Dna Computing

DNA Computing A State Of Art Technology

what is DNA computing ? The field of DNA computing is concerned with the possibility of performing computations using biological molecules. It is also concerned with understanding how complex biological molecules process information here an attempt to gain insight into new models of computation. So,DNA computer can be defined as a computer that “computes” using enzymes that react with DNA strands, causing reactions. These reactions act as a kind of simultaneous computing or parallel processing .

STEPS IN DNA COMPUTING v Here DNA is taken as software and enzymes as hardware.

They are put together in a test tube. The way in which these molecules undergo chemical reactions with each other allows simple operations to be performed as a byproduct of the reactions. The scientists tell the devices what to do by controlling the composition of the DNA software molecules. v To the naked eye, the DNA computer looks like clear water solution in a test tube. There is no mechanical device. A trillion bio-molecular devices could fit into a single drop of water. 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. 

DNA Parallelism FAST

DNA is modified biochemically by a variety of operational proteins called ENZYMES DNA has CUTTING, COPYING ,PASTING , REPAIRING as basic suite operations which allows it to perform even complex calculations. Enzymes work over many DNA molecules simultaneously providing DNA Parallelism.

DNA vs. SILICON n

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Transistor-based computers typically handle operations in a sequential manner. Of course there are multi-processor computers, and modern CPUs incorporate some parallel processing, but in general, in the basic von Neumann architecture computer, instructions are handled sequentially. A von Neumann machine, which is what all modern CPUs are, basically repeats the same "fetch and execute cycle" over and over again. DNA computers, however, are non-von Neuman, machines that approach computation in a different way from ordinary computers for the purpose of solving a different class of problems. When many copies of the replication enzymes are allowed to work on DNA in parallel, what happens after each replication is finished - the number of DNA strands increases exponentially (2^n after n iterations). With each additional strand, the data rate increases by 1000 bits/sec. This is beyond the sustained data rates of the fastest hard drives.

TRAVELLING SALESMAN ALGORITHM A hypothetical salesman tries to find a route through a set of cities so that he visits each city only once

Chicago

Source

Destination

Los Angeles

New York

Dallas

Miami

Adleman’s Experiment

Specifically, the method based on Adleman’s experiment would be as follows:

vGenerate all possible routes. vSelect itineraries that start with a proper city & end with the final city.

vSelect itineraries with correct number of cities.

vSelect itineraries that contain each city only once.

PART I: Generate all possible routes STRATEGY: 1) Encode city names in short DNA sequences. 2) Encode itineraries by connecting the city sequences for which routes exist

City Encoding Los Angeles Chicago Dallas Miami New York

GCTACG CTAGTA TCGTAC CTACGG ATGCCG

Synthesizing short single stranded DNA by

DNA SYNTHESIZER

PART I: Generate all possible routes STRATEGY: 1) Encode city names in short DNA sequences. 2) Encode itineraries by connecting the city sequences for which routes exist

Route Encoding

Miami CTA CGG

CTACGGATGCCG

Miami

New York

CGGATG New York ATG CCG

G C C TA G Hybridized DNA

Miami to New York GC CTAC

Output of Stage I

CTAGTA Chicago

GCTACG

ATGCCG

Los Angeles

New York Destination

Source

Dallas

TCGTAC

Miami

CTACGG

PART II : Select itineraries that start and end with the correct cities STRATEGY : Selectively copy & amplify only selection of DNA that start with Los Angeles & ends with New York .

START PRIMER

END PRIMER

CGATGC

TACGGC

GCTACG

ATGCCG

Los Angeles Source

New York Destination

Technique used is POLYMERASE CHAIN REACTION (PCR) Allows to produce many copies of a specific sequence of DNA

PART III : Select itineraries that contain the correct no. of cities STRATEGY: Sort the DNA by length & select the DNA whose length equals to five cities

+ VOLTAGE

Gel Matrix

DNA Starts here

Long DNA

Short DNA

- VOLTAGE

Generally DNA is –vely charged molecule but with constant charge density. GEL slows down DNA passing through it at different rates depending on it’s lengthProducing BANDS Technique used is: GEL ELECTROPHORESIS Used to resolve size of DNA

PART IV : Select itineraries that have a complete set of cities STRATEGY: Successively filter the DNA molecule by city, one city at a time

CGATGC

GATCAT

AGCATG

GATGCC

TACGGC

GCTACG

CTAGTA

TCGTAC

CTACGG

ATGCCG

LA to CHICAGO

CHICAGO to DALLAS

DALLAS to MIAMI

MIAMI to NEW-YORK

Technique used is: AFFINITY PURIFICATION Uses HYBRIDIZATION of DNA

DNA Computers Vs Classical Computers DNA-based computers

Classical computers

slow at individual operations

fast at individual operations

can do billions of operations simultaneously

can do substantially fewer operations simultaneously

can provide huge memory in small smaller memory. at most 10^14 bits space. One cubic centimeter of DNA soup could store as much as 10^21 bits of information. setting up a problem may involve considerable preparations

setting up only requires keyboard input

DNA is sensitive to chemical deterioration

electronic data are vulnerable but can be backed up easily

Conclusion n

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DNA , the genetic code of life itself , certainly has been the molecule of this century and most likely the next one. The future of DNA manipulation is speed, automation, and miniaturization. Perhaps it wont be used to play games or surf the web–things that traditional computers are good at—but it certainly might be used in the study of logic, encryption, genetic programming and algorithms, automata and lots of other things

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