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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.
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