nsf-itr: eia-0086015: structural dna nanotechnology nadrian c. seeman, subcontractor department of...
TRANSCRIPT
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NSF-ITR: EIA-0086015:Structural DNA Nanotechnology
Nadrian C. Seeman, SubcontractorDepartment of Chemistry
New York UniversityNew York, NY 10003, USA
February 17, 2003
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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
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ReciprocalExchange
Resolve
Reciprocal Exchange:A Theoretical Tool To Generate
New DNA Motifs
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b
a
+Resolve
Reciprocal
Exchange
Resolve
Reciprocal
Exchange
+
Reciprocal Exchange in aDouble Helical Context
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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
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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•
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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
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Qiu, H., Dewan, J.C. & Seeman, N.C. (1997) J. Mol. Biol. 267, 881-898.
Sticky-Ended Cohesion: Structure
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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
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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
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Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, 295-300..
A Method for Organizing Nano-Electronic Components
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Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, 295-300.
A Suggestion for a Molecular Memory DeviceOrganized by DNA (Shown in Stereo)
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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
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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
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Geometrical Constructions(Regular Graphs)
Cube: Junghuei Chen
Truncated Octahedron: Yuwen Zhang
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Chen, J. & Seeman. N.C. (1991), Nature 350, 631-633..
Cube..
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Zhang, Y. & Seeman, N.C. (1994), J. Am. Chem. Soc. 116, 1661-1669.
TruncatedOctahedron
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Constructionof
CrystallineArrays
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REQUIREMENTS FOR LATTICEDESIGN COMPONENTS
PREDICTABLE INTERACTIONS
PREDICTABLE LOCAL PRODUCT STRUCTURES
STRUCTURAL INTEGRITY
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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
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Erik Winfree (Caltech)Furong Liu
Lisa Wenzler
2D DX Arrays
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D X + JD X
+
H P
Resolve
Reciprocal
Exchange
Seeman, N.C. (2001) NanoLetters 1, 22-26.
Derivation of DX+J Molecules
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A B*
Schematic of a Lattice Containing1 DX Tile and 1 DX+J Tile
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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
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D*D*A CB
Schematic of a Lattice Containing 3 DX Tiles and 1 DX+J Tile
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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
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Chengde Mao
Holliday JunctionParallelogram Arrays
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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
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Mao, C., Sun, W & Seeman, N.C. (1999), J. Am. Chem. Soc. 121, 5437-5443.
Holliday Junction Parallelogram Arrays
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Triple Crossover Molecules
Furong Liu, Jens Kopatsch, Hao YanThom LaBean, John Reif
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Triple Crossover Molecules
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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.
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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.
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ProgressToward
Three-DimensionalArrays
Furong LiuJens BirktoftYariv PintoHao YanTong WangBob Sweet
Pam ConstantinouChengde MaoPhil LukemanJens Kopatsch
Bill ShermanMike Becker
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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.
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A 3D Trigonal DX Lattice
Chengde MaoJens BirktoftYariv PintoHao YanBob Sweet
Pam ConstantinouPhil Lukeman
Furong LiuBill ShermanMike Becker
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Algorithmic Assembly
Chengde MaoThom LaBean
John Reif
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A
BA XOR B
A B A XOR B
011
0101
0110
0
The XOR Operation
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A
BA XOR B
C(A XOR B) XOR C
Cumulative XOR
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A Cumulative XOR Calculation: Tiles
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, 493-496.
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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
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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.
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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
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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.
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Natasha JonoskaPhiset Sa-Ardyen
N-Colorability of Graphs
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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.
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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
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Fred MathieuChengde Mao
Six-Helix Bundle
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<----------------7.3 Microns---------------->
Six-Helix DNA Bundle
Fred MathieuShiping Liao
Chengde Mao
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DNANanomechanical
Devices
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B-Z Device
Chengde Mao
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[-] NODE
RIGHT-HANDEDB-DNA
[-] NODES
[+] NODE
LEFT-HANDEDZ-DNA
[+] NODES
Right-Handed and Left-Handed DNA
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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
+++
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.
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.
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Sequence-Dependent Device
Hao Yan
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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
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PX DNA
Seeman, N.C. (2001) NanoLetters 1, 22-26.
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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..
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Switchable Versions of PX and JX2
J X 2
A B
D C
A B
C D
P X
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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
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The PX-JX2 System is Robust
Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.
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System to Test the PX-JX2 Device
JX2
JX2
JX2
PXPXPX
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AFM Evidence for Operationof the PX-JX2 Device
Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.
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NewCohesive Motifs
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Paranemic Cohesion
Xiaoping Zhang
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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.
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+PX Cohesion of DNA Triangles: Theory
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PX Cohesion of DNA Triangles: Experiment
Zhang, X. Yan, H.,Shen, Z. & Seeman, N.C. (2002) J Am. Chem. Soc.124, 12940-12941 (2002)
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Edge-Sharing
Hao Yan
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AA'
~20 nm
One-Dimensional Arrays of Edge-Sharing Triangles(Short Direction)
Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.
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One-Dimensional Arrays of Edge-Sharing Triangles(Long Direction)
BB'
~30 nm
Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.
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One-Dimensional Arrays ofDouble Edge-Sharing Triangles
A
A'
~30 nm
~20 nm
Yan, H. & Seeman, N.C. (2002) J. Supramol. Chem.,in press.
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A Cassette for theInsertion of a PX-JX2 Device into a 2D TX
Array
Baoquan Ding
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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.
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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
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Molecular Models of the 2 states of the Sequence-Driven DNA Devices
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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
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Towards 2D Circuits
Alessandra Carbone (IHES)
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Circuits and triangular patterns
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2 layers assembly
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Tiles
inputs
outputs
operation
TX Molecule
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Molecular Programming: programmed board
4 different states
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PXJXJXJXPX PX PX JX
JXJXPX PX
PXJXPX JX
Possible Components: Programmable Pawns
Possible Components: TX Middle Domains
Possible Arrangement
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(b)
(d)(c)
(a)
templatefirst layer
second layer
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PX Conformation
JX2 Conformation
Control Region & Sticky Ends on the Same Strand
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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
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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.
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Triple Crossover Molecules
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An Algorithmic Arrangement Based on Mix & Split Synthesis
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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.
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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.
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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.
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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.