DNA Computing

1
DNA Computing

• Herman G. Meyer III
• Sept. 28, 2004

2
Overview

• DNA
• DNA/CPU Comparison
• Leonard M. Adleman
• Proof of Concept Experiment

3
DNA

• Adenine, Thymine, Guanine, Cytosine (A,T,C,G)
• Polymerase
• Watson-Crick Pairing (A-T,C-G)
• Cheap
• Compact Data Storage
• 1 cm3 DNA 1012 CDs
• Redundant

4
DNA/CPU Comparison

• CPU
• Sequential Operations
• addition, bit-shifting, logical operations (AND,
  OR, NOT, NOR)
• DNA
• Parallel Operations
• Cut, Copy, Paste, Repair

5
Leonard M. Adleman

• Background in Mathematics Computer Science
• HIV Research
• DNA/Turing Machine similar
• Proof of Concept

6
Proof of Concept Experiment

• Directed Hamiltonian Path
• Pseudo code
• Generate random paths
• For each path
• Check Start/End points
• Check Length
• Check that all vertices exist
• If any path passes all tests, HP exists

7
Programming the DNA

• Cities
• Flights

8
Recipe

• In a test tube add
• 1014 molecules of each city
• 1014 molecules of each flight
• Water, ligase, salt
• Answer generated in about one second
• 100 trillion molecules representing wrong answers
  also generated

9
Ligases

• Bind molecules together
• Concatenates DNA strands

10
Polymerase

• Copies DNA
• Primers (Start, Complement of End)
• PCR

11
Gel Electrophoresis

• Sort molecules by length
• Molecules have a charge
• Magnets used

12
Checking Cities

• Attach city complement to iron ball
• Suspend ball in solution
• Watson-Crick pairing attraction
• Wrong answers poured out
• Repeat for each city

13
Did it work?

• DNA remaining in test tube encoded the valid
  Hamiltonian Path

14
Drawbacks

• The process required much human intervention
• Automation would be required for a real
  computer
• Same method on 200 cities would require more than
  DNA than the mass of Earth

15
Thoughts

• Could a DNA Computer get sick?
• Virus
• Cancer
• Is it biodegradable?
• Could a virus spread from computer to humans?
• If so, could virus writers spread more deadly
  viruses?
• New level of bioterrorism

16
Summary

• DNA can be used for simple calculations
• DNA is a compact form of data storage
• DNA is exponentially parallel
• DNA is redundant

17
References

• Ars Technica. http//arstechnica.com/reviews/2q00/
  dna/dna-5.html
• Scientific American - August 1998. pp 54-61
• Science - Vol. 266. Nov. 11, 1994. pp 1021-1024