DNA COMPUTING

BY
P.Sramika, III B.tech (ECE),
R.V.R. Institute of engineering and tech(Ibp)
S.Amoolya, III B.tech (ECE),
T.K.R. college of engineering and tech

E-mail id:
meerasramika@yahoo.com
samoolya@yahoo.in

ABSTRACT:
 Silicon
microprocessors have been the
heart of computing world for
more than forty years.
Computer chip manufacturers
are furiously racing to make
the next microprocessor that
will topple speed records and
in the process are cramming
more and more electronic
devices onto the
microprocessor. Sooner or
later the physical speed and
limits of silicon
microprocessors is bound to
hit a wall.
Chipmakers
need a new material to
produce faster computing
speed with fewer
complexities. You won’t
believe where scientists have
found this new material.
DNA, the material our genes
are made of, is being used to
build the next generation of
microprocessors. Scientists
are using this genetic material
to create nano-computers that
might take the place of silicon
computers in the next decade.
A nascent
technology that uses DNA
molecules to build computers
that are faster than the world’s
most powerful human-built
computers is called DNA
computing. Molecular
biologists are beginning to
unravel the information
processing tools such as
enzymes, copying tools,
proofreading mechanisms and
so on, that evolution has spent
millions of years refining.
Now we are taking those tools
in large numbers molecules
and using them as biological
computer processors.
DNA computing has
a great deal of advantage over
conventional silicon-based
computing. DNA computers
can store billions of times
more data than your personal
computer. DNA computers
have the ability to work in a
massively parallel fashion,
performing many calculations
simultaneously. DNA
molecules that provide the
input can also provide all the
necessary operational energy.
DNA computing has
made a remarkable progress in
almost every field. It has
found application in fields like
biomedical, pharmaceutical,
information security, cracking
secret codes, etc.
Introduction
Man’s thirst for
knowledge has driven the
information revolution.
Human brain, a master
processor, processes the
information about the internal
and external environment and
sends signals to take
appropriate actions. In nature,
such controls exist at every
level. Even the smallest of the
cells has a nucleus, which
controls the cell. Where does
this power actually come
from? It lies in the DNA. The
ability to harness this
computational power shall
determine the fate of next
generation of computing.
DNA computing is
a novel technology that seeks
to capitalize on the enormous
informational capacity of
DNA, biological molecules
that can store huge amounts of
information and are able to
perform operations similar to
Scientists and
researchers believe that in the
foreseeable future DNA
computing could scale up to
great heights!
that of a computer, through
the deployment of enzymes,
biological catalysts that act
like software to execute
desired operations. The appeal
of DNA computing lies in the
fact that DNA molecules can
store far more information
than any existing conventional
computer chip. Also, utilizing
DNA for complex
computation can be much
faster than utilizing a
conventional computer, for
which massive parallelism
would require large amounts
of hardware, not simply more
DNA.
Structure of DNA
All organisms on
this planet are made of the
same type of genetic blueprint,
which bind us together.
Within the cells of any
organism is a substance called
Deoxyribonucleic Acid
(DNA), which is a double-
stranded helix of nucleotides,
which carries the genetic
information of a cell. The data
density of DNA is impressive.
Just like a string of
binary data is encoded with
ones and zeros, a strand of
DNA is encoded with four
bases, represented by letters A
(Adenine), T (Thymine), C
(Cytosine) and G (Guanine).
Graphical Illustration
representation of of double
inherent bonding helix
properties of DNA shape of
DNA.
The bases
(nucleotides) are spaced every
0.35 nanometers along the
DNA molecule, giving it a
remarkable data density of
nearly 18Mbits per inch.
These nucleotides will only
combine in such a way that C
always pairs with G and T
always pairs with A. This
complementarity makes DNA
a unique data structure for
computation and can be
exploited in many ways.
Computer in a test tube
The idea of
using DNA to store and
process information took off
in the year 1994 when
Leonard Adleman, a computer
scientist at the University of
Southern California, came to
the conclusion that DNA had
computational potential.
Adleman caused an avalanche
in the fields of biology;
mathematics and computers
by solving a problem called
the Directed Hamiltonian Path
problem or sometimes referred
to as the Traveling Salesman
Problem. The ‘salesman’ in
this problem has a map of
several cities that he must visit
to sell his wares where these
cities have only one-way
streets between some but not
all of them. The crux of the
problem is that the salesman
must find a route to travel that
passes through each city (A
through G) exactly once, with
a designated beginning and
end. The salesman does not
want to backtrack or go more
than once through any of the
paths. This is a non-
deterministic polynomial time
problem.
Basic outline of Traveling
Salesman Problem
Adleman used a basic seven
city, thirteen street model for
Traveling Salesman Problem
and created randomly
sequenced DNA strands 20
bases long to chemically
represent each city and a
complementary 20 base strand
that overlaps each city’s
strand half way to represent
each street. This
representation allowed each
multi-city tour to become a
piece of double stranded DNA
with the cities linked in some
order by the streets.
Representation of 20 bases
DNA strand representing a
city showing the bonding
tendencies of nucleotides to
DNA strands representing
pathways between the cities.
By placing a
few grams of every DNA city
and street in a test tube and
allowing the natural bonding
tendencies of the DNA
building blocks to occur, the
DNA bonding created over
10^9 answers in less than one
second. Out of the answers
that came about the correct
answers were determined
considering that the correct
path must start at A and end at
G, it must pass through all
cities at least once and must
contain each city in turn.
The correct
answer was determined by
filtering the strands of DNA
according to their end-bases to
determine which strands
began from A and end in city A Successor to
G. The remaining strands were Silocon
then measured through Silicon
electrophoreic techniques to microprocessors have
determine if the path they been the heart of
represent has passed through computing world for
all seven cities. Finally the more than forty
resulting sets of DNA were years.Computer chip
examined individually to manufacturers are
determine if they contain each furiously racing to make
city in turn. That strand(s) that the next microprocessor
remained was then determined that will topple speed
to be the answer(s). This records and in the process
process took Adleman about a are cramming more and
week. A conventional more electronic devices
computer is better suited for onto the microprocessor.
deterministic computation Many have predicted that
permitting at most one next Moore’s law (which
move at any step in states that the
computation. The inherent microprocessors would
parallel computing ability of double in complexity
DNA, however, is perfectly every two years) will
suited for solving such non- soon reach its end,
deterministic type of because of the physical
problems. speed and miniaturization
limits of silicon
microprocessors.
DNA computers
have the potential to take
computing to new levels,
picking up where Moore’s law
leave off. DNA computers
could surpass their silicon-
based predecessors. The
several advantages of DNA
over silicon are:As long as
there are cellular organisms,
there will 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.
DNA molecules
have a potential to store
extensively large amount of
information. It has been
estimated that a gram of dried
DNA can hold as much
information as a trillion CD’s.
More than 10 trillion DNA
molecules can fit into an area
of 1 cubic centimeter. With
this small amount if DNA a
computer would be able to
hold 10 terabytes of data, and
perform 10 trillion
calculations at a time.
In a biochemical
reaction-taking place in a tiny
surface area, a very large
number of DNA molecules
can operate in concert,
creating a parallel processing
system that mimics the ability
of the most powerful
supercomputer. DNA
computers have the ability to
perform many calculations
simultaneously; specifically,
on the order of 10^9
calculations per ml of DNA
per second! A calculation that
would take 10^22 modern
computers working in parallel
to complete in the span of one
human’s life would take one
DNA computer only 1 year to
polish off!
Scope and recent updates
Scientists have
taken DNA from the free-
floating world of the test tube
and anchored it securely to a
surface of glass and gold.
University of Wiscosnin-
Madison researchers have
developed a thin, gold-coated
plate of glass about an inch
square. They believe it is the
optimum working surface on
which they can attach trillions
of strands of DNA. Putting
DNA computing on a solid
surface greatly simplifies the
complex and repetitive steps
previously used in
rudimentary DNA computers.
Importantly it takes DNA out
of the test tube and puts it on a
solid surface, making the Applications
technology simpler, more DNA logic
accessible and more amenable gates are the first step
to the development of large towards creating a
DNA computers capable of computer that has a
tackling the kind of complex structure similar to that of
problems that conventional an electronic PC. Instead
computers now handle of using electrical signals
routinely. Researchers believe to perform logical
that by the year 2010 the first operations, these DNA
DNA chip will be logic gates rely on DNA
commercially available. code. They detect
fragments of genetic
material as input, splice
together these fragments
and form a single output.
Recent works have shown
how these gates can be
employed to carry out
fundamental
computational operations,
addition of two numbers
expressed in binary. This
invention of DNA logic
gates and their uses are a
breakthrough in DNA
computing.
A group of
researchers at Princeton
University in early 2000
demonstrated an RNA
computer similar to
Adleman’s, which had the
ability to solve a chess
problem involving how many DNA computing is
ways there are to place knights in its infancy, and its
on a chessboard so that none implications are only
can take the others.While a beginning to be explored.
desktop PC is designed to But DNA computing
perform one calculation very devices could
fast, DNA strands produce revolutionize the
billions of potential answers pharmaceutical and
simultaneously. This makes biomedical fields. Some
the DNA computer suitable scientists predict a future
for solving "fuzzy logic" where our bodies are
problems that have many patrolled by tiny DNA
possible solutions rather than computers that monitor
the either/or logic of binary our well-being and
computers. In the future, some release the right drugs to
speculate, there may be hybrid repair damaged or
machines that use traditional unhealthy tissue. They
silicon for normal processing could act as ‘Doctors in a
tasks but have DNA co- cell’. DNA computing
processors that can take over research is going so fast
specific tasks they would be that its potential is still
more suitable for. emerging.
DNA computing can be used
by national governments for
cracking secret codes, or by
airlines wanting to map more
efficient routes. The concept
of using DNA computing in
the fields of cryptography,
steganography and
authentication has been
identified as a possible
technology that may bring
forward a new hope for
unbreakable algorithms in the
world of information security.
Advantages
 The advantage of DNA
approach is that it works in
parallel, processing all
possible answers
simultaneously.
 DNA computing is an
example of computing at a
molecular level, potential a
size limit that may never be
reached by the
semiconductor industry.
 It can be used to solve a
class of problems that are
difficult or impossible to
solve using traditional
computing methods.
 There is no power required
for DNA computing while
the computation is taking
place. The chemical bonds
that are the building blocks
of DNA happen without
any outside power source.
Its energy-efficiency is
more than a million times
that of a PC.
 DNA computing is a cost-
effective method for
solving complex
computational problems.
Disadvantages
 DNA computers require
human assistance.
 Technological challenges
remain before DNA
computing. Researchers
need to develop techniques
to reduce number of
computational errors
produced by unwanted
chemical reactions with the
DNA strands. They need to
eliminate, combine, or
accelerate the steps in
processing the DNA.
 The extrapolation and
practical computational
environment required are
daunting. The ‘test tube’
environment used for DNA
computing is far from
practical for everyday use.
 To the naked eye, DNA
computer looks like clear
water solution in a test tube.
There is no mechanical
device. Hence to make the
output visible, human
manipulation is needed.
Conclusion
The beauty of
DNA research is found in the
possibility of mankind’s newsscientist.com
utilization of its very life iturls.com/English/TechHotsp
building blocks to solve its ot
most difficult problems. DNA theindianprogrammer.com
computing research is going news.bbc.co.uk/hi/english/
so fast that its potential is still sci/tech
emerging. Scientists and chronicle.com/data/articles.dir
mathematicians around the olympus.co.jp/en/magazine/
world are now looking at the TecZone
application of DNA computers
to a whole range of
“intractable” computing
problems. In any case, we will
not be tossing out those PCs
for test tubes of DNA anytime
soon and the use of DNA
computing in every walk of
life is a long way off!

References

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