A Seminar Report

On

DNA COMPUTING

Submitted by

SELAVADI KARTHIK
(189L1A0593)

in partial fulfillment for the award of the degree of

BACHELOR OF TECHNOLOGY
in
Computer Science and Engineering

Under the Guidance of

Mr. D.SURESH REDDY , M.Tech.,

Asst. Professor, Department of CSE.

DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING

SIDDARTHA EDUCATIONAL ACADEMY GROUP OF INSTITUTIONS

(Approved by AICTE & Affiliated to JNTU Anantapur)

C. Gollapalli, Tirupati - 517 505
(2018-2022)
 SIDDARTHA EDUCATIONAL ACADEMY GROUP OF INSTITUTIONS

C. Gollapalli (vi), Tirupati - 517 505

DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING

CERTIFICATE

This is to certify that the project entitled “DNA COMPUTING” is the bonafide

work carried out by SELAVADI KARTHIK , bearing HT. No: 189L1A0593

B.Tech, students of SEAGI, Affiliated to JNTUA, Anantapuramu in partial

fulfillment of the requirements for the award of the Degree of BACHELOR OF
TECHNOLOGY with the specialization in COMPUTER SCIENCE AND ENGINEERING
during the Academic year 2018-2022.

Signature of the Guide Head of the Department

Technical seminar held on

Internal Examiner External Examiner

 ACKNOWLEDGEMENT

All endeavors over a long period can be successful only with the advice
and support of many well-wishers. I take this opportunity to express my
gratitude and appreciation to all of them.

we wish to express deep sense of gratitude to my beloved and respected

guide Mr.D.SURESH REDDY, M.Tech ., Asst.Professor of CSE, Siddartha

Educational Academy Group of Institutions, Tirupati, for his valuable
guidance, suggestions and constant encouragement and keen interest enriched
throughout the course of project work.

We extend sincere thanks to the HOD, Mr.N.ANAND REDDY for his

kind co- operation in completing and making this project a success.

We extend sincere thanks to the Principal, Prof. K. RAJASEKHAR

for his kind co- operation in completing and making this project a success.

We would like to thank the Management for their kind co-operation

and for providing infrastructure facilities.

We extend thanks to all the Teaching staff of the Department of CSE

for their support and encouragement during the course of my project work. I
also thank the Non- Teaching staff of CSE department for being helpful in
many ways in successful completion of my work.

Finally I thank all those who helped me directly or indirectly in

successful completion of this project work.

SELAVADI KARTHIK

(189L1A0523)
 SIDDARTHA EDUCATIONAL ACADEMY GROUP OF INSTITUTIONS

C. Gollapalli (vi), Tirupati - 517 505

DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING

DECLARATION
I hereby declare that the project work entitled “DNA COMPUTING”

is entirely my original work carried out under the guidance of

Mr.D.SURESH REDDY, Asst.Professor, Department of Computer Science and

Engineering, Siddartha Educational Academy Group of Institutions, C.Gollapalli,
Tirupati, JNTU Anantapur, Anantapuramu,A.P,India for the award of the degree of
BACHELOR OF TECHNOLOGY with the specialization in COMPUTER SCIENCE AND
ENGINEERING. The results carried out in this project report have not been
submitted in a part or full for the award of any degree or diploma of this or any
other university or institute.

SELAVADI KARTHIK

(189L1A0523)
 ABSTRACT

In this paper I intend to present the computing technology that has a great future - DNA
COMPUTING. DNA computing can be viewed as a manifestation of an emerging new area
of science made possible by our rapidly developing ability to control the molecular world.
DNA computing is in its infancy and its implications are only beginning to be explored. The
paper begins with a brief description of DNA and its structure. An introduction to DNA
COMPUTING and its origin have been given. Adleman experiment has been discussed,
which gives solution to the “HAMILTONIAN PATH PROBLEM” by the application of
DNA COMPUTING. The salient features of DNA Computer (one that uses DNA
computing as its basic method of problem solving) have been mentioned. An insight into
the advantages, disadvantages, applications and limitations of DNA-computing has been
made. Finally, the paper discusses the various stages in its path of development at present
and the expectations in the near future
 CONTENTS
Page No:

1 INTRODUCTION.........…...........................................1 – 2

2. HISTORY & MOTIVATION.....................................3 – 4

3. DNA FUNDAMENTALS............................................5 – 10
3.1 What is DNA?
3.2 Structure of DNA
4. PRINCIPLES OF DNA COMPUTING.....................11 – 13

5. WHAT IS DNA COMPUTER?...................................14 – 19

5.1 Basic Operations on DNA
6. EXAMPLE OF DNA COMPUTING:
THE HEMILTON PATH PROBLEM.................20 – 23
7. SILICON VS. DNA MICROPROCESSORS.............24
8. COMPARISON WITH CONVENTIONAL
COMPUTERS...................................................................25 – 26
9. ADVANTAGES.............................................................27
10. DISADVANTAGES....................................................28
11. PRESENT AND FUTURE DNA COMPUTER.......29
12. CONCLUSION............................................................30
13. REFERENCES..........................................................31
 List of Figures

1. 3.2.1. Chemical Structure of Nucleotide 6

2. 3.2.2. Phosphodiester 7
3. 3.2.3. Hydrogen Bond 7
4. 3.2.4. Base nucleotide pairings 8
5. 3.2.5. Watson-Crick Model of DNA 9
6. 3.2.6. DNA Structure Hierarchy 10
7. 5.1.1. DNA Synthesis 15
8. 5.1.2. DNA Melting and Annealing 16
9. 5.1.3. DNA Replication 16
10. 5.1.4. Gel Electrophoresis 17
11. 5.1.5. Affinity Purification 17
12. 5.1.6. DNA Cutting 18
13. 5.1.7. Substitution 18
14. 6.1. Directed Graph 20
15. 6.2. Simplified Graph 21
 DNA COMPUTING

1. INTRODUCTION
The twentieth century will be remembered for three major
achievements – The evolution of computers, decoding of the human
genome and evolution from Newtonian physics to quantum physics.
Since the beginning of time man has performed computations or
calculation. The method and nature of these computations has
however changed from manual in the stone ages to mechanical in the
medieval ages to electronic in the new computer age. Computers, by
definition, are machines which receive input, manipulate and store the
input, and produce an output. They've quickly grown in the size and
processing power. Computers are commonly known to consist of
integrated circuits mainly constructed of silicon; however, a computer
is never considered to be "alive". What is going to be the future of
computing systems? Can we look beyond silicon to embrace other
mediums for computing? Computers inspired by biological or
physical systems are possible alternatives. Microprocessors made of
silicon will eventually reach their limits of speed and miniaturization.
Chip makers need a new material to produce faster computing speeds.
You won't 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 (Deoxyribo Nucleic 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.
Technological advances however could use these building blocks of
our genome in creating computer processors and data storage, and
catapult processing speeds to incomprehensible levels not possible by
today's standards. A DNA-based computer has solved a logic problem
that no person could complete by hand, setting a new milestone for
this infant technology that could someday surpass the electronic
digital computer in certain areas. DNA might one day be integrated
into a computer chip to create a so-called Biochip that will push

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 DNA COMPUTING

computers even faster. DNA molecules have already been harnessed

to perform complex mathematical problems. DNA computing is an
alternative to the way computers work today. While this technology is
not readily available, or being mass produced, the theory behind it is
quite old and the development is ongoing and catching more speed.
Companies like IBM are attempting to use DNA to produce the next
generation of processors.

Before discussing how DNA can be used in computers, it's important

to first understand the basic structure of a DNA molecule
The main idea was the encoding of data in DNA strands and the use
of tools from molecular biology to execute computational
operations. Besides the novelty of this approach, molecular computing
has the potential to outperform electronic computers. For example,
DNA computations may use a billion times less energy than an
electronic computer while storing data in a trillion times less space.
Moreover, computing with DNA is highly parallel: In principle there
could be billions upon trillions of DNA molecules undergoing
chemical reactions, that is, performing computations, simultaneously

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 DNA COMPUTING

2. HISTORY & MOTIVATION

"Computers in the future may weigh no more than 1.5 tons." So said Popular Mechanics in
1949. Most of us today, in the age of smart cards and wearable PCs would find that
statement laughable.
We have made huge advances in miniaturization since the days of room sized computers,
yet the underlying computational framework has remained the same.
Today's supercomputers still employ the kind of sequential logic used by the mechanical
dinosaurs of the 1930s. Some researchers are now looking beyond these boundaries and are
investigating entirely new media and computational models.
These include quantum, optical and DNA-based computers. It is the last of these
developments that this paper concentrates on. The current Silicon technology has following
limitations:
Circuit integration dimensions
Clock frequency
Power consumption
Heat dissipation.
The problem's complexity that can be afforded by modern processors grows up, but great
challenges require computational capabilities that neither most powerful and distributed
systems could reach.
The idea that living cells and molecular complexes can be viewed as potential mechanic
components dates back to the late 1950s, when Richard Feynman delivered his famous
paper describing "sub microscopic" computers.
More recently, several people have advocated the realization of massively parallel
computation using the techniques and chemistry of molecular biology. DNA computing was
grounded in reality at the end of 1994, when Leonard Adleman, announced that he had
solved a small instance of a computationally intractable problem using a small vial of DNA.
By representing information as sequences of bases in DNA molecules, Adleman showed
how to use existing DNA-manipulation techniques to implement a simple, massively
parallel random search. He solved the travelling salesman problem also known as the
“Hamiltonian path" problem.

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 DNA COMPUTING

There are two reasons for using molecular biology to solve computational problems. (i) The
information density of DNA is much greater than that of silicon:
1 bit can be stored in approximately one cubic nanometer. Others storage media, such as
videotapes, can store 1 bit in 1,000,000,000,000 cubic nanometer.
(ii) Operations on DNA are massively parallel: 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.

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 DNA COMPUTING

3. DNA FUNDAMENTALS

3.1 WHAT IS DNA?

Like the one ring of power in Tolkien's "Lord of the Rings," deoxyribonucleic acid (DNA)
is the master molecule of every cell. It contains vital information that gets passed on to each
successive generation. It coordinates the making of itself as well as other molecules
(proteins). If it is changed slightly, serious consequences may result. If it is destroyed
beyond repair, the cell dies. Changes in the DNA of cells in multicellular organisms
produce variations in the characteristics of a species. Over long periods of time, natural
selection acts on these variations to evolve or change the species. DNA is one of the nucleic
acids, information-containing molecules in the cell (ribonucleic acid, or RNA, is the other
nucleic acid). DNA is found in the nucleus of every human cell. The information in DNA: *
guides the cell (along with RNA) in making new proteins that determine all of our
biological traits * gets passed (copied) from one generation to the next The key to all of
these functions is found in the molecular structure of DNA, as described by Watson and
Crick

3.2 Structure of DNA

Although it may look complicated, the DNA in a cell is really just a pattern made up of four
different parts called nucleotides. Imagine a set of blocks that has only four shapes, or an
alphabet that has only four letters. DNA is a long string of these blocks or letters. DNA is a
polymer (“large” molecule). DNA is strung together from monomers (“small” molecules):
deoxyribonucleotides.
DNA (deoxyribonucleic acid) is a double stranded sequence of four nucleotides; the four
nucleotides that compose a strand of DNA are as follows: adenine (A), guanine (G),
cytosine (C), and thymine (T); they are often called bases. DNA supports two key functions
for life:
coding for the production of proteins,
Self-replication.
Each deoxyribonucleotide consists of three components:
a sugar — deoxyribosefive carbon atoms: 1´ to 5´

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 DNA COMPUTING

hydroxyl group (OH) attached to 3´ carbon

a phosphate group
a nitrogenous base.

FIG: CHEMICAL STRUCTURE OF A NUCLEOTIDE

DNA nucleotides differ only by their bases (B). There are two classes of nitrogen bases
called purines (double-ringed structures) and pyrimidines (single-ringed structures). The
four bases in DNA's alphabet are: purines pyrimidines Adenine A Thymine T Guanine G
Cytosine C

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 DNA COMPUTING

Linking of Nucleotides

The DNA monomers can link in two ways: Phosphodiester bond and Hydrogen bond.

Fig: Phosphodiester Fig: Hydrogen Bond

Phosphodiester Bond: The 5´-phosphate group of one nucleotide is joined with the 3´-
hydroxyl group of the other - strong (covalent) bond - directionality: 5´—3´ or 3´—5´

Hydrogen Bond: The base of one nucleotide interacts with the base of another - base
pairing (weak bond)

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 DNA COMPUTING

A hydrogen bond is a weak chemical bond that occurs between hydrogen atoms and more
electronegative atoms, like oxygen, nitrogen and fluorine. The participating atoms can be
located on the same molecule (adjacent nucleotides) or on different molecules (adjacent
nucleotides on different DNA strands). Hydrogen bonds do not involve the exchange or
sharing of electrons like covalent and ionic bonds. The weak attraction is like that between
the opposite poles of a magnet. Hydrogen bonds occur over short distances and can be
easily formed and broken. They can also stabilize a molecule.

Fig: Base Nucleotide Pairings

Strands of DNA are made of the sugar and phosphate portions of the nucleotides, while the
middle parts are made of the nitrogenous bases.

Strands of DNA are made of the sugar and phosphate portions of the nucleotides, while the
middle parts are made of the nitrogenous bases.
The nitrogenous bases on the two strands of DNA pair up, purine with pyrimidine (A with
T, G with C), and are held together by weak hydrogen bonds. A — T (2 hydrogen bonds) C
— G (3 hydrogen bonds)

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 DNA COMPUTING

Watson-Crick Model of DNA:

James D. Watson and Francis H. C. Crick deduced double-helix structure of DNA in 1953
and got Nobel Prize in 1962. Adenine and thymine always bond together as a pair, and
cytosine and guanine bond together as a pair. The pairs link together like rungs in a ladder:
Watson and Crick discovered that DNA had two sides, or strands, and that these strands
were twisted together like a twisted ladder -- the double helix. The sides of the ladder
comprise the sugar-phosphate portions of adjacent nucleotides bonded together. The
phosphate of one nucleotide is covalently bound (a bond in which one or more pairs of
electrons are shared by two atoms) to the sugar of the next nucleotide. The hydrogen bonds
between phosphates cause the DNA strand to twist. The nitrogenous bases point inward on
the ladder and form pairs with bases on the other side, like rungs. Each base pair is formed
from two complementary nucleotides (purine with pyrimidine) bound together by hydrogen
bonds. The base pairs in DNA are adenine with thymine and cytosine with guanine.

Fig: Watson-Crick Model of DNA

DNA has a spiral staircase-like structure. The steps are formed by the nitrogen bases of the
nucleotides where adenine pairs with thymine and cytosine with guanine.
DNA is Structured Hierarchically:
DNA is compacted to conserve space. There are several levels at which DNA is compacted:
Levels of Structure
• Double Helix
• Histones / Nucleosomes

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 DNA COMPUTING

• Solenoid Supercoil
• Chromatin

• Chromosomes

Fig: DNA Structure Hierarchy

1. Double Helix — the DNA in a single cell contains 2.9 x 109 base pairs and would be a
meter long. 2. Histones / Nucleosomes — DNA is wound around a histone protein core to
form a nucleosome. This gives a 5- to 9- fold reduction in length.
3. Solenoids — Nucleosomes (beads on a string) supercoil and form solenoid structures. 4-
6-fold reduction in length.
4. Chromatin — Solenoid turns loop around a protein-RNA scaffold to form Minibands.
18-fold reduction in length.
5. Chromosomes — Minibands further condense to form Chromosomes, the form of DNA
as seen during cell division and genetics studies.

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 DNA COMPUTING

4. PRINCIPLES OF DNA COMPUTING

DNA is the major information storage molecule in living cells, and billions of years of
evolution have tested and refined both this wonderful informational molecule and highly
specific enzymes that can either duplicate the information in DNA molecules or transmit
this information to other DNA molecules. Instead of using electrical impulses to represent
bits of information, the DNA computer uses the chemical properties of these molecules by
examining the patterns of combination or growth of the molecules or strings. DNA can do
this through the manufacture of enzymes, which are biological catalysts that could be called
the ’software’, used to execute the desired calculation.

DNA: A unique data structure

The amount of information gathered on the molecular biology of DNA over the last 40
years is almost overwhelming in scope. So instead of getting bogged down in biochemical
and biological details of DNA, we'll concentrate on only the information relevant to DNA
computing.
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 the letters A, T,
C, and G. The bases (also known as nucleotides) are spaced every 0.35 nanometers along
the DNA molecule, giving DNA a remarkable data density of nearly 18 Mbits per inch. In
two dimensions, if you assume one base per square nanometer, the data density is over one
million Gbits per square inch. Compare this to the data density of a typical high
performance hard drive, which is about 7 Gbits per square inch -- a factor of over 100,000
smaller.
Another important property of DNA is its double stranded nature. The bases A and T, and
C and G, can bind together, forming base pairs. Therefore every DNA sequence has a
natural complement. For example if sequence S is ATTACGTCG, its complement, S', is
TAATGCAGC. Both S and S' will come together (or hybridize) to form double stranded
DNA. This complementarities makes DNA a unique data structure for computation and can
be exploited in many ways. Error correction is one example. Errors in DNA happen due to
many factors. Occasionally, DNA enzymes simply make mistakes, cutting where they

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 DNA COMPUTING

shouldn't, or inserting a T for a G. DNA can also be damaged by thermal energy and UV
energy from the sun. If the error occurs in one of the strands of double stranded DNA,
repair enzymes can restore the proper DNA sequence by using the complement strand as a
reference.
In this sense, double stranded DNA is similar to a RAID 1 array, where data is mirrored on
two drives, allowing data to be recovered from the second drive if errors occur on the first.
In biological systems, this facility for error correction means that the error rate can be quite
low. For example, in DNA replication, there is one error for every 10^9 copied bases or in
other words an error rate of 10^-9. (In comparison, hard drives have read error rates of only
10^-13 for Reed-Solomon correction)
Operations in parallel

In the cell, DNA is modified biochemically by a variety of enzymes, which are tiny protein
machines that read and process DNA according to nature's design. There is a wide variety
and number of these "operational" proteins, which manipulate DNA on the molecular level.
For example, there are enzymes that cut DNA and enzymes that paste it back together.
Other enzymes function as copiers, and others as repair units. Molecular biology,
Biochemistry, and Biotechnology have developed techniques that allow us to perform many
of these cellular functions in the test tube. It's this cellular machinery, along with some
synthetic chemistry, that makes up the palette of operations available for computation.
Just like a CPU has a basic suite of operations like addition, bit-shifting, logical operators
(AND, OR, NOT NOR), etc. that allow it to perform even the most complex calculations,
DNA has cutting, copying, pasting, repairing, and many others. And note that in the test
tube, enzymes do not function sequentially, working on one DNA at a time. Rather, many
copies of the enzyme can work on many DNA molecules simultaneously. This is the power
of DNA computing, that it can work in a massively parallel fashion.
DNA as 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.

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 DNA COMPUTING

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 computer screen, results are analyzed using a technique that
allows scientists to see the length of the DNA output molecule. "Once the input, software,
and hardware molecules are mixed in a solution it operates to completion without
intervention," said David Hawksett, the science judge at Guinness World Records. "If you
want to present the output to the naked eye, human manipulation is needed".
A single strand of DNA is similar to a string consisting of a combination of four different
symbols A G C T. Mathematically this means we have at our disposal a letter alphabet, Σ =
{A GC T} to encode information which is more than enough considering that an electronic
computer needs only two digits and for the same purpose. In a DNA computer, computation
takes place in test tubes or on a glass slide coated in 24K gold. The input and output are
both strands of DNA, whose genetic sequences encode certain information. A program on a
DNA computer is executed as a series of biochemical operations, which have the effect of
synthesizing, extracting, modifying and cloning the DNA strands.

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5. WHAT IS DNA COMPUTER

A DNA computer, as the name implies, uses DNA strands to store information and taps the
recombinative properties of DNA to perform operations. A small test tube of DNA strands
suspended in a solution could yield millions to billions of simultaneous interactions at
speeds — in theory — faster than today's fastest supercomputers.
DNA computer uses the recombinative property of dna to perform operations.The main
benefit of using DNA computers to solve complex problems is that different possible
solutions are created all at once. This is known as parallel processing. Humans and most
electronic computers attempt to solve the problem one process at a time (linear processing).
DNA itself provides the added benefits of being a cheap, energy-efficient resource.
In a different perspective, more than 10 trillion DNA molecules can fit into an area no
larger than 1 cubic centimeter. With this, a DNA computer could hold 10 terabytes of data
and perform 10 trillion calculations at a time.
In a traditional computer, data are represented by and stored as strings of zeros and ones.
With a DNA computer, a sequence of its four basic nucleotides — adenine, cytosine,
guanine, and thymine — is used to represent and store data on a strand of DNA.
Calculations in a traditional computer are performed by moving data into a processing unit
where binary operations are performed. Essentially, the operations turn miniaturized circuits
off or on corresponding to the zeros and ones that represent the string of data.

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5.1 BASIC OPERATIONS ON DNA

As concerning the operations that can be performed on DNA strands the proposed models
of DNA computation are based on various combinations of the following primitive bio-
operations:
synthesizing a desired polynomial-length strand used in all models.

Fig: DNA Synthesis

Mixing: combine the contents of two test tubes into a third one to achieve union.
Melting: break apart a double-stranded DNA into its single-stranded complementary
components by heating the solution. Melting in vitro is also known under the name of
denaturation.
Annealing: bond together two single-stranded complementary DNA sequences by cooling
the solution. Annealing in vitro is known as hybridization

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Amplifying (copying): make copies of DNA strands by using the Polymerase Chain
Reaction PCR. The DNA polymerase enzymes perform several functions including
replication of DNA. The replication reaction requires a guiding DNA single-strand called
template, and a shorter oligonucleotide called a primer, that is annealed to it.

 Separating the strands by length using a technique called gel electrophoresis that
makes possible the separation of strands by length

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 DNA COMPUTING

 Extracting those strands that contain a given pattern as a substring by using affinity
purification.

Fig: Gel Electrophoresis

Fig: Affinity Purification

Cutting DNA double-strands at specific sites by using commercially available restriction

enzymes. One class of enzymes, called restriction endonucleases, will recognize a specific
short sequence of DNA, known as a restriction site. Any double-stranded DNA that

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 DNA COMPUTING

contains the restriction site within its sequence is cut by the enzyme at that location.

FIG: DNA Cutting

 Ligating: paste DNA strands with compatible sticky ends by using DNA ligases.
Indeed, another enzyme called DNA ligase, will bond together, or ``ligate'', the end
of a DNA strand to another strand.
 Substituting: substitute, insert or delete DNA sequences by using PCR site-specific

oligonucleotide mutagenesis.
Fig: Substitution

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 DNA COMPUTING

 Marking single strands by hybridization: complementary sequences are attached to

the strands, making them double-stranded. The reverse operation is unmarking of

the double-strands by denaturing, that is, by detaching the complementary strands.

The marked sequences will be double stranded while the unmarked ones will be
single-stranded.
 Destroying the marked strands by using exonucleases, or by cutting all the marked
strands with a restriction enzyme and removing all the intact strands by gel
electrophoresis. (By using enzymes called exonucleases, either double-stranded or
single-stranded DNA molecules may be selectively destroyed. The exonucleases
chew up DNA molecules from the end inward, and exist with specificity to either
single-stranded or double-stranded form.)
 Detecting and Reading: given the contents of a tube, say ``yes'' if it contains at least
one DNA strand, and ``no'' otherwise. PCR may be used to amplify the result and
then a process called sequencing is used to actually read the solution.
In Short, DNA computers work by encoding the problem to be solved in the language of
DNA: the base-four values A, T, C and G. Using this base four number system, the solution
to any conceivable problem can be encoded along a DNA strand like in a Turing machine
tape. Every possible sequence can be chemically created in a test tube on trillions of
different DNA strands, and the correct sequences can be filtered out using genetic
engineering tools.

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 DNA COMPUTING

6. Example of DNA Computing:

The Hamiltonian Path Problem

In 1994 Leonard M. Adleman showed how to solve the Hamilton Path Problem, using DNA
computation. Hamiltonian Path Problem: A directed graph G with designated nodes vin and
vout is said to have a Hamiltonian path if and only if there exists a sequence of compatible
one-way edges e1, e2, ...en that begins at vin, ends at vout and enters every other node
exactly once. A simplified version of this problem, known as the traveling salesman
problem, poses the following question: given an arbitrary collection of cities through which
a salesman must travel, what is the shortest route linking those cities?
This problem is difficult for conventional computers to solve because it is a ”non-
deterministic polynomial time problem”. These problems, when the instance size is large,
are intractable with conventional computers, but can be solved using massively parallel
computers like DNA computers. NP problems are intractable with deterministic
(conventional/serial) computers, but can be solved using nondeterministic (massively
parallel) computers. A DNA computer is a type of non-deterministic computer. The
Hamiltonian Path problem was chosen by Adleman because it is known as ”NP-complete”.

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 DNA COMPUTING

Fig: Simplified graph

Hamiltonian path: Atlanta–Boston–Chicago–Detroit

Adleman´s Algorithm:
Input: A directed graph G with n vertices, and designated vertices vin and vout.

Step 1: Generate paths in G randomly in large quantities.

Step 2: Reject all paths that

do not begin with vin and

do not end in vout.
Step 3: Reject all paths that do not involve exactly n vertices.

Step 4: For each of the n vertices v:

reject all paths that do not involve v.

Output: YES, if any path remains; NO, otherwise.

To implement step 1, each node of the graph was encoded as a random 20-base strand of
DNA. Then, for each edge of the graph, a different 20- base oligonucleotide was generated

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 DNA COMPUTING

that contains the second half of the source code plus the first half of the target node

To implement step 2, the product of step 1 was amplified by PCR using oligonucleotide
primers representing vin and vout and ligase enzyme. This amplified and thus retained only
those molecules encoding paths that begin with vin and end with vout. ~1014 computations
are carried out in a single second.
For implementing step 3, agarose gel electrophoresis allowed separation and recovery of
DNA strands of the correct length. The desired path, if it exists, would pass through all
seven nodes, each of which was assigned a length of 20 bases. Thus PCR products encoding
the desired path would have to be 140 bp.
Step 4 was accomplished by successive use of affinity purification for each node other than
the start and end nodes.
The solution strand has to be filtered from the test tube:
GCAG TCGG ACTG GGCT ATGT CCGA

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Atlanta → Boston → Chicago → Detroit

Thus we see in a graph with n vertices, there are a possible (n-1)! permutations of the
vertices between beginning and ending vertex. To explore each permutation, a traditional
computer must perform O(n!) operations to explore all possible cycles. However, the DNA
computing model only requires the representative oligos. Once placed in solution, those
oligos will anneal in parallel, providing all possible paths in the graph at roughly the same
time. That is equivalent to O(1) operations, or constant time. In addition, no more space
than what was originally provided is needed to contain the constructed paths.

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7. SILICON VS. DNA MICROPROCESSORS

Silicon microprocessors have been the heart of the computing world for more than 40 years.
In that time, manufacturers have crammed more and more electronic devices onto their
microprocessors. In accordance with Moore's Law, the number of electronic devices put on
a microprocessor has doubled every 18 months. Moore's Law is named after Intel founder
Gordon Moore, who predicted in 1965 that microprocessors would double in complexity
every two years. Many have predicted that Moore's Law will soon reach its end, because of
the physical speed and miniaturization limitations of silicon microprocessors.
Surpassing Silicon?

Although DNA computers haven't overtaken silicon-based microprocessors, researchers

have made some progress in using genetic code for computation. In 2003, Israeli scientists
demonstrated a limited, but functioning, DNA computer. You can read more about it at
National Geographic.
The success of the Adleman DNA computer proves that DNA can be used to calculate
complex mathematical problems. However, this early DNA computer is far from
challenging silicon-based computers in terms of speed. The Adleman DNA computer
created a group of possible answers very quickly, but it took days for Adleman to narrow
down the possibilities. Another drawback of his DNA computer is that it requires human
assistance. The goal of the DNA computing field is to create a device that can work
independent of human involvement.
DNA computers have the potential to take computing to new levels, picking up where
Moore's Law leaves off.

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8. COMPARISON WITH CONVENTIONAL COMPUTERS

DNA's key advantage is that it will make computers smaller than any computer that has
come before them, while at the same time holding more data. One pound of DNA has the
capacity to store more information than all the electronic computers ever built; and the
computing power of a teardrop-sized DNA computer, using the DNA logic gates, will be
more powerful than the world's most powerful supercomputer. More than 10 trillion DNA
molecules can fit into an area no larger than 1 cubic centimeter (0.06 cubic inches). With
this small amount of DNA, a computer would be able to hold 10 terabytes of data, and
perform 10 trillion calculations at a time. By adding more DNA, more calculations could be
performed. Unlike conventional computers, DNA computers perform calculations parallel
to other calculations. Conventional computers operate linearly, taking on tasks one at a
time. It is parallel computing that allows DNA to solve complex mathematical problems in
hours, whereas it might take electrical computers hundreds of years to complete them. The
first DNA computers are unlikely to feature word processing, e-mailing and solitaire
programs. Instead, their powerful computing power will be used by national governments
for cracking secret codes, or by airlines wanting to map more efficient routes. Studying
DNA computers may also lead us to a better understanding of a more complex computer --
the human brain. DNA computers will be capable of storing billions of times more data
(say, at a density of 1 bit per cubic nanometer -- a trillion times less space) than your
personal computer. The DNA computer has very low energy consumption, so if it is put
inside the cell it would not require much energy to work. Using DNA logic gates the DNA
computers will be more powerful than the world's most powerful supercomputer. DNA
computers perform calculations parallel to other calculations. Speed: Combining DNA
strands as demonstrated by Dr Adleman, made computations equivalent to 10^9 or
better,arguably over 100 times faster than fastest computer. Minimal storage requirements:
DNA stores memory at a density of about one bit per cubic nanometer where conventional
storage media requires 10^12 cubic nanometers to storage one bit. Minimal power
requirements: No power is required for DNA computing while computation is taking place.
The chemical bonds that are the building blocks of DNA happen without any outside power
source.

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Table 8.1 Comparison of a DNA computer and a Conventional Computer

DNA Computers Conventional Computers

Storage Media Nucleic acids Semiconductors

Nature of Operations Parallel Sequential

Type of Operations Biochemical Operations Logical Operations

Speed of each Operation Slow Fast

Memory Capacity Ultra-High (one bit per cubic High(10^12 cubic nanometers
nanometer) to store one bit)
Data Density One million Gbits per square 7 Gbits per square inch
inch
Computational Power More powerful than any Less powerful
supercomputer
Computer Size Smaller than any computer Larger size
power requirements Not required Required
Cost Cheaper Expensive

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 DNA COMPUTING

9.ADVANTAGES

 Perform millions of operations simultaneously (Parallel Computing).

 Generate a complete set of potential solutions and conduct large parallel searches.
 Capable of storing billions of times more data
 Over 100 times faster than fastest computer
 Minimal storage requirements.
 Minimal power requirements
 They are inexpensive to build, being made of common biological materials.
 The clear advantage is that we have a distinct memory block that encodes bits.
 Using one template strand as a memory block also allows us to use its compliment.
as another memory block, thus effectively doubling our capacity to store
information.
 More powerful than the world's most powerful supercomputer
 DNA computers smaller than any computer

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 DNA COMPUTING

10. DISADVANTAGES

 Generating solution sets, even for some relatively simple problems, may require
impractically large amounts of memory (lots and lots of DNA strands are required)
 Many empirical uncertainties, including those involving: actual error rates, the
generation of optimal encoding techniques, and the ability to perform necessary bio-
operations conveniently in vitro (for every correct answer there are millions of
incorrect paths generated that are worthless).
 DNA computers could not (at this point) replace traditional computers.
 They are not programmable and the average dunce cannot sit down at a familiar
keyboard and get to work.
 It requires human assistance.

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11. Present & Future DNA

Computer A year ago, researchers from the Weizmann Institute of Science in Rehovot,
Israel, unveiled a programmable molecular computing machine composed of enzymes and
DNA molecules instead of silicon microchips. "This re-designed device uses its DNA input
as its source of fuel," said Ehud Shapiro, who led the Israeli research team. This computer
can perform 330 trillion operations per second, more than 100,000 times the speed of the
fastest PC. While a desktop PC is designed to perform one calculation very fast, DNA
strands produce billions of potential answers simultaneously. This makes the DNA
computer suitable for solving "fuzzy logic" problems that have many possible solutions
rather than the either/or logic of binary computers. In the future, some speculate, there may
be hybrid machines that use traditional silicon for normal processing tasks but have DNA
co-processors that can take over specific tasks they would be more suitable for.

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12. CONCLUSION
Before you trash your silicon-based computer and start trying to process words with DNA,
remember that it'll be a while before the wet computers show up in showrooms. DNA
computers can't be found at your local electronics store yet. The technology is still in
development. Biomolecular computers, made of DNA and other biological molecules, only
exist today in a few specialized labs, remote from the regular computer user. DNA
computer components -- logic gates and biochips -- will take years to develop into a
practical, workable DNA computer. If such a computer is ever built, scientists say that it
will be more compact, accurate and efficient than conventional computers. The current
applications of DNA chips are restricted to the field of medicine. Affymetrix Inc pioneered
the research in the field of DNA medicine. However now many companies such as
Motorola and Corning and the Hewlett-Packard spinoff Agilent Technologies have joined
this rapidly growing technology. Each of these challengers is applying its industrial
expertise to making its own DNA microarrays or chips. DNA chips or arrays have been
used to solve many problems in the field of medicine. These DNA computers can be used in
fluids, such as a sample of blood or in the body, and make decisions at the level of a single
cell. DNA computers could conceivably be implanted in the body to both diagnose and kill
cancer cells or monitor and treat diabetes by dispensing insulin when needed. The first DNA
computers are unlikely to feature word processing, e-mailing and solitaire programs.
Instead, their powerful computing power will be used by national governments for cracking
secret codes, or by airlines wanting to map more efficient routes. Studying DNA computers
may also lead us to a better understanding of a more complex computer -- the human brain.
In the future, some speculate, there may be hybrid machines that use traditional silicon for
normal processing tasks but have DNA co-processors that can take over specific tasks they
would be more suitable for.

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13. REFERENCES

[1]. Paun, G., Rozenberg, G., and Salomaa, A., DNA Computing, Springer,1998.
DNA COMPUTING-GRAPH ALGORITHMS [lec-12.pdf] G. P. Raja Sekhar, Dept. of
Mathematics, IIT, Kharagpur
[2]. Leonard M. Adleman, Computing with DNA, Scientific American, August 1998.
From Microsoft to Biosoft Computing with DNA, Lila Kari, Department of Computer
Science University of Western Ontario
[3]. L.Adleman. On constructing a molecular computer. 1st DIMACS workshop on DNA
based computers, Princeton, 1995. In DIMACS series, vol.27 (1996)
[4]. L.Adleman, P.Rothemund, S.Roweis, E.Winfree. On applying molecular computation to
the Data Encryption Standard. 2nd DIMACS workshop on DNA based computers,
Princeton, 1996
WEBSITES:
[1]. http://www.howstuffworks.com/ Structure of DNA
[2]. http://www.rsa.com/ What is DNA computing?
[3]. http://www.features.techworld.com/ Computational nanotechnology
/ Nanobiotechnology
[4]. http://www.networkworld.com/ Are DNA Computer Chips a Reality?
[5]. http://www.ezinearticles.com/ Latest Paper presentation on DNA computing
[6]. http://www.nature.com/Nature Nanotechnology/Nanocomputing/
[7].http://www.latestinfo.com/ Dna-computing.html.

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