ISHA SAXENA

&
Kanika Jain
• DNA Stands for Deoxi-ribonucleic acid.

• It is the genetic material of each individual.

• It contains instructions for assembling cells.

• DNA is unique for each and every individual.

DNA Lab Chip

DNA Molecule
hth
yyh
yhy

DNA strand
• The two strands of DNA are anti parallel
to each other.

• Basic pairing

• Hold by weak hydrogen bonds between

complementary base pairs.
• Also known as MOLECULAR COMPUTING.

• It uses DNA, molecular biology and bio chemistry.

•It perform operations similar to computer by the

use of enzymes, catalyst etc.
 Using a DNA-based cell
adhesion system, researchers
can create cell chips,
analogous to DNA chips, that
could be used as biosensors for
detecting the presence of
pathogens, or for screening
potential new therapeutic
drugs.
DNA HELIX
STRANDS

POLYMERASE
REACTIONS
MOTHERBOARD
 DNA molecule
arrangement
in DNA chip.
 Began in 1994 when Dr. Leonard
Adleman wrote the paper “Molecular
computation of solutions to
combinatorial problems”.
 DNA computers moved from test tubes
onto gold plates.
 First practical DNA computer unveiled in
2002. Used in gene analysis.
 Self-powered DNA computer unveiled
in 2003.

First programmable autonomous computing

machine.
Can perform a billion operations per second
with 99.8% accuracy.
 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.

 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

It utilizes the property of DNA.

 It can solve parallel search problems efficiently.

 Utilizing the DNA computing can solve the

problems more faster.

Father of DNA computing-

Leonard Adleman
 • It shows I gm of DNA and
CD holds 800 MB of data.

•1 gm of DNA = 1*10^14 MB of
data.
• LEONARD
ALDEMAN SOLVED THE
HAMILTONIAN PATH PROBLEM.

• PROBLEM WAS- TO FIND THE

SHORTEST PATH BETWEEN CITIES &
VISITING EACH CITY EXACTLY ONCE.
Given a graph with n vertices
1. Generate a set of random paths
2. For each path in the set
a. Check whether that path starts at the start
vertex and ends with the end vertex
b. Check if that path passes through n vertices
c. Check if that path passes through that vertex
3. If the set is not empty, there is a Hamiltonian path
Strands of DNA depicts the 7 cities. In genes,
genetic coding is represented by the letters A, T,
C and G. Some sequence of these 4 letters
represented each city and possible flight path.

These molecules are then mixed in a test tube,

with some of these DNA strands sticking
together.
Hamilton Path Problem
(also known as the “travelling salesperson
problem”)

DARWIN

BRISBANE
ALICE
PERTH SPRING

SYDNEY
MELBOURNE
 Is there any Hamiltonian path from Darwin to
Alice Spring?
 Within a few seconds, all of the possible
combinations of DNA strands, which represent
answers, are created in the test tube.

 Adleman eliminates the wrong molecules

through chemical reactions, which leaves
behind only the flight paths that connect all
7 cities.
 Solution by inspection is:
 Darwin -> Brisbane -> Sydney -> Melbourne
->Perth->Alice Spring
 BUT, there is no deterministic solution to this
problem, i.e. we must check all possible
combinations.
DARWIN
BRISBANE
PERTH ALICE
SPRING

SYDNEY

MELBOURNE
 Encode each city with complementary base –
vertex molecules

 Sydney - TTAAGG
 Perth - AAAGGG
 Melbourne - GATACT
 Brisbane - CGGTGC
 Alice Spring – CGTCCA
 Darwin - CCGATG
 Encode all possible paths using the
complementary base – edge molecules:

 Sydney -> Melbourne – AGGGAT

 Melbourne-> Sydney – ACTTTA
 Melbourne -> Perth – ACTGGG
etc…
 Merge vertex molecules and edge molecules.
 All complementary base will adhere to each other
to form a long chains of DNA molecules.

MERGE Solution with

Solution with & edge DNA
vertex DNA ANNEAL
molecules
molecules

Long chains of DNA molecules(All possible path

exists in the graph)
 The solution is a double helix molecule:

DARWIN BRISBANE SYDNEY MELBOURNE PERTH ALICE SPRING

CCGATG –CGGTGC –TTAAGG-GATACT – AAAGGG -CGTCCA

TACGCC - ACGAAT - TCCCTA - TGATTT - CCCGCA

DARWIN BRISBANE SYDNEY MELBOURNE PERTH

->BRISBANE ->SYDNEY ->MELBOURNE ->PERTH ->ALICE
SPRING
 They detect fragments of genetic material as input,
splice together these fragments and form a single
output.

 For instance, a genetic gate called the "And gate"

links two DNA inputs by chemically binding them
so they're locked in an end-to-end structure.

 Logic gates might be combined with DNA

microchips to create a breakthrough in DNA
computing
 DNA can be used to calculate complex mathematical
problems.

 University of Rochester developed logic gates made of DNA.

 Currently, logic gates interpret input signals from silicon

transistors, and convert those signals into an output signal
that allows the computer to perform complex functions.

 Logic gates made up DNA instead of using electrical

signals to perform logical, rely on DNA code.
He showed that DNA can be used to solve hard
computational problem…
The power of DNA in view of
computation capability:
 vast parallelism

 exceptional energy efficiency

 extraordinary information density

MELTING

ANNEALING

MERGING

AMPLIFICATION

SELECTION
  Given a test tube T & A
strand S, it is possible to
extract all the possible
strands in T that contain
S as subsequence & to
separate them from
those that do not contain
it.

Formation of a DNA Strand

 Precipitation of more
DNA Strands in alcohol.
 Spooling a DNA with
a metal hook or
similar device.
 Taiwan introduced the world's first DNA
authentication chip.

 The first DNA chip in the world has finally been

developed by Biowell Technology Inc. after 2 years of
research.

 Inside the chip is synthesized DNA, which can be

identified by a device similar to an identification card
or a credit card reader.
 The synthesized DNA inside the chip generates
DNA signals which only the company's readers
can detect and authenticate in two seconds.

 The DNA chip can also be used on passports,

credit cards, membership cards, licenses, CDs,
DVDs, notebooks, PDAs , computer software
etc..
•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.
•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.
 DNA computing involves a relatively large
amount of error.

 Requires human assistance.

•

 Time consuming laboratory procedures.

 No universal method of data

representation.
 DNA chips.

 Genetic programming.

 Pharmaceutical applications.

 Cracking of coded messages.

 Mapping the problem to DNA and DNA
operations.

 Extracting the answer takes time.

 Large problems may not fit into test tube.

 Suited for specific problems, difficult to

generalize
 Error: Molecular operations are not perfect.

 Reversible and Irreversible Error.

 Efficiency: How many molecules contribute?

 Encoding problem in molecules is difficult.

 Scaling to larger problems.

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.
 Cross-fertilization among evolutionary computing,
DNA computing, molecular biology, and computation
biology.

 Niche uses of DNA computers for problems that are

difficult for electronic computers.

 Increased movement into exploring the connection

between life and computation.
 Adleman used the “Traveling Salesman” problem was
simple. As technology becomes more refined, more efficient
algorithms may be discovered.

 In future advances may make DNA computers more efficient.

 The University of Wisconsin is experimenting with chip-based

DNA computers.

Instead, their powerful computing power will be used for areas

of encryption, genetic programming, language systems, and
algorithms or by airlines wanting to map more efficient
routes. Hence better applicable in only some promising areas.
 ANY QUERIES…?

It will take years to develop a practical workable DNA

computer.

But…. Let’s hope that the DREAM come true.