangBob Sweet
Pam ConstantinouChengde MaoPhil LukemanJens Kopatsch
Bill ShermanMike Becker
A 3D TX Lattice
Furong LiuJens BirktoftYariv PintoHao YanBob Sweet
Pam ConstantinouPhil LukemanChengde MaoBill ShermanMike Becker
D D'BA C C'
AB Array
ABC'D' Array
QuickTime™ and aPhoto - JPEG decompressor
are needed to see this picture.
A 3D Trigonal DX Lattice
Chengde MaoJens BirktoftYariv PintoHao YanBob Sweet
Pam ConstantinouPhil Lukeman
Furong LiuBill ShermanMike Becker
Algorithmic Assembly
Chengde MaoThom LaBean
John Reif
A
BA XOR B
A B A XOR B
011
0101
0110
0
The XOR Operation
A
BA XOR B
C(A XOR B) XOR C
Cumulative XOR
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.
S0Pair to C1
C2
Pair to C2
yi = 0
C1
Sixi = 1
1
Si-1
xi = 1
Si-1
Sixi = 0
0
xi = 0
1
yi = 1
xi = 1yi-1 = 0xi = 0
1
yi-1 = 1
yi = 1yi = 0
xi = 1
0
yi-1 = 1
yi = 0
xi = 0
0
yi-1 = 0
yi = 0xi = 1
yi-1 = 1
yi = 1xi = 0
yi-1 = 1
yi = 0xi = 0
yi-1 = 0
yi = 1xi = 1
yi-1 = 0
1
0
X3
X4
1
X1
X2
0
C2
C1
Y11
1
Y2
Y30
0
Y4
0
Y41
1
0
1
C1
C2
1
1
X41
X1
X2
X3
Y1
Y2
Y3
A Cumulative XOR Calculation: Assembly
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, 493-496.
C 1 X 1
X 2
Y 1
C 2
Y 2
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation:Extracting the Answer
A Cumulative XOR Calculation: Data
2,0001,500
800600500
400
300
200
100
X2 = 1
Y1 = 1
Y2 = 0
Y3 = 1
Y4 = 1
X3 = 1X4 = 0
X1 = 1C2
M 1 0
Calculation 1
/01
C2,0001,500800600500
400
300
200
100
X2 = 0
Y1 = 1
Y2 = 1
Y3 = 0
X3 = 1X4 = 0
X1 = 1 C2
MC 1 0
Calculation 2
/01
Y4 = 0
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, 493-496.
Natasha JonoskaPhiset Sa-Ardyen
N-Colorability of Graphs
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
Fred MathieuChengde Mao
Six-Helix Bundle
<----------------7.3 Microns---------------->
Six-Helix DNA Bundle
Fred MathieuShiping Liao
Chengde Mao
DNANanomechanical
Devices
B-Z Device
Chengde Mao
[-] NODE
RIGHT-HANDEDB-DNA
[-] NODES
[+] NODE
LEFT-HANDEDZ-DNA
[+] NODES
Right-Handed and Left-Handed DNA
B-ZZ-B
A Device Based on the B<-->Z Transition
Mao, C., Sun, W., Shen, Z. & Seeman,N.C. (1999), Nature 397, 144-146.
+ Co(NH 3)6+++- Co(NH 3)6
+++
.
0
5
10
15
20
25
B Z
Acceptor Energy Transfer
Solution Conditions
Percent Energy Transfer
Donor Energy Transfer
Solution Conditions
0
5
10
15
20
25
B Z B Z B Z
Percent Energy Transfer
ControlProto-Z
FRET Evidence for Motion Inducedby the B→ Z Transition
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.
+Resolve
Everywhere
Reciprocal
Exchange
Everywhere
Resolve
Everywhere
Reciprocal
Exchange
Everywhere
b
a
+
P X
PX DNA
Seeman, N.C. (2001) NanoLetters 1, 22-26.
C D
P X
A B
J X 2
A B
D C
Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65..
Switchable Versions of PX and JX2
J X 2
A B
D C
A B
C D
P X
Machine Cycle of the PX-JX2 Device
A B
C D
A B
C D
A B
D C
JX2
A B
D C
PX
I II
IV III
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
JX2
JX2
JX2
PXPXPX
AFM Evidence for Operationof the PX-JX2 Device
Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.
NewCohesive 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
AA'
~20 nm
One-Dimensional Arrays of Edge-Sharing Triangles(Short Direction)
Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.
One-Dimensional Arrays of Edge-Sharing Triangles(Long Direction)
BB'
~30 nm
Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.
One-Dimensional Arrays ofDouble Edge-Sharing Triangles
A
A'
~30 nm
~20 nm
Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.
A Cassette for theInsertion of a PX-JX2 Device into a 2D TX
Array
Baoquan Ding
BA C C' D
AB Array
ABC'D Array
TX Array With Rotated Components
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.
1
2A
2B
3
4A
4B
5
P1
P2
J1
J2
4A
5 2A
4B
2B
1
3
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 Devicein a 1D Molecular Pegboard
MARKER ---> MARKEDPX + PX JX INERT
PX JX JX JX PX JX PX PX
+ --->
JXPX
PX JX JX JX PX JX PX PX
1 2 3 4 5 6 7 8
1 2 3 4 5 6 7 8
Towards 2D Circuits
Alessandra Carbone (IHES)
Circuits and triangular patterns
2 layers assembly
Tiles
inputs
outputs
operation
TX Molecule
Molecular Programming: programmed board
4 different states
PXJXJXJXPX PX PX JX
JXJXPX PX
PXJXPX JX
Possible Components: Programmable Pawns
Possible Components: TX Middle Domains
Possible Arrangement
(b)
(d)(c)
(a)
templatefirst layer
second layer
PX Conformation
JX2 Conformation
Control Region & Sticky Ends on the Same Strand
3' 5'Box 1 Box 23' 5'Box 1 Box 23' 5'Box 1 Box 23' 5'Box 1 Box 2
Combine Growing Strand Supports;Repeat Steps 2 and 3 until Boxes are filled.4.
3' 5'Box 1 Box 2
Levulinyl Protected Branch Point
3' 5'Box 1 Box 2
1. Perform Conventional 3'-->5' Synthesisfrom End of Box 1 to Start of Box 2.
Split Growing Strands into A, T, C, GCompartments; Add Base to Box 2.2.
3' 5'Box 1 Box 23' 5'Box 1 Box 23' 5'Box 1 Box 23' 5'Box 1 Box 2
Add Same Base [or F(Base)] with LevulinylProtection and5' Phosphoramidite to Box 1.3.
3' 5'3' 5'3' 5'3' 5'
Complete Conventional Synthesis of theStrands5.
3' 5'3' 5'3' 5'3' 5'
Mix & Split Synthesis -- Central
Mix & Split Synthesis -- Ends
3' Box 1 Box 2 5'
2.
3'
Box 1 Box 2Box 1 Box 2Box 1 Box 2Box 1 Box 2
Combine Growing Strand Supports;Repeat Steps 3 and 4 until Boxes are filled.5.
Box 1Box 1Box 1Box 15'
5'5'5' Box 2
Box 2Box 2Box 2
Add Same Base [or F(Base)] with LevulinylProtection and5' Phosphoramidite to Box 1.4.
5'5'5'5'
5'5'5'5'
5'5'5'5'5'
5'5'5'
5'5'5'5'
5'Box 1 Box 2
Levulinyl Protected Branch Point
1. Perform Conventional 3'-->5' Synthesisfrom End of Box 1 to Start of Box 2.
Reverse Polarity of Strand Growingat Branch; Add Directionality Segment.
Box 1 Box 2 5'5'Split Growing Strands into A, T, C, GCompartments; Add Base to Box 2.3.
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.
CHALLENGES FOR STRUCTURALDNA NANOTECHNOLOGY
TO EXTEND 2-D RESULTS TO 3-D WITH HIGH ORDER --Crystallography.[1]
[2] TO INCORPORATE DNA DEVICES IN 2-D AND 3-D ARRAYS-- Nanorobotics.
[3] TO INCORPORATE HETEROLOGOUS GUESTS IN LATTICES-- Nanoelectronics; Crystallography.
[4] TO EXTEND ALGORITHMIC ASSEMBLY TO HIGHERDIMENSIONS -- Smart Materials; Computation.
[7] TO INTERFACE WITH TOP-DOWN METHODS AND THEMACROSCOPIC WORLD -- Nanoelectronic Reality.
[5] T O ACHI EVE ASSEMBLIES WI T H H IERARCHI CALCHARACTER -- Complex Materials.
[10] T O ADVANCE FROM BIOKLEPT I C SYST EMS T OBIOMIMETIC SYSTEMS -- Chemical Control.
[6] TO ACHIEVE FUNCTIONAL AS WELL AS STRUCTURALSYSTEMS -- Active Materials; Sensor Systems.
[8] TO INCORPORATE COMBINATORIAL APPROACHES IN TILEDESIGN -- Diversity; Programmability.
[9] TO PRODUCE SYSTEMS CAPABLE OF SELF-REPLICATION --Economy; Evolvability.
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