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8/4/2019 Presentation. Raashi
1/23
8/4/2019 Presentation. Raashi
2/23
A DNA computer is a molecularcomputer that worksbiochemically. It "computes"
using enzymes
Concept first thought byLeonard Aldeman, in 1994
To the naked eye, the DNA computer looks like clear
water solution in a test tube.
Instead of showing up on a computer screen, results
are analyzed using a technique that allows scientists
to see the length of the DNA output molecule.
Source : http://www.wiggler.gr/wp-content/maya_ii/
8/4/2019 Presentation. Raashi
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DNA computing was proposed as a means ofsolving a class of intractable computationalproblems ,in which the computing time can grow
exponentially with the problem size.(Liu et al. Nature, 403, 175-179 (13 January 2000)
Use of DNA based computers provides almost 2000
times more data storage capacity .
DNA computations may use a billion times less
energy than an electronic computer while storingdata in a trillion times less space.
Computing with DNA is highly parallel
8/4/2019 Presentation. Raashi
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Integrative knowledge is gaining momentum dayby day. The challenge to integrate biological
systems with the information systems is a huge one.
Molecular biology is a science more closely based
on concepts linked to arithmetic and computation.
The central dogma of life i.e. typically, replication,transcription and translation have the same form:
begin core action check point repeat end
8/4/2019 Presentation. Raashi
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There are two reasons for using molecular biologyto solve computational problems.
1) The information density of DNA is much greaterthan that of silicon : 1 bit can be stored inapproximately 1 nm3. Others storage media, suchas videotapes, can store 1 bit in 1012 nm3.
2) Operations on DNA are massively parallel: a testtube 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.
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Turing machine the simplest form
of a computer. It was the firstcomputer invented on paper(theoretically) (Turing, 1937).
It is a simple machine reading and modifying a tape
carrying a linear sequence of symbols.
Its most important feature is the requirement for aphysical separation between a string of symbols, thedata/program and a machine possessing specificproperties that enable it to manipulate (read andwrite on) the string of symbols.
Source : http://en.wikipedia.org/wiki/Turing_machine
8/4/2019 Presentation. Raashi
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y The genetic program had to be something that hadto continuously passed and in an exact manner
y The discovery of the processes
that organize the regulation of geneexpression
genetic code
Led to the idea that life could be represented asthe result of the expression of a program, viewed as
a linear string of symbols, the chain of nucleotides inDNA.
y Described as a recipe.
8/4/2019 Presentation. Raashi
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Proofs :
1) The basis of genetic engineering is the manipulationof DNA molecules and expression in foreign cells
2) Natural transformation, which identified DNA as thecarrier of the genetic program.
3) Horizontal gene transfer.
Thus, a large number of genes coming from theoutside can be expressed and understood by a ofbacterium.
8/4/2019 Presentation. Raashi
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Concept first thought by
Leonard Aldeman, in 1994
DNA is a double stranded helixwhere the two strands arelinked by base pairs A to T and
G to C. These nucleotideswould essentially take the placeof the binary code of 1's and 0'sused in the computers today.
A single strand of DNA is similarto a string consisting of acombination of four differentsymbols A G C T.
Picture source :
http://www.scq.ubc.ca/a-monks-
flourishing-garden-the-basics-
of-molecular-biology-explained/
8/4/2019 Presentation. Raashi
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Instead of using electrical impulses to represent bitsof information, the DNA computer uses the bio-chemical properties of these molecules by
examining the patterns of combination or growth ofthe molecules or strings.
In a DNA computer, computation takes place in test
tubes or on a glass slide coated in 24K gold.
DNA computers will work through the use of DNA-based logic gates. These would use DNA codes in
place of electrical signals as inputs to the DNA logicgates.
(Aldeman Science 266, 1021 (1994)
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y A program on a DNA computer is executed as aseries of biochemical operations, which have theeffect of
Synthesizing
Extracting
Ligating
Cutting
Modifying
Separating
Amplifying
Annealing
Cloning
8/4/2019 Presentation. Raashi
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The Hamiltonian Path Problem is to
start at node 1, end at node 5, and
visit each node exactly once
while following the available edges.
A DNA based computerProgram
was designed, by engineering
the DNA of Escherichia coli withSalmonella typhimurium Hin/hixC recombinase
system, to find the unique Hamiltonian path.(1472365)
(Baumgardneret al. JournalofBiologicalEngineering 2009)
Baumgardner et al. 2009
8/4/2019 Presentation. Raashi
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ALGORITHM
Input :A directed graph G with nvertices, anddesignated vertices 1 and 5.
Output : YES, if any path remains; NO, otherwise.
Generate paths in G randomly inlarge quantities
Reject all paths that do not beginwith 1 and do not end in 5.
Reject all paths that do notinvolve exactly n vertices.
Reject all paths that do notinvolve designated edges
8/4/2019 Presentation. Raashi
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For step 1, each node of the graph wasencoded as a random 20-base strand of DNA.
Then, for each edge of the graph, a different20-base oligonucleotide was generated thatcontains the second half of the source codeplus the first half of the target node.
For step 2, the product of step 1 was amplifiedby PCR using oligonucleotide primersrepresenting 1 and 5.
This amplified and thus retained only thosemolecules encoding paths that begin with 1and end with 5~1014 computations are carriedout in a single second.
8/4/2019 Presentation. Raashi
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For step 3, agarose gel electrophoresis was donewhich allowed separation and recovery of DNA
strands of the correct length.
The desired path, if it exists, would pass through all
seven nodes, each of which was assigned a length
of 20 bases. Thus PCR products encoding thedesired path would have to be 140 bp.
For step 4, The solution strand was filtered using
affinity chromatography
8/4/2019 Presentation. Raashi
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DNA-based computation in
living cells by engineeringEscherichia coli to address aclassic mathematical puzzle called the
Burnt Pancake Problem (BPP).
The burnt pancake probleminvolves a stack of pancakes of different sizes, each
of which has a golden and a burnt side. The aim isto sort the stack so the largest pancake is on thebottom and all pancakes are golden side up in the
fewest number of flips
(Haynes et al.JournalofBiologicalEngineering 2 2008 )
8/4/2019 Presentation. Raashi
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Flips of the DNA fragmentpancakes are driven by the
S. typhimurium Hin /hix DNArecombinase system in E.coli
DNA segments are sorted by
inversions to producedifferent permutations of apromoter and a tetracyclineresistance coding region;E.coli cells become antibiotic
resistant when the segmentsare properly sorted.
(Haynes et al.JournalofBiologicalEngineering 2 2008 )
8/4/2019 Presentation. Raashi
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8/4/2019 Presentation. Raashi
19/23
The type of bacteria known as magnetotactic bacteria,
contain structures called magnetosomes, In thepresence of a magnetic field, these induce a torque on
the bacteria, making them swim according to thedirection of the field.
An electronic microcircuit that contains both the
bacteria and an array of conductors that produce
magnetic fields has been developed . By carefullycontrolling which conductors are active, themicrocircuit can make the bacteria move in specific
directions.
A computer and an optical microscope provide afeedback loop, tracking the motion of the bacteria and
adjusting the conductors to achieve the desiredbehaviour
(Martel et al. The international journalofrobotics research2009)
8/4/2019 Presentation. Raashi
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E.coli has been programmed
to emit red or green florescentlight in response to varying
concentrations of a signal
chemical emitted by another
of E.coli
The cells glowed green when
they sensed a higher concentration
of the signal chemical and red when
They sensed a lower concentration.
The bulls eye pattern formulation
could help in detection of anthrax
Source : http://www.livescience.com/technology/050428_bacteria_computer.html
8/4/2019 Presentation. Raashi
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Advantages Disadvantages
Can perform millions of operationssimultaneously.
Generating solution sets forrelatively simple problems, mayrequire impractically large
amounts of memory.
Amount of working memoryFor every correct answer there
are millions of incorrect pathsgenerated that are worthless
Conduct large parallel searches.Still at a conceptual stage
Lesser energy dissipation
The first DNA computers are
unlikely to feature wordprocessing, e-mailing and solitaire
programs
Could be used by national
governments for cracking secretcodes, or by airlines wanting to
map more efficient routes etc..
8/4/2019 Presentation. Raashi
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Though still at a conceptual stage, the future of
bacteria as computers and making computersseems very bright owing to the extensive fast-paced research in this direction as the in-silico
technology has almost reached a plateau stage.The DNA based computers will surely be the next
generation computers, which would also be usedfor other allied purposes such as detection ofdiseases and also in intelligence systems for thecountry
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