The Design of Autonomous DNAThe Design of Autonomous DNANanomechanicalNanomechanical Devices: Devices:Walking and Rolling DNAWalking and Rolling DNA

John John ReifReif

Bidirectional RandomTranslational& RotationalMovement

ssDNARoller:ssDNA

Road:

Rolling DNADevice

Bidirectional Translational& Rotational Movement

dsDNAWalker:

ssDNARoad:

Walking DNADevice

HybridizationHybridization of sticky single-strand DNA segments.LigationLigation: If the sticky single-strand segments that anneal abut

doubly stranded segments of DNA, you can use an enzymicreaction known as ligationligation to concatenate these segments.

Prior Nanomechanical Devices built of DNA:

·Seemano used rotational transitions of dsDNA conformations between theB-form (right handed) to the Z-form (left-handed) controlled by ioniceffector molecules and

o extended this technique to be DNA sequence dependant

··YurkeYurke and and TurberfieldTurberfieldoused a fuel DNA strands acting as a hybridization catalyst togenerate a sequence of motions in another tweezers strand of DNA

oextended this technique to be DNA sequence dependant

othe two strands of DNA bind and unbind with the overhangs toalternately open and shut the tweezers.

Other Related Work: Shapiro’s recent autonomous 2 state DNA computing machine

·uses DNA ligase and two restriction enzyme•but distinct technical methods and goals (computation)

Bernard Bernard YurkeYurke’’ss Molecular Tweezers (Bell Lab): Molecular Tweezers (Bell Lab):Composed of DNA and powered by DNA hybridization.Composed of DNA and powered by DNA hybridization. - -Two Two dsDNAdsDNA arms are connected by a arms are connected by a ssDNA ssDNA hinge hinge

- -Two Two ssDNAssDNA ““handleshandles”” at the ends of the arms. at the ends of the arms.

To close tweezers:To close tweezers: -Add a special -Add a special ““fuelfuel”” strand of strand of ssDNA ssDNA.. -The -The ““fuelfuel”” strand attaches to the handles and draws the two strand attaches to the handles and draws the twoarms together.arms together.

B-Z Z-B

D A

D

A

B-Z DNA Nanomechanical Device[Seeman, 1999]

B- ZZ- B

A B

CDC

A

D

B

PX JX2

A B

C D

A B

C D

A B

D C

JX2

A B

D C

PX

I II

IV III

(a) (b)

JX2

JX2

JX2

PXPXPX

Nano Nano-mechanical Rotational Transducers(-mechanical Rotational Transducers(SeemanSeeman, NYU), NYU)(a) DNA(a) DNA nanomechanical nanomechanical motor: Rotation via B-Z transition controlled by motor: Rotation via B-Z transition controlled byconcentration of Co(NHconcentration of Co(NH33 )) 66 C lC l33 . .

(b) Device switches between PX and JX(b) Device switches between PX and JX22 topological states of DNA controlled via topological states of DNA controlled viaintroduction of different strands, using introduction of different strands, using Yu rkeYurkeÕÕ ss Molecular Tweezers. Molecular Tweezers.

(c) A test system where switching states alternates between a(c) A test system where switching states alternates between a 'cis' 'cis' configuration configuration(PX) and a 'trans' configuration (JX(PX) and a 'trans' configuration (JX22 ) .) .

(d) AFM pictures of four successive states through this system.(d) AFM pictures of four successive states through this system.

(a) (a) (b) (b)

(c) (c) (d) (d)

8 turns

10.5 turns

180_ _

Walking Triangles: By binding the short red strand (top figure) versus the long redstrand (bottom figure) the orientation of and distance between the triangular tiles is altered. These changes will be observable by AFM.Applications: Programmable state control for nanomechanical devices.Also as a visual output method.

DNADNA Nanomechanical Nanomechanical Device ( Device (HaoHao, Duke), Duke)

Nanofac toryNanofac tory device( device(SeemanSeeman, NYU):, NYU): PX/JX PX/JX22 devices with 3 cycles of configurations. devices with 3 cycles of configurations.(a) (a) NanogenNanogen electrodes control release of hybridized strands into solution. electrodes control release of hybridized strands into solution.(b) Three augmented device molecules mounted on an lattice.(b) Three augmented device molecules mounted on an lattice.Set strands of device labeled: P(Set strands of device labeled: P(u rp l eu rp l e)-up and G()-up and G(r eenr een) -up .) -up .Cycle 1: -Three G-up set strands on the device,Cycle 1: -Three G-up set strands on the device,

-P-up set strands released into solution.-P-up set strands released into solution.Cycle 2: -G-up strands for molecules 1 and 3 released,Cycle 2: -G-up strands for molecules 1 and 3 released,

-P-up strand for molecule 2 released.-P-up strand for molecule 2 released.Cycle 3: -P-up set strands for molecules 1 and 3 released,Cycle 3: -P-up set strands for molecules 1 and 3 released,

-G-up set strand for molecule 2 released.-G-up set strand for molecule 2 released.

G- U PP- UP

1

2

3

G- UPP- UP

1

2

3

G- UPP- U P

1

2

3

CYCLE 1 CYCLE 2 CYCLE 3

1

2

3

1

2

3

1

2

3

NANOFACTORY

(a) (a)

(b) (b)

Patterned Immobilization of Environmentally-ResponsivePatterned Immobilization of Environmentally-ResponsivePeptides.Peptides. (on-going work in collaboration with (on-going work in collaboration with ChilkotiChilkoti, Dept. of Biomedical Eng., Duke, Dept. of Biomedical Eng., DukeUniversity.)University.)NanoscaleNanoscale actuators that function in an aqueous environment actuators that function in an aqueous environment..Molecular basis ofMolecular basis of nanoactuation nanoactuation:: - - ELPsELPs are are Peptides thatPeptides that undergo a structural transition at a undergo a structural transition at a

characteristic temperature. characteristic temperature. - The end-to-end distance of the ELP decreases by ~50% upon - The end-to-end distance of the ELP decreases by ~50% upon

collapse of the ELP in response to its phase transition.collapse of the ELP in response to its phase transition.Hybrid materialsHybrid materials composed of : composed of :

(a) self-assembling DNA(a) self-assembling DNA nanostructures nanostructures and and(b)(b) elastin elastin-like peptides (ELP)-like peptides (ELP)

-Attachment of ELP to specific sites on DNA lattice results in arrays of peptide in -Attachment of ELP to specific sites on DNA lattice results in arrays of peptide inaa monolayer monolayer of controlled density. of controlled density. -May use layers of DNA sandwiched between layers of ELP. -May use layers of DNA sandwiched between layers of ELP.

Key restrictions on the use of prior DNA nanomechanicaldevices:

Minor Restriction:They can only execute one type of motion(rotational or translational).

Major Restriction:Prior DNA devices require environmental changes

such as temperature cycling orbead treatment of biotin-streptavidin beads

to make repeated motions.

Our Technical Challenge:To make an autonomous DNA nanomechanical device

· that executes cycles of motion (either rotational or translational or both)· without external environmental changes.

Our Results: Designs for the first autonomous DNAnanomechanical devices that execute cycles of motion withoutexternal environmental changes.

Our two DNA Motor Devices:

· Walking DNA device,O Uses ATP consumption by DNA ligase in conjunctionwith restriction enzyme operations.

· Rolling DNA deviceO Uses hybridization energy

These DNA devices translate across a circular strand of ssDNA androtate simultaneously.

Generate random bidirectional movements that acquire after n steps anexpected translational deviation of O(n1/2).

Energy sources that can fuel DNA movements:

(i) ATP consumption by DNA ligase inconjunction with restriction enzymeoperations

(ii) DNA hybridization energy in trapped states

(iii) kinetic (heat) energy

Walking DNA Autonomous Nanomechanical Device:· requires no temperature changes.

Energetics: Uses ATP consumption by DNA ligase in conjunction withrestriction enzyme operations.

Achieves random bidirectional translational and rotational motionaround a circular ssDNA strand.

Bidirectional Translational& Rotational Movement

dsDNAWalker:

ssDNARoad:

Walking DNADevice

Walking DNA Device Construction:

The Road:

·a circular repeating strand R of ssDNA·written in 5’ to 3’ direction from left to right.·consists of an even number n of subsequences, which we callsteppingstones, indexed from 0 to n-1 modulo n.·The ith steppingstone consists of a length L (where L is between 15to 20 base pairs) sequence Ai of ssDNA.·In our constructions, the Ai repeat with a period of 2.

The ith Walker:

A unique a partial duplex DNA strand Wiwith 3’ ends i-1 and i that are hybridized to consecutive i-1th and ith

steppingstones Ai-1 and Ai,

A0 A1 A2 …An-1 An …A...A2...A2 …

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

The Goal of the Device Construction:Bidirectional, translational movement

· both in the 5’ to 3’ direction (from left to right) and· vise versa (in the 3’ to 5’ direction) on the road.

The ith walker Wi will reform to another partial duplex DNA strandcalled the i+1th walker Wi+1 which is:

· shifted one unit over to the left or the right.· Cycle back in 2 stages, so that Wi+2 = Wi for each stage i.

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

Step

Wi+1:

 

A i

 

A i+1A0 A1 … Ai-1 Ai Ai+1

To achieve the movements

·Use 2 distinct types of restriction enzymes.·Use DNA ligase:·provides a source of energy (though ATP consumption) and·a high degree of irreversibility.

Simultaneous Translational and Rotational Movements.·Secondary structure of B-form dsDNA:·Rotates 2PPPP radians every approx 10.5 bases)·So in each step of translational movement, the walker rotates 1/10.5around the axis of the road.

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

Step

Wi+1:

 

A i

 

A i+1A0 A1 … Ai-1 Ai Ai+1

Notation:

(i) use superscript R to denote the reverse of a sequence, and(ii) use overbar to denote the complement of an ssDNA sequence.

Oglionucleotides used in the Walking DNA Construction:

For i = 0, 1, we define ssDNA:· Bi· Ci· Ai

distinct oglionucleotides of low annealing cross-affinity.

To cycle back in 2 stages, subscripts of Ai Bi Ci are taken modulo 2· Ai+1 = Ai-1· Bi+1 = Bi-1· Ci+1 = Ci-1

Avoiding Unwanted Interactions:

· To ensure there is no interaction between a walkerand more than one distinct road at a time:

o we use a sufficiently low road concentration andsolid support attachment of the roads.

· To ensure there is no interaction between a road andmore than one walker:

o we use a sufficiently low walker concentration.

Definition of the Walker Wi

We inductively assume that ith walker Wi has:· the 3’ end i-1 hybridized to steppingstone Ai-1 on the road.· the 3’ end i hybridized to steppingstone Ai on the road.

Definition of the Stepper Si

•The ith steppingstone Ai subsequences will hybridize with acomplementary subsequence i of the ith stepper Si.•We assume that this occurs at each steppingstone, except thesteppingstones where the walker’s ends are hybridized.

BiR Ci

R

 

C i-1

 

A i

 

B iR

 

C iR

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1 …A0 A1 … Ai-1 Ai Ai+1 …

Hybridization of the Walker to steppingstones of the Road:

The ith steppingstone Ai subsequences will hybridize with acomplementary subsequence i of the ith stepper Si.

We assume that this occurs at each steppingstone, except thesteppingstones where the walker’s ends are hybridized.

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1 …A0 A1 … Ai-1 Ai Ai+1 …

The Walker Wi

We use a type two restriction enzyme that:· matches with the duplex subsequence containing Ci-1Bi-1and its complement i-1i-1 within Wi, and· then cleaves Wi just before i and just after Ci.

Restriction Enzyme Cleavage of the Walker:

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1 …A0 A1 … Ai-1 Ai Ai+1 …

RestrictionEnzymeCleavage

 

C i CiR

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1

A0 A1 … Ai-1 Ai Ai+1

The Restriction Enzyme Cleavage of the Walker:

Resulting Products of Cleavage:(1) A ith truncated walker TWi

same as

· still attached to the ith steppingstone Si· · with an ssDNA overhang (Ci)R at one 3’ end

(2) The i-1th stepper Si-1

• still attached to the i-1th steppingstone Si-1• with an ssDNA overhang at one 3’ end.

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1 …A0 A1 … Ai-1 Ai Ai+1 …

RestrictionEnzymeCleavage

BiR Ci

R

 

A i

 

B iR

 

B i

 

A iR

Ci Bi

 

C i CiR

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1

A0 A1 … Ai-1 Ai Ai+1

The Reformation of the Walker.· The i+1th stepper strand Si+1 is already hybridized with a

complementary subsequence i+1 of i+1th stepper Si+1.· This i+1th stepper strand Si+1 can also hybridize with the

truncated walker TWi at their i and Ci ssDNA overhangs

· The DNA ligase concatenates the strands

Resulting transformation of truncated walker TWi into i+1th walker Wi+1with its 3’ ends hybridized to consecutive steppingstones Ai and Ai+1 .

Hybridization

 

B i

 

A iR

Ci Bi

ligation

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1 …A0 A1 … Ai-1 Ai Ai+1 …

 

C i CiR

 

A 0

 

A 1 …

 

A i-1

 

A i

 

A i+1

A0 A1 … Ai-1 Ai Ai+1

Possible Movements of the Walker:(1) Forward:

(2) Stall: The cleavage operation can be reversed by re-hybridization

(3) Reversal: The walker has two possible (dual) restriction enzymerecognition sites which can result in a reversal of movement.

f f f f f f

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

Wi+1:

 

A i

 

A i+1A0 A1 … Ai-1 Ai Ai+1

f f f f f f

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

f f f f f f

Wi+1:

 

A i

 

A i+1A0 A1 … Ai-1 Ai Ai+1

Wi

:

 

A i-1

 

A i

A0 A1 … Ai-1 Ai Ai+1

Rolling DNA Autonomous Nanomechanical Device:•requires no temperature changes.•makes no use of DNA ligase or any restriction enzyme•it uses instead the hybridization energy of DNA in trapped states:Energetics:

•uses fuel DNA strands to store energy•uses the application of DNA catalyst techniques to harness energy•liberates DNA from loops conformations into lower energyconformations

•Achieves random bidirectional motion around a circular ssDNA strand.

Bidirectional RandomTranslational& RotationalMovement

ssDNARoller:ssDNA

Road:

Rolling DNADevice

Oglionucleotides used in the Rolling DNA Construction.

Let A0, A1, B0, B1 each be distinct oglionucleotides:·of low annealing cross-affinity,·consisting of L (L can be between 15 to 20) bases pairs.

Let a0, a1 be oglionucleotides·derived from A0, A1 by changing a small number of bases,·so their annealing affinity with 0

R, 1R

respectively is somewhatreduced, but still moderately high.

Strong Hybridization:Hybridization between A0 and reverse complementary sequence 0

R (orbetween A1 and reverse complementary 1R)

Weak Hybridization:Hybridization between a0 and 0 R (or between a1 and 1R)

Key Idea:A strong hybridization is able to displace a weak hybridization.

Rolling DNA Device

The Road: an ssDNA

·with a0, a1, a0, a1, a0, a1, … in direction from 5’ to 3’,·consisting of a large number of repetitions of the sequences a0, a1.

The Wheel: a cyclic ssDNA· of base length 4L· with 0R,1R,0R, 1R in direction from 5’ to 3’· this corresponds to 1, 0, 1, 0 in direction from 3’ to 5’. Type 0 Wheel Position Type 1 Wheel Position

Note: the wheel DNA strand is intertwined with the road strand of DNA.

a0 a1

a0 a1

a0 a1

……

 

A 0

 

A 1 a0

a1 a0

a1 a0

a1 … …

 

A 1R

 

A 0R

Step

 

A 1

 

A 0 … a0

a1 a0

a1 a0

a1 …

 

A 0R

 

A 1R

Avoiding Unwanted Interactions.

(1)To ensure there is no interaction between a wheel andmore than one distinct road at a time

(e.g., so the wheel is not sandwiched between two roadstrands):

·we use a sufficiently low road concentration and solidsupport attachment of the roads.

(2)To ensure there is no interaction between a road and morethan one wheel:

·we use a sufficiently low wheel concentration.

Wheel Movement Fueled by Heat Energy········Similar to Branch Migrations·Very Slow

Wheel Movement Fueled by DNA Hybridization:·Faster·Used by Yurke and Turberfield [YTM+00,YMT00,TYM00] forDNA tweezer nanomechanical devices but they require heat cycling

We use the hybridization energy of DNA fuel loop strands:

o We require no external environmental changes to induce repetitionsof the motions by our DNA devices (no heat cycling).

o We apply DNA catalyst techniques for liberating DNA from theseloop conformations.

o We harness their energy as they transition into lower energyconformations.

DNA Fuel Loop StrandsType 0 InitialPrimary Fuel Strand Loop Configuration

Type 0 InitialComplementary Fuel Strand Loop Configuration

•Type 1 Primary and Complementary Fuel Strands have 0 and 1 switched.

Duplex DNA: complete hybridization of the type 0 primary and complementary type 0 fuel strands

f f f f f f A1 A0

B0

 

A 1R

Hybridization at the ends of the primary fuel strand.

A0

B0R

 

B 0R

A1

 

A 1

A1 A0

B0

 

A 1R

 

A 1

 

A 0

 

B 0 A1

R

f f f f f f A1

 

A 1

 

A 0

A0

 

B 0R

Hybridization at the ends of the fuel strand.

Duplex DNA: complete hybridizationof the type 0 primary and complementary type 0 fuel strands

Energetics of the Fuel Strands.· The Duplex DNA resulting from hybridization of theprimary and complementary fuel strands of a given type has lowerfree energy

o lowest energy equilibrium state· Over a sufficiently long time interval:

o the free energy will drive these two species to Duplex DNA· By setting a sufficiently low temperature,

o that equilibrium duplex state can be made to take any giventime duration to reach on the average.

A1 A0

B0

 

A 1R

 

A 1

 

A 0

 

B 0 A1

R

The Sequence of Events of a Feasible Movement of the Wheel.Initially Suppose: the wheel is in type 0 position with respect to the road.

(1) Hybridizations of a 0th primary fuel strand:• Initial Hybridization of of the second segment A0 of the 0th primary

fuel strand with the reverse complementary segment 0R of the wheel.• Extension of that initial hybridization to a hybridization of two first

segments A1, A0 of the 0th primary fuel strand with the consecutivereverse complementary segments 1R 0R of the wheel.

Consequences:·The wheel moves by one segment in the 5’ direction along the road,

effecting a transition of the state of the wheel from the type 0 positionto type 1 position.

• Displacement of the prior hybridization of the 5’ end segment A1 withits 3’ end segment 1R of the primary fuel strand, which now is exposed.

Wheel rotationdue to displaced hybridization with primary fuel strand.

The Sequence of Events of a Feasible Movement of the Wheel.

(2) Hybridizations of a type 0 complementary fuel strand:

• Hybridization with reverse complementary subsequences of the type 0primary fuel strand, · first at that fuel strand’s newly exposed 3’ end segment A1

R · then at B0.

· Formation of a type 0 fuel strand duplex removes the type 0 fuelstrands from the wheel, completing the step.

.

Hybridization between primary & complementary fuel strands.

 

A 1

 

A 0 … a0

a1 a0

a1 a0

a1 …

 

A 0R

 

A 1R

Possible Movements of the Walker:(1) Forward: Type 0 Wheel Position Type 1 Wheel Position

(2) Stall: Type 0 Wheel Position Type 0 Wheel Position

(3) Reversal: Type 1 Wheel Position Type 0 Wheel Position

f f f f f f

 

A 0

 

A 1 a0

a1 a0

a1 a0

a1 … …

 

A 1R

 

A 0R

 

A 1

 

A 0 … a0

a1 a0

a1 a0

a1 …

 

A 0R

 

A 1R

f f f f f f

 

A 0

 

A 1 a0

a1 a0

a1 a0

a1 … …

 

A 1R

 

A 0R

 

A 0

 

A 1 a0

a1 a0

a1 a0

a1 … …

 

A 1R

 

A 0R

f f f f f f

 

A 0

 

A 1 a0

a1 a0

a1 a0

a1 … …

 

A 1R

 

A 0R

 

A 1

 

A 0 … a0

a1 a0

a1 a0

a1 …

 

A 0R

 

A 1R

Conclusion: We have given two designs forAutonomous Bidirectional DNA Nanomechanical Devices:(1)Walking DNA Device: Use DNA ligase & restriction

enzymes.

Rolling DNA Device: No Use of DNA ligase or restrictionenzymes.

Bidirectional Translational& Rotational Movement

dsDNAWalker:

ssDNARoad:

Walking DNADevice

Bidirectional RandomTranslational& RotationalMovement

ssDNARoller:ssDNA

Road:

Rolling DNADevice

Expected Drift Via Random Translational Movement:·Both Devices provide random, bidirectional translationalmovements along the road.·Due to the symmetry of the constructions, both translationalmovements have equal probability in either direction.·By the theory of random walks in 1 dimension (Feller [F82]) theexpected deviation after n steps is O(n1/2).

Fixing Translational Movement by Latching:·The designs can be modified to include a “latching mechanism” that fixesthe device(walker or wheel) position at specified locations on road.

·Modifications to allow for Latching:· appending to each 3’ end of the device an additional “latching”sequence and also· inserting the complements of these “latching” sequences at aspecified pair of locations along the road,· This fixes (via their hybridization) the device’s location once thelocations are reached and these “latching” hybridizations occur.

Use of these DNA Autonomous Nanomechanical Devices:· can be incorporated at multiple sites of larger DNA

nanostructures such as self-assembled DNA lattices.

· used to induced movements to hold state information andto sequence between distinct conformations.

Potential Applications.(a) Array Automata: The state information could be stored at each site

of a regular DNA lattices, and additional mechanisms for finite statetransiting would provide for the capability of a cellular arrayautomata.

(b) Nanofabrication: These capabilities might be used to selectivelycontrol nanofabrication stages. The size or shape of the lattice maybe programmed through the control of such sequence-dependentdevices and this might be used to execute a series of foldings (similarto Japanese paper folding techniques) of the DNA lattice to form avariety of 3D confirmations and geometries.

DNA LatticesDNA Lattices A New, Powerful A New, Powerful Technology for Rendering Patterns at the Molecular Level Technology for Rendering Patterns at the Molecular LevelA 2D DNA lattice is constructed by a self-assembly process:A 2D DNA lattice is constructed by a self-assembly process: ---Begins with the assembly of -Begins with the assembly of DNA tile DNA tile nanostructuresnanostructures:: - DNA tiles of size - DNA tiles of size 14 x 7 nanometers14 x 7 nanometers - - Composed of short DNA strands with Holliday junctionsComposed of short DNA strands with Holliday junctions - These - These DNA tiles self-assembleDNA tiles self-assemble to form a to form a 2D lattice:2D lattice:

-The Assembly is -The Assembly is Programmable:Programmable:-Tiles have sticky ends that provide programming for the patterns to be formed.-Tiles have sticky ends that provide programming for the patterns to be formed.

-Alternatively:-Alternatively: tiles self-assemble around segments of a DNA strand encoding a 2D pattern.tiles self-assemble around segments of a DNA strand encoding a 2D pattern.- - Patterning:Patterning: Each of these tiles has a surface perturbation depending on the pixel intensity. Each of these tiles has a surface perturbation depending on the pixel intensity.

-pixel distances 7 to 14 nanometers-pixel distances 7 to 14 nanometers-not diffraction limited-not diffraction limited

Key Application:Key Application: Molecular robotic componentsMolecular robotic components

Applications of Molecular Motors to to DNA arrays:Applications of Molecular Motors to to DNA arrays:

nn Manipulation of molecules using molecular motor devices arrangedManipulation of molecules using molecular motor devices arrangedon DNA tiling arrays.on DNA tiling arrays.

nn Molecular Molecular BabbageBabbage Machines: Machines:nnA DNA array of motors, may offer a mechanism to do DNAA DNA array of motors, may offer a mechanism to do DNAcomputation of arrays whose elements (the tiles) hold state.computation of arrays whose elements (the tiles) hold state.

nn Parallel Cellular Automata computations Parallel Cellular Automata computations may be executed: may be executed:nnarrays of finite state automata each of which holds state.arrays of finite state automata each of which holds state.nnThe transitions of these automata and communication of values toThe transitions of these automata and communication of values totheir neighbors might be done by conformal (geometry) changes,their neighbors might be done by conformal (geometry) changes,again using this programmability.again using this programmability.nnCellular Automata can do computations for which tiling assembliesCellular Automata can do computations for which tiling assemblieswould have required a further dimension.would have required a further dimension.

Challenges in Molecular RoboticsChallenges in Molecular Roboticsnn Challenge: Re-Engineering Biological Molecular MotorsChallenge: Re-Engineering Biological Molecular Motors

nn Construction of these biological molecular motors and theirConstruction of these biological molecular motors and theirlinking chemistry to DNA arrays:linking chemistry to DNA arrays:nn Protein motors are modular and can be re-engineered toProtein motors are modular and can be re-engineered to

accomplish linear or rotational motion of essentially anyaccomplish linear or rotational motion of essentially anytype of molecular component.type of molecular component.

nn Motor proteins have well known transcription sequences.Motor proteins have well known transcription sequences.nn There are also well known proteins (binding proteins) thatThere are also well known proteins (binding proteins) that

provide linking chemistry to DNA.provide linking chemistry to DNA.nn Protein motors and attached linking elements might beProtein motors and attached linking elements might be

synthesized from sequences obtained by concatenation ofsynthesized from sequences obtained by concatenation ofthese transcription sequences.these transcription sequences.

nn Challenge: Programmable Sequence-Specific Control ofChallenge: Programmable Sequence-Specific Control ofNanoMechanicalNanoMechanical Motion. Motion.nn an array of molecular motors would be more useful if theyan array of molecular motors would be more useful if they

can be selectively controlled.can be selectively controlled.nn Manipulate specific molecules: do chemistry at chemicallyManipulate specific molecules: do chemistry at chemically

identical but spatially distinct sites.identical but spatially distinct sites.

Key Open Problemin the design of Autonomous Nanomechanical Devices:

· A DNA Device achieving Unidirectional Movement(translational or rotational)

Conjecture:

· Will need to use irreversible reactions (e.g., ligation)

Another Approach:

· The design of Autonomous Nanomechanical Devicesby use of Protein Motors

Axonemal Dynein Motor [Taylor,2000]

(rotational movement)

ADP Protein Motor [Montemagno, et al,99](rotational movement)

Kinesin [Stracke, 99]walks on microtubules

Biological Protein Motors:manufactured by expression of protein motors and linkers

nn ATP ATP synthasesynthase and ADP act as rotary motors, coupling proton flux through a membrane with the and ADP act as rotary motors, coupling proton flux through a membrane with thephosphorylationphosphorylation of ADP to ATP. of ADP to ATP.

nn KinesinKinesin acts as a molecular walking machine, acts as a molecular walking machine, translocatingtranslocating itself (and any attached components) in step- itself (and any attached components) in step-wise fashion along a microtubule. Each step along the microtubule consumes one ATP molecule.wise fashion along a microtubule. Each step along the microtubule consumes one ATP molecule.

DNA Tile Lattice for DNA Tile Lattice for TemplatingTemplatingMolecular MotorsMolecular Motors(with Dan (with Dan KenanKenan, Duke), Duke)

Motor

DNA tile

Ab

A bifunctional antibody (Ab) is shownbound to a DNA aptamer on a tile and to amotor protein, thus immobilizing the motoronto the tile. An example DNA lattice

More complex patterns of motors on lattices can allow for sophisticatedmolecular robotics tasks.