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INFORMATION TECHNOLOGY

FOR MANAGERS

PROJECT REPORT ON

DNA COMPUTING

MBA-HR (2011-2013)

SUBMITTED TO: RAJEEV GUPTA

FACULTY

ASB

SUBMITTED BY:

ANSHU

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TABLE OF CONTENTS

Topics

Acknowledgement

Chapter-1

Introduction

Chapter-2

DNA Computation technology

Chapter-3 -

A successor of silicon

Chapter-4

Scientists report advance in DNA computing

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ACKNOWLEDGEMENT

I would like to take this opportunity to extend our gratitude to our esteemed faculty Mr.Rajeev Gupta

(Faculty at ABS ) for extending his full support to us throughout this project. My heartiest thanks to

him for giving me the guidance and support to make this project possible.

I feel privileged to offer our sincere thanks and deep sense of gratitude to our respectedA.D.G Sir - Dr.

Sanjay Srivastava , for providing us an environment that helped us in the completion of this project.

We are grateful for the co-operation , valuable suggestions and had work rendered by my classmates.

This has been a tremendous learning experience for me.

I regret any inadvertent omissions.

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Introduction

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INTRODUCTION

DNA computing is a form ofcomputing which uses DNA, biochemistry and molecular biology, instead of

the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular

computing, is a fast developing interdisciplinary area. Research and development in this area concerns

theory, experiments and applications of DNA computing. DNA computing is fundamentally similar

to parallel computing in that it takes advantage of the many different molecules of DNA to try many

different possibilities at once.

DNA computing also offers much lower power consumption than traditional silicon computers. DNA

uses adenosine triphosphate (ATP) as fuel to allow ligation or as a means to heat the strand to cause

disassociation. Both strand hybridization and the hydrolysis of the DNA backbone can occur spontaneously,

powered by the potential energy stored in DNA. Consumption of two ATP molecules releases 1.5 x 1019 J.

Even with a large number of transitions per second using two ATP molecules, power output is still low. For

instance, Kahan reports 109 transitions per second with an energy consumption of 1010 W, and similarly

Shapiro reports a system producing 7.5 x 1011

outputs in 4000 sec resulting in an energy consumption rate of

~ 1010 W.

For certain specialized problems, DNA computers are faster and smaller than any other computer built so

far. Furthermore, particular mathematical computations have been demonstrated to work on a DNA

computer. As an example, Aran Nayebihas provided a general implementation ofStrassen's matrix

multiplication algorithm on a DNA computer, although there are problems with scaling.

But DNA computing does not provide any new capabilities from the standpoint ofcomputability theory, the

study of which problems are computationally solvable using different models of computation. For example,

if the space required for the solution of a problem grows exponentially with the size of the problem on von

Neumann machines, it still grows exponentially with the size of the problem on DNA machines. For very

large EXPSPACE problems, the amount of DNA required is too large to be practical. (Quantum computing,on the other hand, does provide some interesting new capabilities. DNA computing overlaps with, but is

distinct from, DNA nanotechnology. The latter uses the specificity of Watson-Crickbasepairing and other

DNA properties to make novel structures out of DNA. These structures can be used for DNA computing, but

they do not have to be. Additionally, DNA computing can be done without using the types of molecules

made possible by DNA nanotechnology.The Caltech researchers have created a circuit made from 130

unique DNA strands, which is able to calculate the square root of numbers up to 15.

HISTORYThis field was initially developed by Leonard Adleman of the University of Southern California,

in 1994. Adleman demonstrated a proof-of-concept use of DNA as a form of computation which solved the

seven-point Hamiltonian path problem. Since the initial Adleman experiments, advances have been made

and various Turing machines have been proven to be constructible.

In 2002, 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. On

April 28, 2004, Ehud Shapiro, Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, and Rivka Adar at

the Weizmann Institute announced in the journal Nature that they had constructed a DNA computer coupled

with an input and output module which would theoretically be capable of diagnosing cancerous activity

within a cell, and releasing an anti-cancer drug upon diagnosis.

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DNA Computation Technology

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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. In 1994, Leonard Adleman introduced the idea of using

DNA to solve complex mathematical problems. Adleman, a computer scientist at the University of Southern

California, came to the conclusion that DNA had computational potential after reading the book "Molecular

Biology of the Gene," written by James Watson, who co-discovered the structure of DNA in 1953. In fact,

DNA is very similar to a computer hard drive in how it stores permanent information about your genes.

Adleman is often called the inventor of DNA computers. His article in a 1994 issue of the journal Science

outlined how to use DNA to solve a well-known mathematical problem, called the directed Hamilton Path

problem, also known as the "traveling salesman" problem. The goal of the problem is to find the shortest

route between a number of cities, going through each city only once. As you add more cities to the problem,

the problem becomes more difficult. Adleman chose to find the shortest route between seven cities.

You could probably draw this problem out on paper and come to a solution faster than Adleman did using

his DNA test-tube computer. Here are the steps taken in the Adleman DNA computer experiment:

1.Strands of DNA represent the seven cities. In genes, genetic coding is represented by the letters A, T, C

and G. Some sequence of these four letters represented each city and possible flight path.2.These molecules are then mixed in a test tube, with some of these DNA strands sticking together. A chain

of these strands represents a possible answer.

3.Within a few seconds, all of the possible combinations of DNA strands, which represent answers, are

created in the test tube.

4.Adleman eliminates the wrong molecules through chemical reactions, which leaves behind only the flight

paths that connect all seven cities.

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 ofspeed. 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

requireshuman assistance. The goal of the DNA computing field is to create a device that can work

independent of human involvement.

Three years after Adleman's experiment, researchers at the University of Rochester developed logic gates

made of DNA. Logic gates are a vital part of how your computer carries out functions that you command it

to do. These gates convert binary code moving through the computer into a series of signals that the

computer uses to perform operations. Currently, logic gates interpret input signals from silicon transistors,

and convert those signals into an output signal that allows the computer to perform complex functions.The Rochester team's DNA logic gates are the first step toward creating a computer that has a structure

similar to that of an electronic PC. Instead of using electrical signals to perform logical operations, these

DNA logic gates rely on DNA code. They detect fragments ofgenetic material as input, splice together

these fragments and form a single output. For instance, a genetic gate called the "And gate" links two DNA

inputs by chemically binding them so they're locked in an end-to-end structure, similar to the way two Legos

might be fastened by a third Lego between them. The researchers believe that these logic gates might be

combined with DNA microchips to create a breakthrough in DNA computing.

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. In the next section, we'll look at how DNA computers

could surpass their silicon-based predecessors, and what tasks these computers would perform.

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A successor of silicon

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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.

DNA computers have the potential to take computing to new levels, picking up where Moore's Law leaves

off. There are several advantages to using DNA instead of silicon:

1. As long as there are cellular organisms, there will always be a supply of DNA.2. The large supply of DNA makes it a cheap resource.3. Unlike the toxic materials used to make traditional microprocessors, DNA biochips can be made cleanly.4. DNA computers are many times smaller than today's 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 computershundreds 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.

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Scientists report advance in DNA

computing

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Scientists have taken DNA computing from the free-floating world of the test tube and anchored it securely

to a surface of glass and gold. In so doing, they have taken a small but important step forward in the quest to

harness the vast potential of DNA to perform the same tasks that now require silicon and miniature

electronic circuits.

The accomplishment, reported in the Thursday, Jan. 13 issue of the journal Nature by a group of scientists

from the UW-Madison, is an important demonstration that shows DNA computing can be simplified and

scaled up to tackle complex problems, says Lloyd Smith, a UW-Madison professor of chemistry and a co-author of the paper.

DNA computing is a nascent 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 a computer's through the deployment of enzymes, biological catalysts that act like software to

execute desired operations.

The Nature paper describes the development of novel surface chemistry that 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 technology simpler, more accessible and more amenableto the development of larger DNA computers capable of tackling the kinds of complex problems that

conventional computers now handle routinely.

"It demonstrates DNA computing on surfaces, which provides a relatively simple pathway to upscaling

DNA computing to solve large problems," Smith says.

In the Wisconsin experiments, a set of DNA molecules were applied to a small glass plate overlaid with

gold. In each experiment, the DNA was tailored so that all possible answers to a computationally difficult

problem were included. By exposing the molecules to certain enzymes, the molecules with the wrong

answers were weeded out, leaving only the DNA molecules with the right answers.

The appeal of DNA computing lies in the fact that DNA molecules can store far more information than any

existing conventional computer chip. It has been estimated that a gram of dried DNA can hold as much

information as a trillion CDs. Moreover, in a biochemical reaction taking place in a tiny surface area,

hundreds of trillions of DNA molecules can operate in concert, creating a parallel processing system that

mimics the ability of the most powerful supercomputer.

The chips that drive conventional computers represent information as a series of electrical impulses using

ones and zeros. Mathematical formulas are used to manipulate that binary code to arrive at an answer. DNA

computing, on the other hand, depends on information represented as a pattern of molecules arranged on a

strand of DNA. Certain enzymes are capable of reading that code, copying and manipulating it in predictable

ways.

Conventional computing, with ever more and smaller features packed onto the silicon chips that power it, is

approaching the limits of miniaturization. DNA computing, says Smith, is one potential way around that

barrier.

But current DNA computing technology, Smith emphasized, is still far from overtaking the silicon chip. The

new method reported by the Wisconsin scientists, he says, is simply a testbed for working out an improved

and simpler chemistry for DNA computing.

Nevertheless, Smith says, the new surface chemistry provides an opportunity to harnessing DNA to make

the biggest nonconventional computer yet.

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"We're interested in scale up. We believe that based on the principles we've worked out here, we can see

scaling up within a few years a factor of a trillion or more."