DNA BASED COMPUTING

OVERVIEW
Definition DNA structure Solving Hamiltionian Path Problem Different Generations Conclusion

DEFINITION
DNA computers are the computers which using enzymes as a program that processes on the DNA molecules.

NEED OF DNA COMPUTER

Moores Law states that silicon microprocessors double in complexity roughly every two years. One day this will no longer hold true when miniaturisation limits are reached. Intel scientists say it will happen in about the year 2018. Require a successor to silicon.

What is DNA?
Source code to life Instructions for building and regulating cells Data store for genetic inheritance Think of enzymes as hardware, DNA as software

What is DNA made of? Composed of four nucleotides (+ sugarphosphate backbone) A Adenine T Thymine C Cytosine G Guanine Bond in pairs AT CG

STRUCTURE OF DNA

STRUCTURE OF DNA
This DNA structure was first described by James Watson and Francis Crick in 1953. The structure of DNA is illustrated by a right handed double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).

Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three.

DENSE INFORMATION STORAGE

This image shows 1 gram of DNA on a CD. The CD can hold 800 MB of data. The 1 gram of DNA can hold about 1x1014 MB of data.

Can DNA Compute?

DNA itself does not carry out any computation. It rather acts as a massive memory. BUT, the way complementary bases react with each other can be used to compute things. Proposed by Adelman in 1994.

HAMILTON PATH PROBLEM

Solving HPP with DNA

Edges represent nonstop flights Determine whether there is a Hamiltonian Path starting in Atlanta, ending in Detroit
Detroit

Chicago

Bosto n

Atlanta

Solving HPP with DNA (2)

Encode this graph in a DNA Vertices are assigned a random DNA sequence
Atlanta: ACTTGCAG Boston: TCGGACTG

Edges (flights) are formed by concatenating the 2nd half of the originating city and the 1st half of the destination city
Atlanta-Boston: GCAGTCGG

Solving HPP with DNA (3)

Use Polymerase Chain Reaction (PCR) to replicate DNA with the correct start and end city Put one primer on Atlanta and one primer on Detroit The right answer is replicated exponentially, while the wrong paths are replicated linearly or not at all

Solving HPP with DNA (4)

Use gel electrophoresis to identify the molecules with the right length Finally, use affinity separation procedure to weed out paths without all the cities
Iterative procedure (for each vertex/city) Probe molecules attached on iron balls attract the correct strands; the rest is poured out

If any DNA is left in the tube, it is the Hamiltonian Path Overall, this took 7 days in the lab

DNA COMPUTER Vs SILICON COMPUTER

Feature DNA COMPUTER Miniaturization Processing Speed Cost Materials used Unlimited Parallel Very fast Cheaper Non-toxic

SILICON COMPUTER Limited Sequential Slower Costly Toxic

Size

Very small

Large

Data capacity

Very large

Smaller

ADVANTAGES
Conduct large parallel processing Massive amounts of working memory; Perform millions of operations simultaneously; Generate & use own energy source via the input. Four storage bits A T G C . Miniaturization of data storage

LIMITATIONS
DNA computing involves a relatively large amount of error Requires human assistance! Time consuming laboratory procedures. No universal method of data representation.

APPLICATIONS
Pharmaceutical applications DNA chips Genetic programming Cracking of coded messages

Conclusion
o DNA computers showing enormous potential, especially for medical purposes as well as data processing applications. o Many issues to be overcome to produce a useful DNA computer. o Still a lot of work and resources required to develop it into a fully fledged product.

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