Presentation. Raashi

8/4/2019 Presentation. Raashi

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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/


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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


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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


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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


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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.


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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.


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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/


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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


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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


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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


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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.


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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


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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 )


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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 )


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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)


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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


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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..


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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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Presentation. Raashi

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