Seminar Report

titled

DNA Computing

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$%............................................................

1.Introduction

The twentieth century will be remembere for three ma!or achie"ements # The e"olution of computers$ eco in% 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 me ie"al a%es to electronic in the new computer a%e. Computers ha"e &uic'ly %rown in the si(e an commonly 'nown to consist of inte%rate computin% systems? Can we loo' beyon computin%? Computers inspire an processin% power. Computers are of silicon ) circuits mainly constructe

howe"er$ a computer is ne"er consi ere to be *ali"e*. What is %oin% to be the future of silicon to embrace other me iums for by biolo%ical or physical systems are possible a new material to pro uce faster computin%

alternati"es. +icroprocessors ma e of silicon will e"entually reach their limits of spee miniaturi(ation. Chip ma'ers nee spee s. +illions of natural supercomputers e,ist insi e li"in% or%anisms$ inclu in% your bo y. DNA -Deo,yribo Nucleic Aci . molecules$ the material our %enes are ma e 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 buil in% bloc's of our %enome in creatin% computer processors an ata stora%e$ an catapult processin% spee s to incomprehensible le"els not possible by to ay/s stan ar s. 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 some ay 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 1iochip that will push computers e"en faster. DNA molecules ha"e alrea y been harnesse to perform comple, mathematical problems. DNA computin% is an alternati"e to the way computers wor' to ay. While this technolo%y is not rea ily a"ailable$ or bein% mass pro uce $ the theory behin it is &uite ol an the e"elopment is on%oin% an catchin% more spee . Companies li'e 21+ are

attemptin% to use DNA to pro uce the ne,t %eneration of processors. 1efore iscussin% how DNA can be use in computers$ it/s important to first un erstan the basic structure of a DNA molecule. DNA computer

A computer which has DNA molecule as the mo el of its construction is 'nown as DNA computer or we can say that DNA computer is collection of DNA stran s that ha"e been specially selecte to ai in the search of solutions for some problems. DNA base pairs can be translate into 3s an 1s an 1oolean al%ebra can be one with molecules. 4or e,ample$ 5an 6 is one by separatin% DNA stran s by their se&uence while 5or6 is performe by mi,in% two DNA solutions to%ether. 2sraeli scientists ha"e e"ise a computer that can perform 333 trillion operations per sec.$ more than 133$333 times of the fastest 7C. 2n a ifferent perspecti"e$ more than 13 trillion DNA molecules can fit into an area no lar%er than 1 cubic 8 cm. With this$ a DNA computer coul hol 13 terabytes of ata an perform 13 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 that woul ta'e to ay9s con"entional computers hun re s of years to sol"e. The importance of DNA computer can be un erstoo by 'nowin% the problems with the current semicon uctor base technolo%ies which are as follows: ; <i%her power issipation ; Don9t allow parallel processin% ; =olatile memory ; >ower chip ensity ; >ar%e in si(e ; +anufacturin% ifficulties ; ?,pensi"e

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. 2t etermines e"erythin% from what color of eyes the person will ha"e to whether they will be pre ispose to a certain isease or not. A DNA -Deo,yribose Nucleic Aci . molecule is a pair of interwine parallel stran s 'nown as ouble heli,. ?ach stran has a phosphate then a su%ar an then a base. The @ bases -A enine$ Thymine$ Auanine an Cytosine. are calle nucleoti es) 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 A$ there is a C attache . Due to its typical structure DNA can be use for computin%.B2C The followin% is the picture of DNA an how it is bon e -4i%.1.. There are two chains lin'e to%ether by wea'er bon s. These chains are calle stran s. 2t is sort of a la er$ but it is also twiste in a ouble heli, pattern. 2t also illustrates the wea'er bon s containin% complementary molecules by lin'in% all of the C9s to A9s an all of the A9s to T9s.

4i%. 1. Structure of DNA

2.2 (tructure of DNA

The nucleoti e is the basic buil in% bloc' of nucleic aci s. ?ach nucleoti e consists of 3 components : 1. a su%ar eo,yribose E fi"e carbon atoms: 1F to DF E hy ro,yl %roup -G<. attache to 3F carbon 2. a phosphate %roup attache to D/ carbon an 3. a nitro%enous base attache to 1/ carbon. -4i%. 2.

4i%. 2. 1asic buil in% bloc' of a nucleoti e DNA nucleoti es iffer only by their bases -1.. There are two classes of nitro%en bases calle purines - ouble0rin%e structures. an pyrimi ines -sin%le0rin%e structures.. The four bases in DNA/s alphabet are: purines pyrimi ines A enine A Thymine T Auanine A Cytosine C )in$ing of Nucleotides The DNA monomers can lin' in two ways: 7hospho iester bon an <y ro%en bon . 7hospho iester 1on The DF0phosphate %roup of one nucleoti e is !oine with the 3F0hy ro,yl %roup of the other 0 stron% -co"alent. bon 0 irectionality: DF3F or 3FDF <y ro%en 1on The baA hy ro%en bon is a wea' chemical bon that occurs between hy ro%en atoms an more electrone%ati"e atoms$ li'e o,y%en$ nitro%en an fluorine. The participatin% atoms can be locate on the same molecule -a !acent nucleoti es. or on ifferent DNA stran s.. <y ro%en bon s ifferent o not molecules -a !acent nucleoti es on

in"ol"e the e,chan%e or sharin% of electrons li'e co"alent an ionic bon s. The wea' attraction is li'e that between the opposite poles of a ma%net. <y ro%en bon s occur o"er short istances an can be easily forme an bro'en. They can also stabili(e a molecule. Stran s of one nucleoti e interacts with the base of another 0 base pairin% -wea' bon . Stran s of DNA are ma e of the su%ar an phosphate portions of the nucleoti es$ while the mi le parts are ma e of the nitro%enous bases. Stran s of DNA are ma e of the su%ar an phosphate portions of the nucleoti es$ while the mi le parts are ma e of the nitro%enous bases. The nitro%enous bases on the two stran s of DNA pair up$ purine with pyrimi ine -A with T$ A with C.$ an are hel to%ether by wea' hy ro%en bon s. A I T -2 hy ro%en bon s. 3. an C I A -3 hy ro%en bon s..B1JC -4i%.

4i%. 3. Stran s of DNA

2.3 &hat is DNA Computer%

A DNA computer$ as the name implies$ uses DNA stran s to store information an taps the recombinati"e properties of DNA to perform operations. A small test tube of DNA stran s suspen e in a solution coul yiel millions to billions of simultaneous interactions at spee s$ in theory$ faster than to ay/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%. <umans an most electronic computers attempt to sol"e the problem one process at a time -linear processin%.. DNA itself pro"i es the a e benefits of bein% a cheap$ ener%y0efficient resource. 2n a ifferent perspecti"e$ more than 13 trillion DNA molecules can fit into an area no lar%er than 1 cubic centimeter. With this$ a DNA computer coul hol 13 terabytes of ata an perform 13 trillion calculations at a time. 2n a tra itional computer$ ata are represente by an store as strin%s of (eros an ones. With a DNA computer$ a se&uence of its four

basic nucleoti es I a enine$ cytosine$ %uanine$ an thymine I is use to represent an store ata on a stran of DNA. Calculations in a tra itional 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 correspon in% 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 won erful 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. 2nstea 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$use to e,ecute the esire calculation. DNA + A uni,ue data structure The amount of information %athere on the molecular biolo%y of DNA o"er the last @3 years is almost o"erwhelmin% in scope. So instea of %ettin% bo%%e own in biochemical an biolo%ical etails of DNA$ 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 enco e with ones an (eros$ a stran of DNA is enco e with four bases$ represente by the letters A$ T$ C$ an A. The bases -also 'nown as nucleoti es. are space e"ery 3.3D nanometers alon% the DNA molecule$ %i"in% DNA a remar'able ata ensity of nearly 1K +bits per inch. 2n two imensions$ if you assume one base per s&uare nanometer$ the ata ensity is o"er one million Abits per s&uare inch. Compare this to the ata ensity of a typical hi%h performance har o"er 133$333 smaller. Another important property of DNA is its ouble stran e nature. The bases A an T$ an C an A$ 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 ATTACATCA$ its complement$ S/$ is TAATACAAC. 1oth S an S/ will come to%ether -or hybri i(e. to form ouble stran e DNA. This complementarity ma'es DNA a uni&ue ata structure for computation an can ri"e$ which is about J Abits per s&uare inch 00 a factor of

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 shoul n/t$ or insertin% a T for a A. DNA can also be ama%e by thermal ener%y an N= ener%y from the sun. 2f the error occurs in one of the stran s of ouble stran e DNA$ repair en(ymes can restore the proper DNA se&uence by usin% the complement stran as a reference. 2n this sense$ ouble stran e DNA is similar to a OA2D 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. 2n 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 13PM copie bases or in other wor s an error rate of 13P0M. -2n comparison$ har rates of only 13P013 for Oee 0Solomon correction.. perations in parallel 2n the cell$ DNA is mo ifie biochemically by a "ariety of en(ymes$ which are tiny protein machines that rea an process DNA accor in% to nature/s esi%n. There is a wi e "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$ 1iochemistry$ an 1iotechnolo%y ha"e e"elope techni&ues that allow us to perform many of these cellular functions in the test tube. 2t/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 C7N has a basic suite of operations li'e a ition$ 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. ri"es ha"e rea error

DNA as a soft#are

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Thin' of DNA as software$ an en(ymes as har ware. 7ut them to%ether in a test tube. The way in which these molecules un er%o chemical reactions with each other allows simple operations to be performe as a by0pro uct of the reactions. The scientists tell the e"ices what to o by controllin% the composition of the DNA software molecules. 2t/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. 2nstea 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 har ware molecules are mi,e in a solution it operates to completion without inter"ention$* sai nee e .* A sin%le stran of DNA is similar to a strin% consistin% of a combination of four ifferent symbols A A C T. +athematically this means we ha"e at our isposal a letter alphabet$ Q R SA AC TT to enco e information which is more than enou%h consi erin% that an electronic computer nee s only two i%its an for the same purpose. 2n a DNA computer$ computation ta'es place in test tubes or on a %lass sli e coate in 2@U %ol . The input an output are both stran s of DNA$ whose %enetic se&uences enco e certain information. A pro%ram on a DNA computer is e,ecute as a series of biochemical operations$ which ha"e the effect of synthesi(in%$ e,tractin%$ mo ifyin% an clonin% the DNA stran s.B3$@C Da"i <aw'sett$ the science !u %e at Auinness Worl Oecor s. *2f you want to present the output to the na'e eye$ human manipulation is

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3. perations on DNA

As concernin% the operations that can be performe on DNA stran s the propose mo els of DNA computation are base on "arious combinations of the followin% primiti"e bio0 operations: ('nthesi-ing a esire polynomial0len%th stran use in all mo els

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 ouble0stran e DNA into its sin%le0stran e complementary components by heatin% the solution. +eltin% in "itro is also 'nown un er the name of enaturation. Annealing : bon to%ether two sin%le0stran e complementary DNA se&uences by coolin% the solution. Annealin% in "itro is 'nown as hybri i(ation.

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

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Amplif'ing -copyin%.: ma'e copies of DNA stran s by usin% the 7olymerase Chain Oeaction 7CO. The DNA polymerase en(ymes perform se"eral functions inclu in% replication of DNA. The replication reaction re&uires a %ui in% DNA sin%le0stran calle template$ an a shorter oli%onucleoti e calle a primer$ that is anneale to it.

4i%. H. DNA Oeplication

1@

(eparating + the stran s by len%th usin% a techni&ue calle %el electrophoresis that ma'es possible the separation of stran s by len%th.

4i%. J. Separatin% DNA

1D

0/tracting + those stran s that contain a %i"en pattern as a substrin% by usin% affinity purification.

4i%. K. DNA ?,traction

1H

Cutting : DNA ouble0stran s at specific sites by usin% commercially a"ailable restriction en(ymes. Gne class of en(ymes$ calle restriction en onucleases$ will reco%ni(e a specific short se&uence of DNA$ 'nown as a restriction site. Any ouble0 stran e 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 stran s with compatible stic'y en s by usin% DNA li%ases. 2n ee $ another en(yme calle DNA li%ase will bon to%ether the en of a DNA stran to another stran .

1J

(ubstituting : substitute$ insert or elete DNA se&uences by usin% 7CO site0specific oli%onucleoti e muta%enesis.

4i%.13. DNA Substitution .ar$ing : sin%le stran s by hybri i(ation: complementary se&uences are attache to the stran s$ ma'in% them ouble0stran e . The re"erse operation is unmar'in% of the ouble0 stran s by enaturin%$ that is$ by etachin% the complementary stran s. The mar'e se&uences will be oublestran e while the unmar'e ones will be sin%le0stran e . Destro'ing : the mar'e stran s by usin% e,onucleases$ or by cuttin% all the mar'e stran s with a restriction en(yme an remo"in% all the intact stran s by %el electrophoresis. -1y usin% en(ymes calle e,onucleases$ either ouble0stran e or sin%le0 stran e 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%le0stran e or ouble0stran e form..

1K

Detecting and 1eading : %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. 2n Short$ DNA computers wor' by enco in% the problem to be sol"e in the lan%ua%e of DNA: the base0four "alues A$ T$ C an A. Nsin% this base four number system$ the solution to any concei"able problem can be enco e 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 stran s$ an the correct se&uences can be filtere out usin% %enetic en%ineerin% tools.atible stic'y en s by usin% DNA li%ases. 2n ee $ 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$%

1M

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 won erful informational molecule an hi%hly specific en(ymes that can uplicate information in DNA molecules or transmit this information to other DNA molecules. 2nstea 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 A -a enine. C -cytosine. A -%uanine. T -thymine. as the memory units an recombinant DNA techni&ues alrea y in e,istence carry out the fun amental operations. ; 2n a DNA computer$ computation ta'es place in test tubes or on a %lass sli e coate in 2@' %ol . ; The input an output both are stran s of DNA$ whose %enetic se&uences enco e 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%$ mo ifyin% an clonin% the DNA stran s. ; Their potential power un erscores how nature coul be capable of crunchin% number better an faster than the most a "ance silicon chips. ; The stu y 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 stran s of ouble0stran e DNA at ifferent positions lea"in% o"erhan%s of sin%le0stran e DNA. Two pieces of DNA may be re!oine if their terminal o"erhan%s are complementary. Complements are referre to as Wstic'y en s9. Nsin% these operations$ fra%ments of DNA may be inserte or elete from the DNA. be calle the Wsoftware9 use to e,ecute the esire calculation. A DNA computer uses the @ eo,yribonucleic aci s:

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; As state earlier DNA represent information as a pattern of molecules on a stran . ?ach stran represents one possible answer. ; 2n each e,periment$ the DNA is tailore so that all concei"able answers to a particular problem are inclu e . Oesearchers then sub!ect all the molecules to precise chemical reactions that imitate the computational abilities of a tra itional computer. 1ecause molecules that ma'e up DNA bin to%ether in pre ictable ways$ it %i"es a powerful 5search6 function. ; 2f the e,periment wor's$ the DNA computer wee s 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 13 trillion calculations %oin% on at the same time in "ery little space. ; DNA computin% is a fiel that hol s the promise of ultra0 ense 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 ma e 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 co e 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. 2nstea of usin% electrical si%nals to perform lo%ical operations$ these DNA lo%ic %ates rely on DNA co e. 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 bin in% them so they/re loc'e in an en 0to0en 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. 2f such a computer is e"er built$ scientists say that it will be more compact$ accurate an efficient than con"entional computers.

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