DNA Computing - Copy

8/6/2019 DNA Computing - Copy

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DNA COMPUTING

SUBMITTED BYRASHID ANWAR

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PRESENTATION OUTLINE

Basic concepts of DNA

Origin of DNA Computing

Solution for NP-Complete Problems

Advantages of DNA Computing

Problems with Adleman¶s Experiment

DNA Computers

Current research

Conclusion2



WHAT IS DNA?

DNA stands for Deoxyribonucleic Acid

DNA represents the genetic blueprint of living creatures

DNA contains ³instructions´ for assembling cells

Every cell in human body has a complete set of DNA

DNA is unique for each individual

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DOUBLE HELIX STRUCTURE OFDNA

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DOUBLE HELIX SHAPE OF

DNA The two strands of a DNA molecule areanti parallel where each strand runs in anopposite direction.

Complementary base pairs Adenine & T hymineGuanine & C ytosine

Two strands are held together by weakhydrogen bonds between thecomplementary base pairs

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PHYSICAL S`TRUCTURE OFDNA

NitrogenousBase

34 Å

Major Groove

Minor Groove

Central Axis

Sugar-PhosphateBackbone

20 Å 5¶ C 3¶ OH

3¶ 0HC 5¶

5¶

3¶

3¶

5¶

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INSTRUCTIONS IN DNA

Instructions are coded in a sequence of the DNAbases

A segment of DNA is exposed, transcribed andtranslated to carry out instructions

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The use of biological molecules, primarilyDNA, DNA analogs, and RNA, for computational purposes.

What is DNA Computing (DNAC) ?

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Great advances in molecular biologyP CR (Polymerase C hain R eaction)DNA Microarrays

New enzymes and proteinsBetter understanding of biological molecules

Ability to produce massive numbers of DNAmolecules with specified sequence and size

DNA molecules interact through template

matching reactions

What makes DNAC possible

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BASICS AND ORIGIN OF DNA

COMPUTING "In order to do computations, you only needtwo things: a means of storing information

and a means of manipulating information,"says Lloyd Smith [Sal2000], one of thescientists who worked on the project on DNACO MPU TI NG at the University of Wisconsin atMadison. "Any system that has those twoproperties one can set up to do thosecomputations. And DNA has them."

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BASICS CONT..

DNA computing is utilizing the property of DNA for massively parallel computation.With an appropriate setup and enough DNA, one canpotentially solve huge problems by parallel search.

Utilizing DNA for this type of computation can be muchfaster than utilizing a conventional computer

Leonard Adleman proposed that the makeup of DNAand its multitude of possible combining nucleotidescould have application in computational researchtechniques

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DENSESTORAGE

T his image shows 1 gram of DNA on a C D. T he C D canhold 8 00 MB of data.

T he 1 gram of DNA can holdabout 1x101 4 MB of data.

The number of CDs requiredto hold this amount of information, lined up edge toedge, would circle the Earth375 times, and would take163,000 centuries to listento!!

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ENORMOUS PARALLELISM

A test tube of DNA can contain trillions of strands. Eachoperation on a test tube of DNA is carried out on all

strands in the tube in parallel !C heck this out««. We T ypically use

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INVENTOR OF DNA COMPUTING ADLEMAN

Adleman is often called the inventor of DNA computers.

His article in a 1 99 4 issue of the journal Science outlinedhow to use DNA to solve a well-known mathematicalproblem, called the directed H amilton Path problem, alsoknown as the "traveling salesman " problem.

The goal of the problem is to find the shortest routebetween a number of cities, going through each city onlyonce. As you add more cities to the problem, theproblem becomes more difficult. Adleman chose to findthe shortest route between seven cities

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Solution to Hamiltonian path problemT he H amilton path problem commonly known as the

traveling salesman problem is a hard NP problemIf there are N cities then , there are N! /2 possible paths and

the goal is to find a path from the start city to the end city

going through every city only once.

STEP 1: Represent each city by a single DNA strandcontaining 20 randomly chosen amino acid base . eg

Sydney -TT

AAGGPerth - AAAGGGMelbourne - GA T ACT

Brisbane - C GG T GC

Alice Spring ± C GTCC A

Darwin - CC GAT G 15



STEP 2: Represent the route between any twocities by a single DNA strand where the 1st 10

amino acid bases are the complementary bases tothe last 10 bases in City 1 and the 2nd 10 bases arethe complementary bases to the first 10 bases

Sydney Melbourne ± AGGGA T

Melbourne Sydney ± A CTTT AMelbourne Perth ± A CT GGGetc«

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STEP 3: Millions of stands of DNA representing every cityand every possible route between any two cities are placedin a test tube where the strands combine. The end result is

a large number of lon strings of variable lengths formed bythe strands combining.The solution is a double helix molecule:

CCGATG ± CGGTGC ± TTAAGG ± GATACT ± AAAGGG ± CGTCCA

TACGCC ± ACGAAT ± TCCCTA ± TGATTT ± CCCGCASolution with vertex DNA molecules

Darwin _Brisbane _Sydney _Melbourne _Perth _Alice Spring _Darwin

Solution with edge DNA molecules

Brisbane - BrisbaneSydney - SydneyMelbourne ±Melbourne

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To determine the solution:

Look only for strings that have C ity 1 at oneend and C ity 7 at the other

Among these strands look for only the stringsthat had seven cities

Among what was left, look for a string withseven different cities and that is the solution

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1.CITIES2.FLIGHTS

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C hecking C ities

Attach city complement to iron ball

Suspend ball in solution

Watson- C rick pairing attraction

Wrong answers poured out

Repeat for each city

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T he success of the Adleman DNA computer provesthat DNA can be used to calculate complex

mathematical problems.T hree years after Adleman's experiment, researchers

at the University of R ochester developed logic gates

made of DNA.T he researchers believe that these logic gates might

be combined with DNA microchips to create a

breakthrough in DNA computing

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Finite Au tomaton in DNA M olec u les and E nzymes

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Advantages of a DNA Computer

Parallel C omputing- DNA computers are massively

parallel.

Incredibly light weight- With only 1 LB of DNA youhave more computing power than all the computers ever made.

Low power- T he only power needed is to keep DNAfrom denaturing.

Solves C omplex Problems quickly- A DNA computer can solve hardest of problems in a matter of weeks.

C lean, C heap and Available :-clean because people do notuse any harmful material to produce it and cheap and availablebecause you can easily find DNA from nature

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DISADVANTAGESO ccasionally Slow

Hydrolysis :-

The DNA molecules can fracture.

Over the six months you¶re

C omputing your DNA system is gradually turning to water

Information Untransmittable :- C urrent DNA algorithms compute successfully

Without passing any information from one processor to the next in a

Multiprocessor connection-busR eliability Problems

Errors in DNA C omputers happen due to many factors Annealing (or

hybridization) Errors while combine with the proper DNA complements`

Size restrictions :-Adleman¶s process to solve the traveling salesmanproblem for 200 cities would require an amount of DNA that weighed morethan the Earth.

T he computation time required to solve problems with a DNA computer does not grow exponentially, but amount of DNA required D O ES.

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What developments can we expect in the near-

term?Increased use of molecules other than DNA

Evolutionary approachesC ontinued impact by advances in molecular biology

Some impact on molecular biology by DNAcomputation

Increased error avoidance and detection27



FUTURE development cont..!

Algorithm used by Adleman for the traveling salesman problem wassimple. As technology becomes more refined, more efficient algorithmsmay be discovered.

DNA Manipulation technology has rapidly improved in recent years,

and future advances may make DNA computers more efficient.

T he University of Wisconsin is experimenting with chip-based DNAcomputers.

DNA computers are likely to feature word processing, emailing andsolitaire programs.

Instead, their powerful computing power will be used for areas of encryption, genetic programming, language systems, and algorithms

by airlines wanting to map more efficient routes.28



Application of DNA Based Computation

Massively Parallel Processing

Solving NP- C omplete and H ard C omputational

Problems

Storage and Associative Memory

DNA2DNA Applications

Implications to Biology, C hemistry, and Medicine

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THANK YOU!!!!!It will take years to develop a practical,

workable DNA computer.But«Let¶s all hope that this D R EAMcomes true!!!

QUES TIO NS ?

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DNA Computing - Copy