DNA COMPUTING

By : Suresh Kr. Verma Cs 3rd year

Outline of Topic
Definition DNA structure Solving Hamiltonian Path problem Different generations Conclusion

DEFINITION

DNA computers are the computers which using enzymes as a program that processes on the DNA molecules (input data)

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.

FEATURERS OF DNA

What is DNA?
DNA stands for Deoxyribonucleic Acid. 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 (+ sugar-phosphate backbone)

A Adenine T Thymine C Cytosine G Guanine

Bond in pairs

AT

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.

How enormous is the parallelism?

A test tube of DNA can contain trillions of strands. Each operation on a test tube of DNA is carried out on all strands in the tube in parallel ! Check this out. We Typically use

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

Detroit

Chicago Atlanta

Boston

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

Solving HPP with DNA (2)

Encode this graph in a DNA Vertices are assigned a random DNA sequence oAtlanta: ACTTGCAG oBoston: TCGGACTG Edges (flights) are formed by concatenating the 2nd half of the originating city and the 1st half of the destination city oAtlanta-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 path 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

Technological Developments.
US team shows that DNA computing can be simplified by attaching the molecules to a surface.

DNA molecules were applied to a small glass plate overlaid with gold.
Exposure to certain enzymes, destroyed the molecules with wrong answers leaving only the DNA with the right answers.

Evolution of the DNA computer

Evolution of the DNA computer (1)

Began in 1994 when Dr. Leonard Adleman wrote the paper Molecular computation of solutions to combinatorial problems. He then carried out this experiment successfully although it took him days to do so!

Evolution of the DNA computer (2)

DNA computers moved from test tubes onto gold plates.

Evolution of the DNA computer (3)

First practical DNA computer unveiled in 2002. Used in gene analysis.

Evolution of the DNA computer (4)

Self-powered DNA computer unveiled in 2003.

First programmable autonomous computing machine in which the input, output, software and hardware were all made of DNA molecules. Can perform a billion operations per second with 99.8% accuracy.

Evolution of the DNA computer (5)

Biological computer developed that could be used to fight cancers.

Designer DNA identifies abnormal and is attracted to it. The Designer molecule then releases chemicals to inhibit its growth or even kill the malignant cells. Successfully tested on animals.

DNA COMPUTER Vs SILICON COMPUTER

Feature Miniaturization

DNA COMPUTER Unlimited

SILICON COMPUTER Limited

Processing
Speed Cost Materials used Size Data capacity

Parallel
Very fast Cheaper Non-toxic Very small Very large

Sequential
Slower Costly Toxic Large Smaller

ADVANTAGES
Perform millions of operations simultaneously; Conduct large parallel processing

Massive amounts of working memory;

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

DNA chips Genetic programming Pharmaceutical applications 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.

THANK YOU!
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