DNA Computing

A State Of Art Technology

COMPILED BY:
LIPSA PRADHAN
T. AMRITA RAO
CET BBSR
 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
 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.
 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
 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:

Generate all possible routes.

Select itineraries that start with a proper
city & end with the final city.
Select itineraries with correct number of
cities.
Select 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 GCTACG

Chicago CTAGTA
Dallas TCGTAC
Miami CTACGG
New York 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 CTACGGATGCCG
CTA CGG
Miami New York Miami to New York
GC CTAC
CGGATG
New York
G C C TA G
ATG CCG
Hybridized DNA
 Output of Stage I

CTAGTA
Chicago

GCTACG ATGCCG
Los Angeles New York

Source Destination

Dallas Miami
TCGTAC 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 END
PRIMER PRIMER
CGATGC TACGGC

GCTACG ATGCCG
Los Angeles New York

Source 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
Generally DNA is –vely charged
DNA Starts here molecule but with constant
charge density.
Gel Matrix

GEL slows down DNA passing

Long DNA through it at different rates
depending on it’s length-
Producing BANDS

Short DNA Technique used is: GEL

ELECTROPHORESIS
- VOLTAGE 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 to DALLAS to MIAMI to
CHICAGO DALLAS MIAMI 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 can do substantially fewer

simultaneously 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 setting up only requires keyboard

considerable preparations input

DNA is sensitive to chemical electronic data are vulnerable but

deterioration can be backed up easily
Conclusion
 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 that haven’t even been
invented yet.