DNA Computing

By: Libin Lukose Emmanuel

1NH05IS020
 Fundamentals about
DNA Structure
ØDNA is Deoxyribo Nucleic Acid and is the building
block of all living beings
Ø
ØIt is a polynucleotide and has a double helical structure
Ø
ØIt is made of nucleotides
Adenine(A),Guanine(G),Thiamine(T) and Cytosine( C)
Ø
ØAdenine bonds only with Thiamine and Guanine bonds
only with Cytosine
Ø
ØThe two helix are complimentary of each other
Basics and Origin of DNA
Computing
Ø In 1994, Leonard Adleman, scientist at the university of
 California, introduced the idea of using DNA to solve
 complex mathematical problems
Ø
Ø Leonard Adleman proposed that the makeup of DNA
 and its multitude of possible combining nucleotides
 could have application in computational research techniques
Ø
Ø DNA computing is utilizing the property of DNA for massively parallel computation
Ø
Ø With an appropriate setup and enough DNA, one can potentially solve huge problems
by parallel search
Ø
Ø Utilizing DNA for this type of computation can be much faster than utilizing a
conventional computer

 What is DNA Computing
Ø The field of DNA computing is concerned with the possibility of
performing computations using biological molecules.


Ø It is also concerned with understanding how complex biological

molecules process information here an attempt to gain insight
into new models of computation.
Ø
Ø 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.
 How does it work?
Ø Use specially coded DNA as initial conditions for biological
reaction
Ø
Ø DNA is taken as software and enzymes as hardware.


Ø Natural enzymes duplicate DNA



Ø Matching DNA base pairs attach to each other



Ø Find answer in resulting soup of DNA strands


 Why is it interesting?
Ø Cross-discipline (CS meets Molecular Biology)


Ø High data density



Ø Massively parallel


Ø Energy efficient


Ø Potential to perform computation inside the body

 Dense Information
Storage
ØThis image shows 1 gram of DNA on a
CD.The CD can hold 800 MB of data.
Ø
ØThe 1 gram of DNA can hold about 1x1014
MB of data.
Ø
ØThe number of CDs required to hold this
amount of information, lined up edge to edge,
would circle the Earth 375 times, and would
take 163,000 centuries to listen to.
Ø
ØWith bases spaced at 0.35 nm along DNA,
data density is over a million Gbits/inch
compared to 7 Gbits/inch in typical high
performance HDD
Ø
 How enormous is the
parallelism?
Ø A test tube of DNA can contain trillions of strands. Each
operation on a test tube of DNA is carried out on all strands in
the tube in parallel !
Ø Enzymes work over many DNA molecules simultaneously
providing DNA Parallelism.
Ø Each DNA strand represents a processor !
Ø
Ø Desktop PC : 109 ops/sec
Ø Supercomputer : 1012 ops/sec
Ø 1 µmol of DNA : 1026 reactions…(isn’t amazing)




 How extraordinary is the
energy efficiency?
ØAdleman figured out that his computer was running 2 x
1019 operations per joule.

 Inventor Of DNA
Computing:
Leonard Adleman
Ø Adleman is often called the inventor of DNA computers. His
article in a 1994 issue of the journal Science outlined how to
use DNA to solve a well-known mathematical problem, called
the directed Hamilton Path problem, also known as the
"traveling salesman" problem.
Ø
Ø The goal of the problem is to find the shortest route between a
number of cities, going through each city only once. As you
add more cities to the problem, the problem becomes more
difficult. Adleman chose to find the shortest route between
seven cities using a brute force approach.

RAVELLING 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
Steps in Adleman’s
experiment would be
as follows:
1)Generate all possible routes
2)
3)Select itineraries that start and end with the correct cities
4)
5)Select itineraries that contain the correct number of cities
6)
7)Select itineraries that have a complete set of cities
 Generate all possible
STEP I:
routes
STRATEGY: 1)Encode city names in short DNA sequences.
2)Encode itineraries by connecting the city sequence for
 which routes exist

City Encodings

Los Angeles GCTACG

Chicago CTAGTA
Dallas TCGTAC
Miami CTACGG
New York ATGCCG

Synthesizing short single stranded DNA by DNA SYNTHESIZER

G e n e ra tio n o f d iffe re n t
Itin e ra rie s
Route Encoding

Miami
C T A C G G A T G C CG
CTA CGG
Miami New York Miami to New York
GC CTAC
CGG ATG
New York
G C C TA C
ATG CCG
Hybridized DNA
 Output of Step I

C T A G T A

Chicago
G C T A C G A T G C C G
Los Angeles New York
Source Destinatio
n

Dallas Miami
T C G T A C C T A C G G
 S T E P II: Select itineraries that
start and end with the correct
cities
Technique used is: POLYMERASE CHAIN REACTION (PCR)
Allows to produce many copies of a specific sequence of DNA
ØPolymerase Chain Reaction is iterative and uses an enzyme called polymerase
ØPolymerase copies a section of single stranded DNA starting at the position of
the primer, which is DNA complimentary to one end of the interested section.

START END
PRIMER PRIMER
CGATGC TACGGC

GCTACG ATGCCG
Los Angeles New York

Source Destination
 STEP III : Select itineraries that
contain the correct number of
cities
STRATEGY: Sort the DNA by length & select the DNA whose length equals to
five cities
Technique used is: GEL ELECTROPHORESIS
Used to resolve size of DNA
+ VOLTAGE
DNA Starts here ØGel Electrophoresis force the DNA through
a gel matrix by using an electric field.
Ø
ØGenerally DNA is –vely charged molecule
Gel Matrix

but with constant charge density.

Ø
Long DNA ØGEL slows down the DNA passing through
it at different rates depending on it’s length
producing DNA bands.

Short DNA
- VOLTAGE
 Select itineraries that
STEP IV :
have a complete set of cities
Technique used is: AFFINITY PURIFICATION
Uses HYBRIDIZATION of DNA

CGATGC GATCAT AGCATG GATGCC TACGGC

GCTACG CTAGTA TCGTAC CTACGG ATGCCG

LA to CHICAGO to DALLAS to MIAMI to

CHICAGO DALLAS MIAMI NEW-YORK
ØAffinity purification is done by attaching the compliment of the sequence in question to a
substrate like magnetic bead.
ØThe DNA which contains the sequence hybridizes with the complement sequence on the
beads
ØGraduated PCR can also be used if we already have the sequence of city encodings.
 First DNA computer
:-MAYA II
Ø Stand for (Molecular Array of YES and AND logic gate )
Ø Replacing the normally silicon-based circuits, this chip has DNA
strands to form the circuit
Ø MAYA-II has more than 100 DNA circuits

 Applications

Ø DNA sequencing
Ø DNA fingerprinting
Ø DNA mutation detection
Ø The fabrication of nanoscale objects
Ø The replacement of silicon devices
Ø Design of expert systems
Ø Medical diagnosis, drug discovery
Ø To Solve NP-Complete Problems
 LIMITATIONS
Ø The computation time required to solve problems with a DNA computer does
not grow exponentially, but amount of DNA required DOES.
Ø
Ø DNA computing involves a relatively large amount of error
Ø
Ø High cost is time.
Ø
Ø Different problems need different approaches.
Ø
Ø Requires human assistance!
Ø
Ø No efficient implementation has been produced for testing, verification and
general experimentation

 THE FUTURE!
Ø Algorithm used by Adleman for the traveling salesman problem was simple.
As technology becomes more refined, more efficient algorithms may be
discovered.
Ø
Ø DNA Manipulation technology has rapidly improved in recent years, and
future advances may make DNA computers more efficient.
Ø
Ø The University of Wisconsin is experimenting with chip-based DNA
computers.
Ø
Ø DNA computers are unlikely to feature word processing, emailing and
solitaire programs.
Ø
Ø Instead, their powerful computing power will be used for areas of encryption,
genetic programming, language systems, and algorithms or by airlines
wanting to map more efficient routes. Hence better applicable in only some
promising areas.

 Conclusion
ØThe paradigm of DNA computing has lead to a very important theoretical
research.
Ø
ØThe beauty of DNA research trends is found in the possibility of mankind’s
utilization of its very life building blocks to solve its most difficult problems.
Ø
Ø
ØThe field of DNA computing is still in its infancy and the applications for this
technology are still not fully understood.
Ø
ØIs DNA computing viable – perhaps, but the obstacles that face the field such as
the extrapolation and practical computational environments required are daunting.

Queries?