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Compact Error Resilient Computational DNA Tiling Assemblies. John Reif, Sudheer Sahu, Peng Yin Department of Computer Science, Duke University. 2. Self-Assembly of DNA Tiles. Perform universal computation. Manufacture patterned nanostructures from smaller unit nanostructures.

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compact error resilient computational dna tiling assemblies

Compact Error Resilient Computational DNA Tiling Assemblies

John Reif, Sudheer Sahu, Peng Yin

Department of Computer Science, Duke University

self assembly of dna tiles

2

Self-Assembly of DNA Tiles
  • Perform universal computation.
  • Manufacture patterned nanostructures from smaller unit nanostructures.
assembly of binary counter winfree
Assembly of Binary Counter (Winfree)

Computationaltiles

Seedtile

Frametiles

Binarycounter

errors in self assembly of dna tiles
Errors in Self-Assembly of DNA Tiles
  • Binding rules are not strict.
  • A tile might get assembled to a binding site where it was not supposed to go.
example of a computational error
Example of a Computational Error

Computationaltiles

Seedtile

Error!

Frametiles

how to decrease errors
How to Decrease Errors?
  • Errors can be arbitrarily decreased by
    • Decreasing concentration of tiles.
    • Increasing binding strengths.
    • Drawback : Reduce speed.
  • Another approach:
    • Change the logical design of the tiles.
slide7

Error Resilient Tilings by Winfree

Original tiles:

Error resilient tiles:

(Excerpted from Winfree 03)

  • Error rate  => 2
  • Assembly size increased by 4
slide8

Originaltiles:

A

B

C

AB

BC

Errorresilienttiles:

slide9

Original tiles:

A

B

C

AB

BC

Error resilient tiles:

slide10

Originaltiles:

A

B

C

AB

BC

Errorresilienttiles:

Error checking pads

compact error resilient construction
Compact Error Resilient Construction
  • Wholeness of pad: Single pad per side.
result of compact error resilient scheme
Result of Compact Error Resilient Scheme
  • We saw:
    • Two way overlay scheme.
    • One mismatch caused at least one more mismatch.
    • Error is reduced from  to 2.
  • Next we will see:
    • Three way overlay scheme.
    • One mismatch will cause at least two more mismatches.
    • Error will reduce from  to 3.
slide21

Computer Simulation (Xgrow, Winfree)

Three way overlay

Winfree 3x3 construction

Winfree 2x2 construction

Two way overlay

No error correction

conclusions
Conclusions
  • Assembly size not increased.
  • Two way overlay: error rate (5%) => 2(0.25%).
  • Three way overlay: error rate  (5%) => 3 (0.0125%).
  • Open question: error rate  => k ?