DNA COMPUTING

Swati Bandhewal
CSE 2nd yr
GS10UE0409

Overview
Introduction to DNA
What is DNA computing
Adlemans Hamiltonian path problem.
Cutting Edge Technologies
Pros and Cons
DNA Vs Electronic Computers
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
Sides
Sugar-phosphate backbones
ladders
complementary base pairs
Adenine & Thymine
Guanine & Cytosine
Two strands are held together by
weak hydrogen bonds between the
complementary base pairs

Uniqueness of DNA
Why is DNA a Unique Computational
Element???
Extremely dense information storage.
Enormous parallelism.
Extraordinary energy efficiency.

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

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.

Instructions in DNA
Sequence to indicate
the start of an
instruction

Instruction that
Instruction for hair cells
triggers
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

A Little More
Basic suite of operations:
AND,OR,NOT & NOR in CPU while cutting,
linking, pasting, amplifying and many
others in DNA.
Complementarity makes DNA unique.

Can DNA compute?

DNA itself does not carry out any

computation. It rather acts as a massive

memory.
BUT, the way complementary bases react
with each other can be used to compute
things.
Proposed by Adelman in 1994

DNA COMPUTING
Acomputerthat uses DNA

(deoxyribonucleic acids) to store

information and perform complex
calculations.
The main benefit of using DNA computers
to solve complex problems is that different
possible solutions are created all at once.
This is known asparallel processing.

Adlemans 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?

Adlemans Experiment
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
Perth

Brisbane
Alice Spring
Sydney
Melbourne

Adlemans Experiment
1. Encode each city with complementary base vertex molecules
Sydney - TTAAGG
Perth - AAAGGG
Melbourne - GATACT
Brisbane - CGGTGC
Alice Spring CGTCCA
Darwin - CCGATG

Adlemans Experiment
(Contd)

2. Encode all possible paths using the

complementary base edge molecules
Sydney Melbourne AGGGAT
Melbourne Sydney ACTTTA
Melbourne Perth ACTGGG
etc

Adlemans Experiment
(Contd)

3. Merge vertex molecules and edge molecules.

All complementary base will adhere to each other to
form a long chains of DNA molecules
Solution with
vertex DNA
molecules

Merge
&
Anneal

Solution with
edge DNA
molecules

Long chains of DNA molecules (All

possible paths exist in the graph)

Adlemans Experiment
(Contd)

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
Alice Spring
Brisbane Sydney Melbourne Perth

Operations (Contd)
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

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.

DNA Chip

Chemical IC

The Smallest Computer

The smallest programmable DNA computer
was developed at Weizmann Institute in
Israel by Prof. Ehud Shapiro last year
It uses enzymes as a program that
processes on 0n the input data (DNA
molecules).

Pros and Cons

+ Massively parallel processor
DNA computers are very good to solve Nondeterministic Polynomial problems such as
DNA analysis and code cracking.
+ Small in size and power consumption

Pros and Cons (Contd)

- Requires constant supply of proteins and
enzymes which are expensive
- Errors occur frequently
a complex selection mechanism is required
and errors increase the amount of DNA
solutions needed to compute
- Application specific
- Manual intervention by human is required

DNA Vs Electronic
computers

At Present, NOT competitive with the state-

of-the-art algorithms on electronic

computers
Only small instances of HDPP can be
solved. Reason?..for n vertices, we require
2^n molecules.
Time consuming laboratory procedures.
Good computer programs that can solve
HSP for 100 vertices in a matter of
minutes.
No universal method of data

Conclusion
Many issues to be overcome to produce a
useful DNA computer.
It will not replace the current computers
because it is application specific, but has a
potential to replace the high-end research
oriented computers in future.

Thank you