A

Seminar Report On

“DNA Computing”

Submitted in the partial fulfillment of Bachelor of engineering

degree of Visweswaraya Technological University (VTU)

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 DNA Computing

Abstract
Deoxyribonucleic acid (DNA) containing all the genetic information required for the
development and functioning of all living organisms is capable of performing the calculations
many times faster than the world’s fastest human built computers.DNA Computing which is still
in its infancy will be used to store billions of times more data than our personal computers used
in the present. Their powerful computing power can be used by national governments to crack
secret codes or by airlines to map more efficient routes. Studying DNA computers may also lead
to a better understanding of more complex computer –human brain.

1. Introduction DNA is a type of nucleic acid that is

responsible for carrying the genetic
Microprocessors made of silicon will information required for the development
eventually reach their limits of speed and and functioning of all possible life forms
miniaturization. Chip makers need a new other than RNA viruses. The main role of
material to produce faster computing speeds. DNA is the long term storage information.
It is hard to believe where scientists have
found the new material they need to build
the next generation of microprocessors.
Millions of natural supercomputers exist
inside living organisms, including your
body. DNA (deoxyribonucleic acid)
molecules, the material our genes are made
of, have the potential to perform calculations
many times faster than the world's most
powerful human-built computers.
DNA computing is the alternative to the
way computers work today. DNA
computing is a kind of computing which
makes use of DNA, biochemisty, molecular
biology. While this technology is not yet
readily available, the development is
ongoing and catching more speed.

2. Deoxyribonucleic acid (DNA)

2.1 What is DNA?

DOUBLE HELIX STRUCTURE OF DNA
 Genes are sections of DNA that code for redundancy of the genetic code. By allowing
a defined biochemical function, usually the more than one codon to specify
production of a protein. The DNA of an
organism may contain anywhere from a
dozen genes, as in a virus, to tens of
thousands of genes in higher organisms like
humans. The structure of a protein
determines its function. The sequence of
bases in a given gene determines the
structure of a protein. Thus the genetic code
determines what proteins an organism can
make and what those proteins can do. It is
estimated that only 1-3% of the DNA in our
cells codes for genes; the rest may be used
as a decoy to absorb mutations that could
otherwise damage vital genes.

2.2 Structure of DNA

-
In living organisms DNA usually exists as
a pair of molecules which are tightly held
together as two strands each coiled around
the same axis with a pitch of 3.4 Angstroms
and radius of 10 Angstroms and is called the
“double-helix” structure.DNA strands are
connected by base pairs. Each base will pair
with only one other. Adenine(A) pairs with
thymine (T) and guanine (G) pairs with
cytosine (C). STRUCTURE OF DNA
The genetic code is the language used by
living cells to convert information found in each amino acid, mutations can occur in the
DNA into information needed to make sequence of a gene without affecting the
proteins. A protein's structure, and therefore resulting protein.
function, is determined by the sequence of
amino acid subunits. The amino acid
sequence of a protein is determined by the
2.3 Operations on DNA
sequence of the gene encoding that protein.
The "words" of the genetic code are called 1. Annealing- Double stranded DNA is
codons. Each codon consists of three dissolved into single strands by breaking of
adjacent bases in an mRNA molecule. Using the hydrogen bonds between the strands.
combinations of A, U, C and G, there can be
sixty four different three-base codons. There 2. Hybridization-Base pairing between
are only twenty amino acids that need to be two complementary single strand to form a
coded for by these sixty four codons. This double stranded DNA molecule.
excess of codons is known as the
 3. Ligation- Ligase enzymes are used to
concatenate free floating double stranded 4. Adleman’s Experiment
DNA.
In 1994, Leonard M. Adleman solved a
4. Replication- DNA replication taking computational problem with a remarkable
a single strand and producing thousands of technique. It took Adleman, however, seven
replicas can be made possible by days to find a solution to the famous
Polymerase Chain Reaction (PCR) problem called Hamiltonian Path (HP)
problem but more popularly called
5. Sorting/Gel electrophoresis- This is a “travelling salesman problem” (TSP). This
process of sorting the DNA strands based on work was exceptional because he solved the
their size.DNA strands are negatively problem at the molecular level with DNA.
charged. Smaller molecules migrate faster in Suppose that I live in LA, and need to
the gel compared to the larger ones. The gel visit four cities: Houston, Chicago, Miami,
is made up of agarose and polyacrylamide. and NY, with NY being my final
destination. The airline I’m taking has a
6. Filtering/Affinity Purification -This specific set of connecting flights that restrict
refers to filtering of DNA with a specific which routes I can take (i.e. there is a flight
sequences.For this complementary sequence from L.A. to Chicago, but no flight from
is used. The DNA with the required Miami to Chicago).
sequence hybridizes with the
complementary sequence.

3. DNA as a software
Think of DNA as software, and
enzymes as hardware. Put them together in a
test tube. The way in which these molecules
undergo chemical reactions with each other
allows simple operations to be performed as
a by-product of the reactions. The scientists
tell the devices what to do by controlling the
composition of the DNA software
molecules. It's a completely different
approach to pushing electrons around a dry
circuit in a conventional computer. To the
naked eye, the DNA computer looks like
clear water solution in a test tube. There is
no mechanical device. A trillion bio-
molecular devices could fit into a single
drop of water. Instead of showing up on a It should take you only a moment to see that
computer screen, results are analyzed using there is only one route. Starting from L.A.
a technique that allows scientists to see the you need to fly to Chicago, Dallas, Miami
length of the DNA output molecule. and then to N.Y. Any other choice of cities
will force you to miss a destination, visit a
city twice, or not make it to N.Y. For this
example you obviously don’t need the help
of a computer to find a solution. For six, Part I: Generate all possible routes
seven, or even eight cities, the problem is
still manageable. However, as the number of Strategy: Encode city names in short
cities increases, the problem quickly gets out DNA sequences. Encode itineraries by
of hand. connecting the city sequences for which
routes exist.
As the number of cities increases, the DNA can simply be treated as a string of
problem becomes more difficult and hence data. For example, each city can be
computationally expensive making it represented by a "word" of six bases:
impractical to solve even on the latest super-
computer. Adleman’s demonstration only Los Angeles GCTACG
involves seven cities, making it in some Chicago CTAGTA
sense a trivial problem that can easily be Dallas TCGTAC
solved by inspection. Miami CTACGG
His work is significant for a number of New York ATGCCG
reasons
 It illustrates the possibilities of using TSP – CITY ENCODING
DNA to solve a class of problems that is
Almost impossible to solve using traditional The entire itinerary can be encoded by
computing methods. simply stringing together these DNA
 It's an example of computation at a sequences that represent specific cities.
molecular level, potentially a size limit that For example, the route from L.A -->
may never be reached by the semiconductor Chicago--> Dallas --> Miami --> New York
industry. would simply be GCTACG CTAGTA
 It demonstrates that computing with DNA TCGTAC CTACGG ATGCCG or
can work in a massively parallel fashion. equivalently it could be represented in
Specifically, the method based on double stranded form with its complement
Adleman’s experiment would be as follows: sequence. So how do we generate this?
Synthesizing short single stranded DNA is
1. Generate all possible routes. now a routine process, so encoding the city
names is straightforward. The molecules can
2. Select itineraries that start with the proper be made by a machine called a DNA
city and end with the final city. synthesizer or even custom ordered from a
third party. Itineraries can then be produced
3. Select itineraries with the correct number from the city encodings by linking them
of cities. together in proper order. To accomplish this
you can take advantage of the fact that DNA
4. Select itineraries that contain each city hybridizes with its complimentary sequence.
only once. For example, you can encode the routes
between cities by encoding the compliment
All of the above steps can be accomplished of the second half (last three letters) of the
with standard molecular biology techniques. departure city and the first half (first three
letters) of the arrival city. For example the
route between Miami (CTACGG) and NY
(ATGCCG) can be made by taking the
second half of the coding for Miami (CGG)
and the first half of the coding for NY
(ATG). This gives CGGATG. By taking the
complement of this you get, GCCTAC,
which not only uniquely represents the route
from Miami to NY, but will connect the
DNA representing Miami and NY by
hybridizing itself to the second half of the
code representing Miami (CGG) and the
first half of the code representing
NY (ATG...). TSP – ROUTE ENCODING

For example: We can be confident that we have all

possible combinations including the correct
one by using an excess of DNA encodings,
say 10^13 copies of each city and each route
between cities. Remember DNA is a highly
compact data format, so numbers are on our
side.

Part II: Select itineraries that start and

end with the correct cities

Strategy: Selectively copy and amplify only

the section of the DNA that starts with LA
and ends with NY by using the Polymerase
Chain Reaction.

After Part I, we now have a test tube full

of various lengths of DNA that encode
TSP – City Encoding possible routes between cities. What we
want are routes that start with LA and end
Random itineraries can be made by mixing with NY. To accomplish this we can use a
city encodings with the route encodings. technique called Polymerase Chain Reaction
Finally, the DNA strands can be connected (PCR), which allows you to produce many
together by an enzyme called ligase. What copies of a specific sequence of DNA. PCR
we are left with are strands of DNA is an iterative process that cycle through a
representing itineraries with a random series of copying events using an enzyme
number of cities and random set of routes. called polymerase. Polymerase will copy a
section of single stranded DNA starting at
the position of a primer, a short piece of
DNA complimentary to one end of a section
of the DNA that you're interested in. By
selecting primers that flank the section of
DNA you want to amplify, the polymerase
preferentially amplifies the DNA between
these primers, doubling the amount of DNA with each band corresponding to a certain
containing this sequence. length. We can then simply cut out the band
of interest to isolate DNA of a specific
After many iterations of PCR, the length. Since we known that each city is
DNA you're working on is amplified encoded with 6 base pairs of DNA, knowing
exponentially. So to selectively amplify the the length of the itinerary gives us the
itineraries that start and stop with our cities number of cities. In this case we would
of interest, we use primers that are isolate the DNA that was 30 base pairs long
complimentary to LA and NY. What we end (5 cities times 6 base pairs).
up with after PCR is a test tube full of
double stranded DNA of various lengths,
encoding itineraries that start with LA and
end with NY.

Part III: Select itineraries that contain the

correct number of cities.

Strategy: Sort the DNA by length and

select the DNA whose length corresponds to
5 cities. Our test tube is now filled with
DNA encoded itineraries that start with LA
and end with NY, where the number of
cities in between LA and NY varies. We
now want to select those itineraries that are
five cities long. To accomplish this we can GEL ELECTROPHORESIS
use a technique called Gel Electrophoresis,
which is a common procedure used to Part IV: Select itineraries that have a
resolve the size of DNA. The basic principle complete set of cities
behind Gel Electrophoresis is to force DNA
through a gel matrix by using an electric Strategy: Successively filter the DNA
field. DNA is a negatively charged molecule molecules by city, one city at a time. Since
under most conditions, so if placed in an the DNA we start with contains five cities,
electric field it will be attracted to the we will be left with strands that encode each
positive potential. However since the charge city once.
density of DNA is constant (charge per DNA containing a specific sequence can
length) long pieces of DNA move as fast as be purified from a sample of mixed
short pieces when suspended in a fluid. DNA by a technique called affinity
This is why you use a gel matrix. The gel purification. This is accomplished by
is made up of a polymer that forms attaching the compliment of the sequence in
meshwork of linked strands. The DNA now question to a substrate like a magnetic bead.
is forced to thread its way through the tiny The beads are then mixed with the DNA.
spaces between these strands, which, slows DNA, which contains the sequence you're
down the DNA at different rates depending after then hybridizes with the complement
on its length. What we typically end up with sequence on the beads. These beads can then
after running a gel is a series of DNA bands, be retrieved and the DNA isolated.
 team, led by Ehud Shapiro, has announced a
novel model of its bio molecular machine
- that no longer requires an external energy
source and performs 50 times faster than its
predecessor did. The Guinness Book of
World Records has crowned it the world's
smallest biological computing device. Many
designs for minuscule computers aimed at
harnessing the massive storage capacity of
DNA have been proposed over the years.
Earlier schemes have relied on a molecule
known as ATP, which is a common source
of energy for cellular reactions, as a fuel
source. But in the new set up, a DNA
molecule provides both the initial data and
sufficient energy to complete the
computation.

AFFINITY PURIFICATION Three years after Adleman's experiment,

researchers at the University of Rochester
So we now affinity purify five times, using a developed logic gates made of DNA. Logic
different city complement for each run. For gates are a vital part of how your computer
example, for the first run we use L.A.'-beads carries out functions that you command it to
to fish out DNA sequences which contain do. These gates convert binary code moving
the encoding for L.A. (which should be the through the computer into a series of signals
entire DNA because of step 3), the next run that the computer uses to perform
we use Dallas'-beads, and then Chicago'- operations. Currently, logic gates interpret
beads, Miami'-beads, and finally NY'-beads. input signals from silicon transistors, and
The order isn’t important. If an itinerary is convert those signals into an output signal
missing a city, then it will not be "fished that allows the computer to perform
out" during one of the runs and will be complex functions. The Rochester team's
removed from the candidate pool. What we DNA logic gates are the first step toward
are left with are the itineraries that start in creating a computer that has a structure
LA, visit each city once, and end in NY. similar to that of an electronic PC. Instead of
This is exactly what would retrieve it at this using electrical signals to perform logical
step. operations, these DNA logic gates rely on
5. Other References. DNA code. They detect fragments of genetic
material as input, splice together these
In 2001, scientists at the Weizmann fragments and form a single output.
Institute of Science in Israel announced that
they had manufactured a computer so small
that a single drop of water would hold a
trillion of the machines. The devices used
DNA and enzymes as their software and
hardware and could collectively perform a
billion operations a second. Now the same
 from the sun. If the error occurs in one of
the strands of double stranded DNA, repair
6. Significance of DNA enzymes can restore the proper DNA
sequence by using the complement strand as
6.1 DNA- A unique structure a reference. In this sense, double stranded
DNA is similar to a RAID 1 array, where
The amount of information gathered on data is mirrored on two drives, allowing data
the molecular biology of DNA over the last to be recovered from the second drive if
40 years is almost overwhelming in scope. errors occur on the first. In biological
So instead of getting bogged down in systems, this facility for error correction
biochemical and biological details of DNA, means that the error rate can be quite low.
we'll concentrate on only the information
relevant to DNA computing. The data 6.2 Operations in parallel
density of DNA is impressive. Just like a
string of binary data is encoded with ones In the cell, DNA is modified
and zeros, a strand of DNA is encoded with biochemically by a variety of enzymes,
four bases, represented by the letters A, T, which are tiny protein machines that read
C, and G. The bases (also known as and process DNA according to nature's
nucleotides) are spaced every design. There is a wide variety and number
0.35nanometres along the DNA molecule, of these "operational" proteins, which
giving DNA a remarkable data density of manipulate DNA on the molecular level. For
nearly 18 Mbits per inch. In two dimensions, example, there are enzymes that cut DNA
if you assume one base per square and enzymes that paste it back together.
nanometre, the data density is over one Other enzymes function as copiers and
million Gbits per square inch. Compare this others as repair units. Molecular biology,
to the data density of a typical high Biochemistry, and Biotechnology have
performance hard drive, which is about 7 developed techniques that allow us to
Gbits per square inch -- a factor of over perform many of these cellular functions in
100,000 smaller. the test tube. It's this cellular machinery,
Another important property of DNA is along with some synthetic chemistry, that
its double stranded nature. The bases A and makes up the palette of operations available
T, and C and G, can bind together, forming for computation.
base pairs. Therefore every DNA sequence Just like a CPU has a basic suite of
has a natural complement. For example if operations like addition, bit-shifting, logical
sequence S is ATTACGTCG, its operators (AND, OR, NOT NOR), etc. that
complement, S', is TAATGCAGC. Both S allow it to perform even the most complex
and S' will come together (or hybridize) to calculations, DNA has cutting, copying,
form double stranded DNA. This makes pasting, repairing, and many others. And
DNA a unique data structure for note that in the test tube; enzymes do not
computation and can be exploited in many function sequentially, working on one DNA
ways. at a time. Rather, many copies of the
Errors in DNA happen due to many enzyme can work on many DNA molecules
factors. Occasionally, DNA enzymes simply simultaneously. This is the power of DNA
make mistakes, cutting where they shouldn't, computing, that it can work in a massively
or inserting a T for a G. DNA can also be parallel fashion.
damaged by thermal energy and UV energy
 7. DNA vs. Silicon operations per second with 99.8%
accuracy.
DNA Conventional
computers computers
Storage Nucleic Semiconductors
Media acids 8. Advantages
Memory Ultra high High
Capacity  Perform millions of operations
Type of Biochemical Logical simultaneously
operations
Nature of Parallel Sequential  Conduct large parallel processing
Operation
Speed of Slow Fast  Massive amounts of working
Each memory
operation
Process Stochastic Deterministic  Generate & use own energy source
via the input.
COMPARISON BETWEEN A DNA
COMPUTER AND CONVENTIONAL  Four storage bits A T G C.
COMPUTER.
 Miniaturization of data storage

9. Limitations
 A single gram of dried DNA is
capable of storing the same amount of
information as could fit on one trillion
 DNA computing involves relatively
large scale of error.
CDs which is 1014 MB of data.

 More than 10 trillion DNA  Requires human assistance.

molecules can fit into an area no larger
than 1 cubic centimeter (0.06 cubic  Time consuming laboratory
inches) procedures.

 With this small amount of DNA, a  No universal method of data

computer would be able to hold 10 representation.
terabytes of data, and perform 10 trillion
calculations at a time.

 Abundance of availability of DNA is 10.Applications

another advantage of DNA computers.
 DNA chips.
 DNA is comparatively very cheap.
 Genetic Programming.
 Self powered computer unveiled in
2003 was capable of performing billion  Pharmaceutical applications.
  Cracking of coded messages.

11.Conclusion

The most significant technology in the

future of engineering is DNA computers.
DNA is what makes up your genes and
stores all the information about you inside
your cells. It is the instructions for what you
look like and how your function. Each
microscopic cell in your body contains the
entire DNA needed to build you, which is a
lot of information. DNA not only has huge
data storage potential but also the potential
to solve complicated calculations and
mathematical problems.
DNA computers are a very new
concept. The idea was conceived just few
years ago. But in these few years, scientists
have already been able to use DNA to solve
moderately difficult math problems. DNA
computers are still decades away from being
able to compete with silicon based
computers, but will eventually be much
more powerful than silicon based computers.
The first DNA computers will not be like a
home PC. They will be used to solve huge,
complicated mathematical problems, such as
breaking codes.
DNA computers will be thousands of
times smaller and more powerful than
silicon based computers. One pound of
DNA has ability to store more data than
every electronic devices ever made to date.
A water droplet sized DNA computers will
have more computing power than today's
most powerful supercomputers. Another
advantage of DNA computing over silicon
based computers is the ability to do parallel
calculations. Silicon based microprocessors
can only do on calculation at a time while
DNA computer will be able to do many
simultaneous calculations.