DNA COMPUTING

RINIL MG
S7 EC
NO:38
 Outline of Lecture

 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?

 Moore’s 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?

 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
 A–T
 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 Boston

Atlanta

•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 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
 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 DNA COMPUTER SILICON COMPUTER

Miniaturization Unlimited Limited

Processing Parallel Sequential

Speed Very fast Slower

Cost Cheaper Costly

Materials used Non-toxic Toxic

Size Very small Large

Data capacity Very 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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