DNA Computing Introductory seminar

8/13/2019 DNA Computing Introductory seminar

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Seminar ReportSeminar Report

titled

DNA Computing


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Table of Contents

1.0 Introduction.................................................

2.0 Architecture of DNA Computer.......................

2.1 What is DNA?

2.2 Structure of DNA

2.3 What is DNA Computer?

3.0 perations on DNA computer...

!.0 "o# DNA computer #ill #or$%............................................................

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1.Introduction

The twentieth century will be remembere for three ma!or achie"ements # The e"olution

of computers$ ecoin% of the human %enome an e"olution from Newtonian physics to

&uantum physics.Since the be%innin% of time man has performe computations or

calculation. The metho an nature of these computations has howe"er chan%e from

manual in the stone a%es to mechanical in the meie"al a%es to electronic in the new

computer a%e.Computers ha"e &uic'ly %rown in the si(e an processin% power. Computers are

commonly 'nown to consist of inte%rate circuits mainly constructe of silicon )

howe"er$ a computer is ne"er consiere to be *ali"e*. What is %oin% to be the future of

computin% systems? Can we loo' beyon silicon to embrace other meiums for

computin%? Computers inspire by biolo%ical or physical systems are possible

alternati"es. +icroprocessors mae of silicon will e"entually reach their limits of spee

an miniaturi(ation. Chip ma'ers nee a new material to prouce faster computin%

spees.

+illions of natural supercomputers e,ist insie li"in% or%anisms$ incluin% your boy.

DNA -Deo,yribo Nucleic Aci molecules$ the material our %enes are mae of$ ha"e the

potential to perform calculations many times faster than the worl/s most powerful

human0built computers. Technolo%ical a"ances howe"er coul use these builin% bloc's

of our %enome in creatin% computer processors an ata stora%e$ an catapult processin%

spees to incomprehensible le"els not possible by toay/s stanars.

A DNA0base computer has sol"e a lo%ic problem that no person coul complete by

han$ settin% a new milestone for this infant technolo%y that coul someay surpass the

electronic i%ital computer in certain areas. DNA mi%ht one ay be inte%rate into a

computer chip to create a so0calle iochip that will push computers e"en faster. DNA

molecules ha"e alreay been harnesse to perform comple, mathematical problems.

DNA computin% is an alternati"e to the way computers wor' toay. While this

technolo%y is not reaily a"ailable$ or bein% mass prouce$ the theory behin it is &uite

ol an the e"elopment is on%oin% an catchin% more spee. Companies li'e + are

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attemptin% to use DNA to prouce the ne,t %eneration of processors. efore iscussin%

how DNA can be use in computers$ it/s important to first unerstan the basic structure

of a DNA molecule.

DNA computer

A computer which has DNA molecule as the moel of its construction is 'nown as DNA

computer or we can say that DNA computer is collection of DNA strans that ha"e been

specially selecte to ai in the search of solutions for some problems.

DNA base pairs can be translate into s an 1s an oolean al%ebra can be one with

molecules. 4or e,ample$ 5an6 is one by separatin% DNA strans by their se&uence

while 5or6 is performe by mi,in% two DNA solutions to%ether. sraeli scientists ha"e

e"ise a computer that can perform 33 trillion operations per sec.$ more than 1$

times of the fastest 7C. n a ifferent perspecti"e$ more than 1 trillion DNA molecules

can fit into an area no lar%er than 1 cubic 8 cm. With this$ a DNA computer coul hol 1

terabytes of ata an perform 1 trillion of calculations at a time.

&h' DNA computers%

A DNA computer woul nee !ust a few hours to analy(e a floo of information thatwoul ta'e toay9s con"entional computers hunres of years to sol"e.

The importance of DNA computer can be unerstoo by 'nowin% the problems with the

current semiconuctor base technolo%ies which are as follows:

; ower chip ensity

; >ar%e in si(e

; +anufacturin% ifficulties

; ,pensi"e

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2.Architecture of DNA Computers

2.1&hat is DNA %

"ery li"in% thin% such as person has DNA$ an this DNA is the blueprint use to buil

each an e"ery li"in% or%anisms. t etermines e"erythin% from what color of eyes the

person will ha"e to whether they will be preispose to a certain isease or not.

A DNA -Deo,yribose Nucleic Aci molecule is a pair of interwine parallel strans

'nown as ouble heli,. ach stran has a phosphate then a su%ar an then a base. The @

bases -Aenine$ Thymine$ uanine an Cytosine are calle nucleoties) they are the 'ey

components for computin%. They are 'nown as complementary molecules because e"ery

where that there is an A$ there is a T lin'e to it$ as well as$ e"erywhere there is a $ there

is a C attache. Due to its typical structure DNA can be use for computin%.B2

The followin% is the picture of DNA an how it is bone -4i%.1. There are two chains

lin'e to%ether by wea'er bons. These chains are calle strans. t is sort of a laer$ butit is also twiste in a ouble heli, pattern. t also illustrates the wea'er bons containin%

complementary molecules by lin'in% all of the C9s to 9s an all of the A9s to T9s.


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4i%. 1. Structure of DNA

2.2 (tructure of DNA

The nucleotie is the basic builin% bloc' of nucleic acis. ach nucleotie consists of 3

components :

1 a su%ar eo,yribose

E fi"e carbon atoms: 1F to F

E hyro,yl %roup -G


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4i%. 2. asic builin% bloc' of a nucleotie

DNA nucleoties iffer only by their bases -. There are two classes of nitro%en bases

calle purines -ouble0rin%e structures an pyrimiines -sin%le0rin%e structures. The

four bases in DNA/s alphabet are: purines pyrimiines

Aenine A Thymine T

uanine Cytosine C

)in$ing of Nucleotides

The DNA monomers can lin' in two ways: 7hosphoiester bon an


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4i%. 3. Strans of DNA

2.3 &hat is DNA Computer%

A DNA computer$ as the name implies$ uses DNA strans to store information an taps

the recombinati"e properties of DNA to perform operations. A small test tube of DNA

strans suspene in a solution coul yiel millions to billions of simultaneous

interactions at spees$ in theory$ faster than toay/s fastest supercomputers. DNA

computer uses the recombinati"e property of na to perform operations.The main benefit

of usin% DNA computers to sol"e comple, problems is that ifferent possible solutions

are create all at once. This is 'nown as parallel processin%.


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basic nucleoties I aenine$ cytosine$ %uanine$ an thymine I is use to represent an

store ata on a stran of DNA. Calculations in a traitional computer are performe by

mo"in% ata into a processin% unit where binary operations are performe. ssentially$

the operations turn miniaturi(e circuits off or on corresponin% to the (eros an ones that

represent the strin% of ata

*rinciples of DNA Computing

DNA is the ma!or information stora%e molecule in li"in% cells$ an billions of years of

e"olution ha"e teste an refine both this wonerful informational molecule an hi%hly

specific en(ymes that can either uplicate the information in DNA molecules or transmit

this information to other DNA molecules. nstea of usin% electrical impulses to represent

bits of information$ the DNA computer uses the chemical properties ofthese molecules by

e,aminin% the patterns of combination or %rowth of the molecules or strin%s. DNA can o

this throu%h the manufacture of en(ymes$ which are biolo%ical catalysts that coul be

calle the software$use to e,ecute the esire calculation.

DNA + A uni,ue data structure

The amount of information %athere on the molecular biolo%y of DNA o"er the last @

years is almost o"erwhelmin% in scope. So instea of %ettin% bo%%e own in biochemical

an biolo%ical etails of DNA$ we/ll concentrate on only the information rele"ant to DNA

computin%.The ata ensity of DNA is impressi"e. Lust li'e a strin% of binary ata is

encoe with ones an (eros$ a stran of DNA is encoe with four bases$ represente by

the letters A$ T$ C$ an . The bases -also 'nown as nucleoties are space e"ery .3

nanometers alon% the DNA molecule$ %i"in% DNA a remar'able ata ensity of nearly 1K

+bits per inch. n two imensions$ if you assume one base per s&uare nanometer$ the ataensity is o"er one million bits per s&uare inch. Compare this to the ata ensity of a

typical hi%h performance har ri"e$ which is about J bits per s&uare inch 00 a factor of

o"er 1$ smaller.

Another important property of DNA is its ouble strane nature. The bases A an T$ an

C an $ can bin to%ether$ formin% base pairs. Therefore e"ery DNA se&uence has a

natural complement. 4or e,ample if se&uence S is ATTACTC$ its complement$ S/$ is

TAATCAC. oth S an S/ will come to%ether -or hybrii(e to form ouble strane

DNA. This complementarity ma'es DNA a uni&ue ata structure for computation an can

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be e,ploite in many ways. rror correction is one e,ample. rrors in DNA happen ue

to many factors. Gccasionally$ DNA en(ymes simply ma'e mista'es$ cuttin% where they

shouln/t$ or insertin% a T for a . DNA can also be ama%e by thermal ener%y an =

ener%y from the sun.

f the error occurs in one of the strans of ouble strane DNA$ repair en(ymes can

restore the proper DNA se&uence by usin% the complement stran as a reference.

n this sense$ ouble strane DNA is similar to a OAD 1 array$ where ata is mirrore

on two ri"es$ allowin% ata to be reco"ere from the secon ri"e if errors occur on the

first. n biolo%ical systems$ this facility for error correction means that the error rate can

be &uite low. 4or e,ample$ in DNA replication$ there is one error for e"ery 1PM copie

bases or in other wors an error rate of 1P0M. -n comparison$ har ri"es ha"e rea error

rates of only 1P013 for Oee0Solomon correction.

perations in parallel

n the cell$ DNA is moifie biochemically by a "ariety of en(ymes$ which are tiny

protein machines that rea an process DNA accorin% to nature/s esi%n. There is a wie

"ariety an number of these *operational* proteins$ which manipulate DNA on the

molecular le"el. 4or e,ample$ there are en(ymes that cut DNA an en(ymes that paste it

bac' to%ether. Gther en(ymes function as copiers$ an others as repair units. +olecular

biolo%y$ iochemistry$ an iotechnolo%y ha"e e"elope techni&ues that allow us to

perform many of these cellular functions in the test tube. t/s this cellular machinery$

alon% with some synthetic chemistry$ that ma'es up the palette of operations a"ailable for

computation.

Lust li'e a C7 has a basic suite of operations li'e aition$ bit0shiftin%$ lo%ical operators

-AND$ GO$ NGT NGO$ etc. that allow it to perform e"en the most comple, calculations$

DNA has cuttin%$ copyin%$ pastin%$ repairin%$ an many others. An note that in the test

tube$ en(ymes o not function se&uentially$ wor'in% on one DNA at a time. Oather$ many

copies of the en(yme can wor' on many DNA molecules simultaneously. This is the

power of DNA computin%$ that it can wor' in a massi"ely parallel fashion.

DNA as a soft#are

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Thin' of DNA as software$ an en(ymes as harware. 7ut them to%ether in a test tube.

The way in which these molecules uner%o chemical reactions with each other allows

simple operations to be performe as a by0prouct of the reactions. The scientists tell the

e"ices what to o by controllin% the composition of the DNA software molecules. t/s a

completely ifferent approach to pushin% electrons aroun a ry circuit in a con"entional

computer.

To the na'e eye$ the DNA computer loo's li'e clear water solution in a test tube. There

is no mechanical e"ice. A trillion bio0molecular e"ices coul fit into a sin%le rop of

water. nstea of showin% up on a computer screen$ results are analy(e usin% a techni&ue

that allows scientists to see the len%th of the DNA output molecule. *Gnce the input$

software$ an harware molecules are mi,e in a solution it operates to completion

without inter"ention$* sai Da"i


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3.perations on DNA

As concernin% the operations that can be performe on DNA strans the propose moels

of DNA computation are base on "arious combinations of the followin% primiti"e bio0

operations:

('nthesi-inga esire polynomial0len%th stran use in all moels

4i%. @. DNA Synthesis

i/ing : combine the contents of two test tubes into a thir one to achie"e union.

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elting : brea' apart a ouble0strane DNA into its sin%le0strane complementary

components by heatin% the solution. +eltin% in "itro is also 'nown uner the name of

enaturation.

Annealing : bon to%ether two sin%le0strane complementary DNA se&uences by

coolin% the solution. Annealin% in "itro is 'nown as hybrii(ation.

4i%. . DNA +eltin% an Annealin%

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Amplif'ing -copyin%: ma'e copies of DNA strans by usin% the 7olymerase Chain

Oeaction 7CO. The DNA polymerase en(ymes perform se"eral functions incluin%

replication of DNA. The replication reaction re&uires a %uiin% DNA sin%le0stran calle

template$ an a shorter oli%onucleotie calle a primer$ that is anneale to it.

4i%. H. DNA Oeplication

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(eparating +the strans by len%th usin% a techni&ue calle %el electrophoresis that ma'es

possible the separation of strans by len%th.

4i%. J. Separatin% DNA

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/tracting +those strans that contain a %i"en pattern as a substrin% by usin% affinity

purification.

4i%. K. DNA ,traction

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Cutting: DNA ouble0strans at specific sites by usin% commercially a"ailable

restriction en(ymes. Gne class of en(ymes$ calle restriction enonucleases$ will

reco%ni(e a specific short se&uence of DNA$ 'nown as a restriction site. Any ouble0

strane DNA that contains the restriction site within its se&uence is cut by the en(yme at

that location.

4i%. M. DNA Cuttin%

)igating: paste DNA strans with compatible stic'y ens by usin% DNA li%ases. nee$

another en(yme calle DNA li%ase will bon to%ether the en of a DNA stran to another

stran.

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(ubstituting : substitute$ insert or elete DNA se&uences by usin% 7CO site0specific

oli%onucleotie muta%enesis.

4i%.1. DNA Substitution

ar$ing: sin%le strans by hybrii(ation: complementary se&uences are attache to the

strans$ ma'in% them ouble0strane. The re"erse operation is unmar'in% of the ouble0

strans by enaturin%$ that is$ by etachin% the complementary strans. The mar'e

se&uences will be oublestrane while the unmar'e ones will be sin%le0strane.

Destro'ing: the mar'e strans by usin% e,onucleases$ or by cuttin% all the mar'e

strans with a restriction en(yme an remo"in% all the intact strans by %el

electrophoresis. -y usin% en(ymes calle e,onucleases$ either ouble0strane or sin%le0

strane DNA molecules may be selecti"ely estroye. The e,onucleases chew up DNA

molecules from the en inwar$ an e,ist with specificity to either sin%le0strane or

ouble0strane form.

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Detecting and eading: %i"en the contents of a tube$ say VVyes// if it contains at least one

DNA stran$ an VVno// otherwise. 7CO may be use to amplify the result an then a

process calle se&uencin% is use to actually rea the solution.

n Short$ DNA computers wor' by encoin% the problem to be sol"e in the lan%ua%e of

DNA: the base0four "alues A$ T$ C an . sin% this base four number system$ the

solution to any concei"able problem can be encoe alon% a DNA stran li'e in a Turin%

machine tape. "ery possible se&uence can be chemically create in a test tube on

trillions of ifferent DNA strans$ an the correct se&uences can be filtere out usin%

%enetic en%ineerin% tools.atible stic'y ens by usin% DNA li%ases. nee$ another

en(yme calle DNA li%ase$ will bon to%ether$ or VVli%ate//$ the en of a DNA stran to

another stran.

!."o# DNA Computers #ill #or$%

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DNA is the ma!or information stora%e molecule in li"in% cells$ an billions of years of

e"olution ha"e teste an refine both this wonerful informational molecule an hi%hly

specific en(ymes that can uplicate information in DNA molecules or transmit this

information to other DNA molecules.

nstea of usin% electrical impulses to represent bits of information$ the DNA computer

uses chemical properties of these molecules by e,aminin% the patterns of combination or

%rowth of the molecules or strin%s. DNA can o this throu%h the manufacture of the

en(ymes$ which are biolo%ical catalysts that coul be calle the software9 use to

e,ecute the esire calculation. A DNA computer uses the @ eo,yribonucleic acis:

A -aenine

C -cytosine

-%uanine

T -thymine

as the memory units an recombinant DNA techni&ues alreay in e,istence carry out the

funamental operations.

; n a DNA computer$ computation ta'es place in test tubes or on a %lass slie coate in

2@' %ol.

; The input an output both are strans of DNA$ whose %enetic se&uences encoe certain

information.

; A pro%ram on a DNA is e,ecute as a series of biochemical operations$ which ha"e the

effect of synthesi(in%$ e,tractin%$ moifyin% an clonin% the DNA strans.

; Their potential power unerscores how nature coul be capable of crunchin% number

better an faster than the most a"ance silicon chips.

; The stuy of bacteria has shown that restriction en(ymes can be employe to cut DNA

at a specific wor -W. +any restriction en(ymes cut the 2 strans of ouble0strane

DNA at ifferent positions lea"in% o"erhan%s of sin%le0strane DNA. Two pieces of

DNA may be re!oine if their terminal o"erhan%s are complementary. Complements are

referre to as stic'y ens9. sin% these operations$ fra%ments of DNA may be inserte orelete from the DNA.

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; As state earlier DNA represent information as a pattern of molecules on a stran. ach

stran represents one possible answer.

; n each e,periment$ the DNA is tailore so that all concei"able answers to a particular

problem are inclue. Oesearchers then sub!ect all the molecules to precise chemical

reactions that imitate the computational abilities of a traitional computer. ecause

molecules that ma'e up DNA bin to%ether in preictable ways$ it %i"es a powerful

5search6 function.

; f the e,periment wor's$ the DNA computer wees out all the answers$ lea"in% one

molecule or more with the ri%ht answer.

; All these molecules can wor' to%ether at once$ so you coul theoretically ha"e 1

trillion calculations %oin% on at the same time in "ery little space.

; DNA computin% is a fiel that hols the promise of ultra0ense systems that pac'

me%abytes of information into e"ices the si(e of a silicon transistor. ach molecule of

DNA is rou%hly e&ui"alent to little computer chip.

. Oochester e"elope lo%ic %ates mae of DNA. >o%ic %ates are a "ital part of how your

computer carries out functions that you comman it to o. These %ates con"ert binary

coe mo"in% throu%h the computer into a series of si%nals that the computer uses to

perform operations. Currently$ lo%ic %ates interpret input si%nals from silicon transistors$

an con"ert those si%nals into an output si%nal that allows the computer to perform

comple, functions.

. The Oochester team/s DNA lo%ic %ates are the first step towar creatin% a computer that

has a structure similar to that of an electronic 7C. nstea of usin% electrical si%nals to

perform lo%ical operations$ these DNA lo%ic %ates rely on DNA coe. They etect

fra%ments of %enetic material as input$ splice to%ether these fra%ments an form a sin%le

output. 4or instance$ a %enetic %ate calle the *An %ate* lin's two DNA inputs by

chemically binin% them so they/re loc'e in an en0to0en structure$ similar to the way

two >e%os mi%ht be fastene by a thir >e%o between them.

. DNA computer components 00 lo%ic %ates an biochips 00 will ta'e years to e"elop into

a practical$ wor'able DNA computer. f such a computer is e"er built$ scientists say that it

will be more compact$ accurate an efficient than con"entional computers.

DNA Computing Introductory seminar

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