Dna Computing

By: PRASHANTH T
1NH02EC033
• As long as there are cellular organisms, there will always be
a supply of DNA.
• The large supply of DNA makes it a cheap resource.
• Unlike the toxic materials used to make traditional

microprocessors, DNA biochips can be made cleanly.
• DNA computers are many times smaller than today's

computers.
* Purifying silicon is very expensive, hence the chip making.
However, for DNA sequencing corroborates to purity, which is
very cheap.
•MOORE’S LAW establishes a limit on the miniaturization of
silicon chips, but there are no limits DNA density in DNA
computing.
FUNDAMENTALS ABOUT DNA STRUCTURE
DNA is deoxyribo nucleic acid and is the building block of all living
beings
It is a polynucleotide and has a double helical structure.
It is made of nucleotides adenine(A),guanine(G),Thiamine(T) and
cytosine( C).
Adenine bonds only with thiamine and guanine bonds only with
cytosine.
The two helix are complimentary of each other
{To find the shortest path covering all cities only
once.}
To find a route between
DELHI Mumbai and Kolkata
MUMBAI KOLKATA
BANGALORE
CHENNAI
• Generate all possible routes.
• Select itineraries that start with the proper city and
end with the final city.
• Select itineraries with the correct number of cities.
• Select itineraries that contain each city only once.
STEP1:Encode the city names in short DNA sequences.Encode the
Itineraries by connecting the city sequences for which the routes exist
MUMBAI GCTACG
DELHI CTAGTA
BANGALORE TCGTAC
CHENNAI CTACGG
KOLKATA ATGCCG
The DNA molecules are generated by a machine called DNA
synthesizer
GENERATION OF DIFFERENT ITINERARIES
Polymerase chain reaction is used to produce many copies of the DNA

PCR is iterative and uses an enzyme called polymerase
Polymerase copies a section of single stranded DNA starting at the
position of the primer,which is DNA complimentary to one end of the
Interested section.
Step 2: Sort the DNA by length and select the DNA whose length
Corresponds to 5 cities.
Gel electrophoresis force the DNA through a gel matrix by using an

electric field.
DNA forces its way through the gel which slows down the DNA at
different rates
STEP 3:Successively filter the DNA molecules by city,one city at a
Time.
Affinity purification is done by attaching the compliment of the

sequence in question to a substrate like magnetic bead.
The DNA which contains the sequence hybridizes with the
complement sequence on the beads
Graduated PCR can also be used if we already have the sequence of
city encodings.
As the complexity of the problem increases the
amount of DNA required also increases exponentially.
Since the operations are not deterministic but
stochastically driven,there will be some statistical errors
which limits the number of iterations.
It could not operate on a surface, limiting its applications
It required human intervention
Prof Lloyd Smith,Robert corn and Liman
Wang of University of Wisconsin
-Madison,US
Published a paper in the journal NATURE
on Jan 13,2000
Millions of DNA was anchored on

a surface of glass coated with gold
Invented in 2001 by researchers in Weizmann
Institute of science in Rehovot,Israel
The team was headed by Prof Ehud Shapiro
A single drop of water could hold trillion of
machines.
It could perform a billion operations per second
It relied on ATP(adenosine triphosphate) for
fuel
It used DNA and enzymes as hardware
,software ,input and output
Invented in 2002 by scientists at Weizmann Institute of
science,Israel
Team led by Prof Ehud Shapiro
The DNA molecule provides both the initial data and
energy to complete computation
An enzyme known as FOKL cleaves a piece of input
molecule and releases the energy stored in the bonds
It performs 330 trillion operations per second which is
more than 1,00,000 times the fastest PC
Dr Leonard Adleman of University of Southern
California,USA designed a DNA computer in 2002
The computer solves a complex problem with more than
one million possible solutions.
One strand of DNA was used to represent a problem
It in turn generated trillions of other strands
The computer weeds out invalid solutions until it is left
with the correct solution.
In 2003,Columbia University researcher Milan Strojanovic
developed a DNA computer used by NASA for health
maintenance of astronauts.
Richard J.Lipton,Daniel Boneh and Christopher
T.Dunworth designed a DNA computer that cracked the US
defence messages.
Albert Libchaber of NEC research institute,Princeton,NJ
used DNA to solve maximal clique problem.
Wisconsin Researchers solved “satisfiability”problem
Harold Craighead of Cornell Nanobiotechnology center has
developed silicon alternatives for DNA electrophoresis.
Nadrian C.Seeman of New York University used DNA to
mimick the XOR gate behaviour.
The inputs are replaced by DNA.If the
DNA at the input are a complementary
strands they combine to give a 1.
On April 28,2004 Ehud Shapiro
constructed a DNA computer which when
coupled with a input and output module is
capable of diagnosing cancerous activity
within a cell and release an anti-cancer
drug.
Feature DNA SILICON
COMPUTER 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
Features DNA SILICON
COMPUTER COMPUTER
Capability Highly Complex Complex
computations computations
Flexibility Less Good
Raw material Grows Remains stable

requirement exponentially
Energy Very negligible Comparatively
consumption higher
Control systems for chemical and biological processes
Gene validation
Lithography for nanotechnology and semiconductor
applications
Food traceability and safety
DNA chips
Study of logic
Encryption of data for security
Genetic programming and algorithms
Design of Bio-chips
Pharmaceutical applications
Airline and communication routing
Cracking of coded messages
1.news.nationalgeographic.com/ news/2003/02/0224_030224_
DNAcomputer.html - 38k
2.www.cnn.com
3. http://www.wisegeek.com/what-is-a-dna-computer.htm
4. http://www.tpgi.com.au/users/aoaug/dna_comp.html
5.http://www.sciam.com/article.cfm?articleID=000A4F2E-781B-1E5A-
A98A809EC5880105
6. http://unisci.com/stories/20021/0315023.htm
7.www.howstuffworks.com
8.www.bbcworld.com
9.www.wikipedia.com
10.Bio spectrum magazine-January 2006
11.DIGIT magazine-November 2005

Dna Computing

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Dna Computing

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By: PRASHANTH T

• The large supply of DNA makes it a cheap resource.

• Unlike the toxic materials used to make traditional

• DNA computers are many times smaller than today's

Polymerase chain reaction is used to produce many copies of the DNA

Gel electrophoresis force the DNA through a gel matrix by using an

Affinity purification is done by attaching the compliment of the

Millions of DNA was anchored on

Raw material Grows Remains stable

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