NSF-ITR: EIA-0086015: Structural DNA Nanotechnology

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.