Abstract: Self-assembly is beginning to be seen as a practical vehicle for computation. The assembly of DNA-based tiles into 2D periodic arrays had been reported several times with a variety of motifs. In our work, one layer of self-assembled DNA 2-D array will be used as the programmable template. Sequence dependent nano-mechanical DNA devices will be inserted into the array. Each device can enter into a bi-stable state, and that this state could be controlled as well by the sequences of DNA. This system can lead to the computation of an arbitrary boolean function or creation of 2D DNA layers satisfying specific properties.

A DNA Motif to Insert a Sequence-Driven Device into a DNA Array

Baoquan Ding, Nadrian Seeman

Structures of of the 2 states of the Sequence-Driven DNA Devices

1

2A

2B

3

4A

4B

5

P1

P2

J1

J2

4A

5 2A

4B

2B

1

3

TPX

TJX

Molecular Models of the 2 states of the Sequence-Driven DNA Devices

Simple Model of the Device and the Inserting into Array

M A R K E R ---> M A R K E DP X + P X J X IN E R T

P X J X J X J X P X J X P X P X

+ - - - >

J XP X

P X J X J X J X P X J X P X P X

1 2 3 4 5 6 7 8

1 2 3 4 5 6 7 8

Model of the Array that Contain Different State Devices

ABC'D' Array--All JX

ABC'D' Array--Specifically Mixed as JX and PX

ABC'D' Array--PX-State Tiles Marked

Cj'Cp'

Dp' Dj'Dp

Cp Cj

Dj

BA

AB Array

Cj'+MCp'+M Dp'+M Dj'+M

Electrophoresis Analysis of the Formation of the Device

Electrophoresis Analysis of Operation of the Device

TX 2D DNA Array that Works as the Template

2D Array with Protruding Marker Tiles

One State of Modified Device that Will be Inserted into Array

Template Array that Contain Different States Devices

Summary:

Sequence-driven DNA devices that will be inserted into 2D DNA array have been constructed. The template array has been designed, and construction and AFM analysis are currently in progress.