​A

Technical Report

On

DNA COMPUTING
Submitted to Jawaharlal Nehru Technological University for the Partial fulfillment of the requirement

for the Award of Degree in

BACHELOR OF TECHNOLOGY
In

COMPUTER SCIENCE & ENGINEERING

Submitted by

P.VIDYA (16QK1A0560)

DEPARTMENT OF COMPUTER SCIENCE & ENGINEERING

JYOTHISHMATHI INSTITUTE OF TECHNOLOGICAL SCIENCES
(Approved by AICTE, Delhi, Affiliated to JNTU, HYDERABAD)

Rama Krishna Colony, Karimnagar- 505481. T.S. INDIA

(2016-2020)
 DEPARTMENT OF COMPUTER SCIENCE & ENGINEERING
JYOTHISHMATHI INSTITUTE OF TECHNOLOGICAL SCIENCES
(Approved by AICTE, Delhi, ​Affiliated to JNTU, HYDERABAD​)
RAMA KRISHNA COLONY, KARIMNAGAR, T.S - 505481

​CERTIFICATE

This is to certify that ​P.VIDYA (16QK1A0560) ​is a bonafide student of ​Jyothismathi

Institute of Technological Sciences​, Karimnagar, and submitted the technical seminar report
on ​“DNA COMPUTING” in partial fulfillment of the requirement for the award of
BACHELOR OF TECHNOLOGY ( B.TECH) ​D​egree In COMPUTER SCIENCE AND
ENGINEERING (CSE) ​T​hrough ​Jawaharlal Nehru Technological University (J.N.T.U)
HYDERABAD for the academic year ​2016-2020.

SEMINAR SUPERVISOR SENIOR FACULTY Head of Department

Mr. N.THIRUPATHI Mr. N.THIRUPATHI Mrs .A.MANJULA
Designation, Associate Professor, Associate Professor,
Dept of CSE Dept of CSE Dept of CSE
 ACKNOWLEDGEMENT

I would like to express my sincere gratitude to my advisor, ​Mr. N.THIRUPATHI​ ​, ​Associate

Professor​, CSE Dept., whose knowledge and guidance has motivated me to achieve goals I never thought
possible. The time I have spent working under his supervision has truly been a pleasure.

It is my privilege and pleasure to express my profound sense of respect, gratitude and indebtedness to
my coordinator ​Mr. N.THIRUPATHI, ​Associate Professor​, Department of CSE, for his constant guidance,
inspiration, and constant encouragement throughout this technical work.

The experience from this kind of work is great and will be useful to me in future. I thank ​Mrs.
A.MANJULA Associate Professor & HOD​, CSE Department, for encouraging me to do such work and for
providing all the facilities to carry out this work.

It is a great pleasure to convey my thanks to my principal Dr. K.VAISHALI​, ​Principal​,

Jyothishmathi Institute of Technological Sciences and the College Management for permitting me to
undertake this work and providing excellent facilities to carry out my work.

I thank all the ​Faculty members of the Department of Computer Science & Engineering for sharing
their valuable knowledge with me. I extend my thanks to the ​Technical Staff of the department for their
valuable suggestion to technical problems.

Finally, special thanks to my parents, brothers for their support and encouragement through out my
life and this course .Thanks to all my friends and well wishers for their constant support
 DECLARATION

We hereby declare that the work which is being presented in this dissertation entitled, “​DNA
COMPUTING​”, submitted towards the partial fulfillment of the requirements for the award of the degree of
Bachelor ​of Technology ​in ​Computer Science & Engineering​, ​Jyothismathi Institute of Technological
Sciences​, Karimnagar is an authentic record of our own work carried out under the supervision of ​Mr. N.
THIRUPATHI​, Asst. Prof., Department of CSE, Jyothismathi Institute of Technological Sciences,
Karimnagar.

To the best of our knowledge and belief, this project bears no resemblance with any report submitted
to JNTUH or any other University for the award of any degree or diploma.

P.VIDYA (16QK1A0560)

Date:

Place:Karimnagar
 ​TABLE OF CONCPTS

S.No Title page.No.

1. Introduction 1

2. What is DNA 2

2.1 Structure of DNA 3-4

3. What is DNA computing 5

3.1 Operation with DNA 5-6

4. Origin of DNA computing 7-8

5. Silicon vs DNA computing 8-9

6 Evolution of DNA computing 10

7. Conclusion 11
 LIST OF FIGURES

S.No Figure.No Figure.Name Page.No

1. 1 DNA 2

2. 2 Structure of DNA 3

3. 3 Structure of nucleotide 3

4. 4 Phosphodiester Bound 4

5. 5 Hydrogen Bound 4

6. 6 Chromatin 4

7. 7 Chemical structure of nucleotide 6

8 8 Hamiltonian path 8

9. 9 Silicon Chip 9
 ​1.INTRODUCTION

​DNA computing is the idea of using chemical reactions on biological molecules to perform computation,
rather than silicon and electricity. We often hear about quantum computers, and there is a lot of discussion
about whether it will actually work, or crack RSA, stuff like that. In the domain of alternative computers,
DNA computers are often overlooked, but they’re easy to understand (none of the quantum weirdness), and
have potential to do massively parallel computations efficiently.

I first heard about DNA computers when doing my undergrad research project this term. I won’t bore you
with the details, but it has to do with the theoretical aspects of DNA self-assembly which we will see is
related to DNA computing.

The study of DNA computing is relatively new: the field was started by Leonard Adleman who published a
breakthrough paper in Science in 1994. In this paper, he solved the directed Hamiltonian Path problem on 7
vertices using DNA reactions. This was the first time anything like this had been done. In this article, I will
summarize this paper.

DNA computing ​ is a branch of ​computing​ which uses ​DNA​, ​biochemistry​, and ​molecular biology​ hardware,
instead of the traditional silicon-based ​computer​ ​technologies​. Research and development in this area
concerns theory, experiments, and applications of DNA computing. The term "molectronics" has sometimes
been used, but this term has already been used for an earlier technology, a then-unsuccessful rival of the
first ​integrated circuits this term has also been used more generally, for molecular-scale electronic
technology.

It is interesting to compare DNA computing to the Turing Machine. Two things are needed to build a
universal computer: storage and processing. In the case of the Turing Machine, the storage takes the form of
the tape. In DNA computing, the DNA itself is a storage medium, one of the densest known. The processing
of the Turing Machine is done by what Turing called the "Finite Control," or what we might think of as the
state machine. The processing of DNA computing is a bit more complicated, and explained in the demo.

2.WHAT IS DNA

Deoxyribonucleic acid, or DNA, is a molecule that contains the instructions an organism needs to develop,
live and reproduce. These instructions are found inside every cell, and are passed down from parents to their
children.
Deoxyribonucleic acid, more commonly known as DNA, is a complex molecule that contains all of the
information necessary to build and maintain an organism. All living things have DNA within their cells. In
fact, nearly every cell in a multicellular organism possesses the full set of DNA required for that organism.

However, DNA does more than specify the structure and function of living things — it also serves as the
primary unit of heredity in organisms of all types. In other words, whenever organisms reproduce, a portion
of their DNA is passed along to their offspring. This transmission of all or part of an organism's DNA helps
ensure a certain level of continuity from one generation to the next, while still allowing for slight changes
that contribute to the diversity of life.

But what, exactly, is DNA? What smaller elements make up this complex molecule, how are these elements
arranged, and how is information extracted from them? This unit answers each of these questions, and it also
provides a basic overview of the process of DNA discovery.

2.1 STRUCTURE OF DNA

​Although it may look complicated, the NA in a cell is really just an pattern made up of four different
patterns called nucleotides. Imagine a set of blocks that has only four shapes, or an alphabets that has only
four letters.NA is a long string of these blocks or letters.
Structure of a nucleotide-DNA Monomer

The nucleotide is the basic building block of nucleic acids. Each nucleotide consists of 3 components:1.a
sugar-deoxyribose (five carbon atoms:1to5)

2.a phosphate group attached to 5’ carbon and

3.a nitrogen base attached ti 1’ carbon

LINKING OF NUCLEOTIDS:

The DNA monomer can link in two ways: phosphodiester bound and Hydrogen bond

Phosphodiester bound Hydrogen bound

DNA is structured hierarchically:

DNA is composed to conserve space. There are several levels at which DNA is compacted.

Levels of structure:

● Double Helix
● Histones/Nucleosome
● Solenoid Supercoil
● Chromatin
● Chromosomes

​ 3.WHAT IS DNA COMPUTING

DNA computing is the use of bio molecular components rather than standard artificial hardware (such as
silicon chips) in computer technology. In place of traditional code (such as the common binary variety),
DNA computing utilizes the four-character genetic alphabet, which consists of:

● A – Adenine
● G – Guanine
● C – Cytosine
● T – Thymine

For the past decade, engineers have come up against the harsh reality of physics in the pursuit of more
powerful computers: transistors, the on-off switches that power the computer processor, cannot be made any
smaller than they currently are. Looking beyond the silicon chip, an intuitive alternative is currently being
developed using DNA to perform the same kinds of complex calculations that silicon transistors do now. But
what is DNA computing, how does DNA computing work, and why is it such a big deal?

A computer that uses DNA to store information and also perform complex calculations. The main benefit of
using DNA computer to solve complex problems is that different possible solutions are created all at once.
This is called parallel processing.

3.1 Operations with DNA

In an electronic computer an operator is succinctly represented by a truth table, a table of all possible
combinations of the input bit values and their corresponding output values, as shown in table 1 A. Our
approach is to encode these truth tables in DNA using a three-level scheme. An operation is represented in
terms of DNA hybridization. For each binary operation, the two bit strings are represented with two different
DNA single strands​.

The first string is called the “input” and the second the “operand” strand. Each bit is represented with a
dinucleotide unit, and a bit string with a sequence of dinucleotides. The natural DNA bases Adenine (A),
Thymine (T), Uracil (U) and a non-natural base 7-deaza-adenine (P) (shown in figure 1) are used for
constructing the dinucleotides. A non-natural base is needed in order to realize all possible input and operand
bit values in DNA; a base which can pair with the specificity of A and yet is chemically distinct.
7-deaza-adenine 2 base-pairs selectively with U and T just like A which makes it ideal for our application.

The input DNA strand is constructed with dinucleotides 5’-AU representing bit 1, and 5’-UA, the bit 0,
where 5’ and 3’ denote directionality of the DNA strand. The operand strand is constructed with 2
2-aminopurine and 2-aminoadenine could potentially be used too. dinucleotides 3’-TA and 3’-PT,
representing bit 0, and the dinucleotides 3’-AT and 3’-TP, representing bit 1. The table 1 B shows how these
dinucleotides can base-pair to allow for all possible combinations of the input strand and the operand strand.

Since, as we will show later in the paper, the operand strands do not have to be sequenced to obtain the final
result, but instead carry an output strand, we do not have to chemically distinguish between A and P at any
stage. DNA strands carrying TA (similarly AT) might have a different output appended to it than the DNA
strand carrying TP (similarly PT) depending upon the result of the calculation. If the input strand is
constructed in the 5’ to 3’ direction the operand strand is constructed in the 3’ to 5’ direction and vice versa.
The input strand is constructed using only A and U (level 1), while the operand strand with A, T, and P
(level 2).

This keeps the input distinct from the operand, yet retains the same base-pairing structure and allows all
possible combinations of the input and operand bits (see table 1). As a result of an operation the input strand
hybridizes with its complementary operand strand to form a double stranded DNA complex. This output is
interpreted according to the truth table (level 3) of the operator applied. Table 1 B shows our encoding
scheme along with the truth tables for different boolean and arithmetic operations such as NAND, AND,
XOR and ADD (addition). The truth table encoding can easily be extended to a number of other operators.

Figure 1: Chemical structure of the bases used; Adenine (A), Thyamine (T), Uracil (U), 7-deaza-adenine (P), Guanine
(G), Cytidine (C), iso-Guanine (M) and iso-Cytidine (N). Also shown are some example base-pairs, and a dinucleotide
“bit” unit.

4.ORIGION OF DNA COMPUTER

DNA computers can’t be found at your local electronics store yet. The technology is still in development and
didn’t even exist as a concept a decade ago. The concept of DNA computing was born in1993,whwn
professor Lenard Adleman, a mathematician specializing in computer science and cryptography at the
Laboratory of Molecular Science, Department of Computer Science, University of Southern California
accidentally stumbled upon the similarities between conventional computers and DNA while reading the
book “Molecular Biology of the Gene” written by James Watson who co-discovered the structured of DNA
in 1953. Adelman came to the conclusion that DNA had computational to solve complex mathematical
problems.

In 1994, Leonard Aldeman introduced the idea of using DNA to solve complex mathematical problems. In
fact, DNA is very similar to a computer hard drive in how it stores permanent information about your genes.

The Adleman Experiment-

In Adleman's 1994 paper (​archived​), he describes a method of manipulating DNA molecules in a lab that
results in a solution to the Hamiltonian Path problem with high probability.
He claims that "The number of different oligonucleotides required should grow linearly with the number of
edges", and this makes sense given the molecular encoding of the edges described in the paper, but he also
claims that "the number of procedures required should grow linearly with the number of ​vertices​ in the
graph". Why is this last claim true? In other words, why isn't the assembly of edge molecules counted
towards this calculation? If it were, the complexity of lab procedures would be O (|V|2)O(|V|2), as the
number of edges in a graph is bound by this function​.

Example:
The Hamiltonian Path Problem asks whether there is a route in a directed graph from a beginning node to an
ending node, visiting each node exactly once. The Hamiltonian Path Problem is NP complete, achieving
surprising computational complexity with modest increases in size. This challenge has inspired researchers
to broaden the definition of a computer. DNA computers have been developed that solve NP complete
problems. Bacterial computers can be programmed by constructing genetic circuits to execute an algorithm
that is responsive to the environment and whose result can be observed. Each bacterium can examine a
solution to a mathematical problem and billions of them can explore billions of possible solutions. Bacterial
computers can be automated, made responsive to selection, and reproduce themselves so that more
processing capacity is applied to problems over time.
 5.silicon vs. DNA microprocessor

Silicon microprocessor have been the heart of the computing world for more than 40 years. In that time,
manufactures have crammed more electronic devices onto their microprocessor. In accordance with Moore’s
Law, the number of electronic devices put on a microprocessor has doubled every 18 months. Moor’s Law is
named after Intel founder Gordon Moore, who predicted in 1965 that microprocessor 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

As mentioned in previous sections sequentially. A modern CPU basically repeats the same “fetch and
execute (fetches an instruction and the appropriate data from main memory and executes it) cycle” over and
over again. This process is repeated many, many times in a row, and really, really fast. Typically, increasing
performance of silicon computing means faster clock cycles, placing emphasis on the speed of the CPU and
not on the size of the memory. Oppositely, the power of DNA computing comes from its memory capacity
and parallel processing. In other words, DNA loses its appeal if forced to behave sequentially.

Silicon chips:

A ​silicon chip​ is an ​integrated circuit​ made primarily of silicon. Silicon is one of the most common
substances used to develop computer chips. The picture shows an example of a silicon wafer with dozens of
individual silicon chips.

An integrated circuit or monolithic integrated circuit (also referred to as an IC, a chip, or a microchip) is a set
of ​electronic circuits on one small flat piece (or "chip") of ​semiconductor material that is normally ​silicon.
The integration of ​large numbers of tiny ​MOS transistors ​into a small chip results in circuits that are orders
of magnitude smaller, faster, and less expensive than those constructed of discrete ​electronic components.
The IC's ​mass production​ capability, reliability, and building-block approach to ​circuit design​ has ensured
the rapid adoption of standardized ICs in place of designs using discrete ​transistors​. ICs are now used in
virtually all electronic equipment and have revolutionized the world of ​electronics​. ​Computers​, ​mobile
phones​, and other digital ​home appliances​ are now inextricable parts of the structure of modern societies,
made possible by the small size and low cost of ICs.

Advantages of DNA Computing:

The massively parallel processing capabilities of DNA computers has the potential of speeding up large, but
otherwise solvable, polynomial time problems requiring relatively few operations (Adams). For instance, a
mix of 1,018 strands of DNA could operate at 10,000 times the speed of today’s advanced supercomputers.

​Performing millions of operations simultaneously allows the performance rate of DNA strands to increase
exponentially. Adleman’s experiment was executed at 1,014 operations per second, a rate of 100 Teraflops
(100 trillion floating point operations per second). The world’s fastest supercomputer runs at just 35.8
Teraflops.

Traditional storage media, such as videotapes, require 10^12 cubic nanometers of space to store a single bit
of information; DNA molecules require just one cubic nanometer per bit (Parker). In other words, a single
cubic centimeter of DNA holds more information than a trillion CDs (Johnson). This is because the data
density of DNA molecules approaches 18 Mbits per inch, whereas today’s computer hard drives can only
store less than 1/100,000 of this information in the same amount of space.

6.EVOLUTION OF DNA COMPUTING

The DNA computer has clear advantages over conventional computers when applied to problems that can be
divided into separate, non-sequential tasks. The reason is that DNA strands can hold so much data in
memory and conduct multiple operations at once, thus solving decomposable problems much faster. On the
other hand, non-decomposable problems, those that require many sequential operations are much more
efficient on a conventional computer due to the length of time required to conduct the biochemical
operations.

LIMIOTATIONS:

Each stage of parallel operations requires time measured in hours or days, with extensive human or
mechanical intervention between stepssince a set of DNA strands is tailored to a specific problem, a new set
would have to be made for each new problem.

Algorithms can be executed in polynomial time due to the massive parallelism inherent in DNA
computation, but they are limited in applicability to small instances of these problems because they require
the generation of an unrestricted solution space. For example, the DNA encoding of all paths of a Traveling
Salesman problem with 200 cities would weigh more than the earth.
DNA synthesis is liable to errors, such as mismatching pairs, and is highly dependent on the accuracy of the
enzymes involved . In addition, the chance of errors increases exponentially, limiting the number of
operations you can do successively before the probability becomes greater than producing the correct result

Generating solution sets, even for some relatively simple problems, may require impractically large amounts
of memory . Although DNA can store a trillion times more information than current storage media, the way
in which the information is processed necessitates a massive amount of DNA if larger-scale problems are to
be solved..
 7.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.

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.

Many issues to be overcome to produce a

useful DNA computer.