SEMINAR

ON
DNA COMPUTING
 Presentation Outline

 Basic concepts of DNA

 Origin of DNA Computing
 Solution for NP-Complete Problems
 Advantages of DNA Computing
 Problems with Adleman’s Experiment
 DNA Computers
 Current research
 Conclusion
 What is DNA?
 DNA stands for Deoxyribonucleic Acid
 DNA represents the genetic blueprint of living
creatures
 DNA contains “instructions” for assembling
cells
 Every cell in human body has a complete set
of DNA
 DNA is unique for each individual
Double Helix shape of DNA

 The two strands of a DNA

molecule are anti parallel
where each strand runs in an
opposite direction.
 Complementary base pairs
Adenine & Thymine
Guanine & Cytosine
 Two strands are held together
by weak hydrogen bonds
between the complementary base
pairs
Graphical Representation of inherent bonding
properties of DNA
 Instructions in DNA
Sequence to indicate the
start of an instruction

………

Instruction that triggers

Instruction for hair cells
Hormone injection
 Instructions are coded in a sequence of the DNA
bases
 A segment of DNA is exposed, transcribed and
translated to carry out instructions
DNA Duplication
 Protein Synthesis
 DNA  RNA  Proteins  actions
 Basics and
Origin of DNA Computing
 DNA computing is utilizing the property of DNA for
massively parallel computation.

 With an appropriate setup and enough DNA, one can

potentially solve huge problems by parallel search.

 Utilizing DNA for this type of computation can be much

faster than utilizing a conventional computer

 Leonard Adleman proposed that the makeup of DNA and

its multitude of possible combining nucleotides could
have application in computational research techniques
 Dense Information Storage
 This image shows 1 gram
of DNA on a CD. The CD
can hold 800 MB of data.

 The 1 gram of DNA can

hold about 1x1014 MB of
data.

 The 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.
 How Dense is the Information Storage?

 with 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.
 Check this out………..
 How enormous is the parallelism?

 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 !

 Check this out……. We Typically use

 How extraordinary is the energy
efficiency?
 Adleman figured his computer was running
2 x 1019 operations per joule.
 NP Complete Problems
 A hard NP problem is one in which the time required
for algorithms to find a solution increases exponentially
with the number of variables involved.
 A hard NP problem can eat up a lot of computer cycles
if carried out by brute force. For example, the Hamilton
path problem —commonly known as the traveling
salesman problem —is a hard NP problem.
 If there are N cities in a Hamilton path problem, there
are N!/2 possible paths, where N! is N factorial, which
is the multiplication of every integer from 1 to N —for
example, 4!= 1 x 2 x 3 x 4.
 Inventor Of DNA Computing: Adleman

 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.
 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.
 Steps for Adleman’s Experiment

 Strands of DNA represent the seven cities. In genes,

genetic coding is represented by the letters A, T, C and
G. Some sequence of these four letters represented
each city and possible flight path.
 These molecules are then mixed in a test tube, with
some of these DNA strands sticking together. A chain of
these strands represents a possible answer.
 Within a few seconds, all of the possible combinations of
DNA strands, which represent answers, are created in
the test tube.
 Adleman eliminates the wrong molecules through
chemical reactions, which leaves behind only the flight
paths that connect all seven cities.
 Adleman’s Experiment
 Hamilton Path Problem
(also known as the travelling salesperson problem)
Darwin

Perth Alice Spring Brisbane

Sydney

Melbourne

Is there any Hamiltonian path from Darwin to Alice Spring?

 Adleman’s Experiment (Cont’d)
 Solution by inspection is:
Darwin  Brisbane  Sydney  Melbourne  Perth 
Alice Spring
 BUT, there is no deterministic solution to this
problem, i.e. we must check all possible
combinations. Darwin
Brisbane
Perth
Alice Spring

Sydney

Melbourne
 Adleman’s Experiment (Cont’d)
• Encode each city with complementary base -
vertex molecules
Sydney - TTAAGG
Perth - AAAGGG
Melbourne - GATACT
Brisbane - CGGTGC
Alice Spring – CGTCCA
Darwin - CCGATG
 Adleman’s Experiment (Cont’d)

• Encode all possible paths using the

complementary base – edge molecules
Sydney  Melbourne – AGGGAT
Melbourne  Sydney – ACTTTA
Melbourne  Perth – ACTGGG
etc…
 Adleman’s Experiment (Cont’d)
• Merge vertex molecules and edge molecules.

All complementary base will adhere to each other to

form a long chains of DNA molecules
Solution with Merge Solution with
vertex DNA & edge DNA
molecules Anneal molecules

Long chains of DNA molecules (All

possible paths exist in the graph)
 Adleman’s Experiment (Cont’d)

 The solution is a double helix molecule:

Darwin Brisbane Sydney Melbourne Perth Alice Spring
CCGATG – CGGTGC – TTAAGG – GATACT – AAAGGG – CGTCCA

TACGCC – ACGAAT – TCCCTA – TGATTT – CCCGCA

Darwin Brisbane Sydney Melbourne Perth

Brisbane Sydney Melbourne Perth Alice Spring
The success of the Adleman DNA computer proves that
DNA can be used to calculate complex mathematical
problems.
Three years after Adleman's experiment, researchers at
the University of Rochester developed logic gates made of
DNA.
Currently, logic gates interpret input signals from silicon
transistors, and convert those signals into an output signal
that allows the computer to perform complex functions.
But the logic gates made up DNA instead of using
electrical signals to perform logical, rely on DNA code.
They detect fragments of genetic material as input, splice
together these fragments and form a single output.
 For instance, a genetic gate called the "And gate" links
two DNA inputs by chemically binding them so they're
locked in an end-to-end structure.

 The researchers believe that these logic gates might be

combined with DNA microchips to create a breakthrough
in DNA computing.
 Operations
 Melting
breaking the weak hydrogen bonds in a double helix
to form two DNA strands which are complement to
each other
 Annealing
reconnecting the hydrogen bonds between
complementary DNA strands
 Operations (Cont’d)
 Merging
mixing two test tubes with many DNA molecules
 Amplification
DNA replication to make many copies of the original
DNA molecules
 Selection
elimination of errors (e.g. mutations) and selection of
correct DNA molecules
 Extraction
 given a test tube T and a strand s, it is possible to extract all the strands in T
that contain s as a subsequence, and to separate them from those that do not
contain it.

Spooling the DNA with a metal

hook or similar device

Precipitation of more DNA

strands in alcohol
Formation of DNA strands.
 Advantages of a DNA Computer
 Parallel Computing- DNA computers are massively
parallel.

 Incredibly light weight- With only 1 LB of DNA you

have more computing power than all the computers ever
made.

 Low power- The only power needed is to keep DNA

from denaturing.

 Solves Complex Problems quickly- A DNA computer

can solve hardest of problems in a matter of weeks.
 Cont……
 Perform millions of operations simultaneously.

 Generate a complete set of potential solutions.

 Efficiently handle massive amounts of working memory.

 cheap, clean, readily available materials.

 amazing ability to store information.

Current Research
 Soft Molecular Computing
 DNA Computing utilizes the complex interaction of bio
molecules and molecular biology to effect computation

 Lab experiments in DNA Computing are unreliable,

inefficient, unscalable and expensive compared to
conventional computing standards

 A critical issue in DNA Computing is to test protocols

 So we will describe a platform EDNA, to address this

problem.
 EDNA,integrated software platform
 Address the basic problems of reliability, efficiency and
scalability for molecular protocols using DNA molecules.

 Allows to take advantage of digital computers to gain

realistic insights on actual test tube performance of a
protocol before they are carried out in the lab.

 It is a research tool that makes it possible to use the

advantages of conventional computing to bring to DNA
computing comparable levels of reliability and efficiency.
 EDNA
 EDNA is object oriented and extensible, so that it can
easily evolve as the field progresses.

 EDNA is therefore a research tool that makes it possible

to use the advantages of conventional computing to
make DNA computing reliable.

 EDNA includes graphical interfaces and click-and-drag

facilities to enable easy use.
 DNA Authentication
 Taiwan introduced the world's first DNA authentication
chip.

 The first DNA chip in the world has finally been

developed by Biowell Technology Inc. after two years of
research.

 Inside the chip is synthesized DNA, which can be

identified by a device similar to an identification card or a
credit card reader.

 Suggestions have been made to make use of DNA chips

on national identification cards in order to crack down on
frauds using fake ID cards.
 DNA Authentication
 The synthesized DNA inside the chip generates DNA
signals which only the company's readers can detect and
authenticate in two seconds.

 The DNA chip can also be used on passports, credit

cards, debit cards, membership cards, driver's licenses,
automobile license plates, CDs, VCDs, DVDs,
notebooks, PDAs, computer software.

 In addition to the absolute security of the DNA

authentication systems, the price of the DNA
authentication product is comparable to that of IC chip.
DNA Chip
 What are the challenges?
 Error: Molecular operations are not perfect.

 Reversible and Irreversible Error

 Efficiency: How many molecules contribute?

 Encoding problem in molecules is difficult

 Scaling to larger problems

What are the challenges for
Computer Science?
 Discover problems DNA Computers are
good at
o Messy reactions as positive
o Evolvable, not programmable
 Characterize complexity for DNA
computations with bounded resources
 New notions of what a “computation” is?
 What are the challenges for
molecular biology?
 Develop computation-specific protocols
 Better understanding of basic mechanisms
and properties
 Better characterization of processes
 Measures of reliability and efficiency
 Advanced understanding of biomolecules
other than DNA and RNA
 What developments can we
expect in the near-term?
 Increased use of molecules other than DNA
 Evolutionary approaches
 Continued impact by advances in molecular
biology
 Some impact on molecular biology by DNA
computation
 Increased error avoidance and detection
 What are the long-term
prospects?
 Cross-fertilization among evolutionary
computing, DNA computing, molecular
biology, and computation biology

 Niche uses of DNA computers for problems

that are difficult for electronic computers

 Increased movement into exploring the

connection between life and computation?
LIMITATIONS
 DNA Vs Electronic computers

 At Present,NOT competitive with the state-of-the-

art algorithms on electronic computers
o Only small instances of HDPP can be solved.Reason?..for
n vertices, we require 2^n molecules.
o Time consuming laboratory procedures.
o Good computer programs that can solve TSP for 100
vertices in a matter of minutes.
o No universal method of data representation.
 Size restrictions
 Adleman’s process to solve the traveling
salesman problem for 200 cities would require
an amount of DNA that weighed more than the
Earth.

 The computation time required to solve

problems with a DNA computer does not grow
exponentially, but amount of DNA required
DOES.
 Error Restrictions
 DNA computing involves a relatively large
amount of error.

 As size of problem grows, probability of

receiving incorrect answer eventually becomes
greater than probability of receiving correct
answer
 Cont…..

High cost is time.

Occasionally slower-Simple problems are solved

much faster on electronic computers.

Reliability- There is sometime errors in the pairing

of DNA strands
 Some more……….

 Different problems need different approaches.

 requires human assistance!

 DNA in vitro decays through time,so lab procedures should

not take too long.

 No efficient implementation has been produced for testing,

verification and general experimentation.
 THE FUTURE!
 Algorithm used by Adleman for the traveling salesman problem was simple. As
technology becomes more refined, more efficient algorithms may be discovered.

 DNA Manipulation technology has rapidly improved in recent years, and future
advances may make DNA computers more efficient.

 The University of Wisconsin is experimenting with chip-based DNA computers.

 DNA computers are unlikely to feature word processing, emailing and solitaire
programs.

 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.
 THANK YOU!!!!!

It will take years to develop a practical,

workable DNA computer.

But…Let’s all hope that this DREAM comes

true!!!

Pratibha Rathore
VIII Sem