DNA Computing

Sanjib Mondal
Student, MCSE 2010-11
Roll- 001010502031
Introduction:
What is DNA computing ?
Around 1950 first idea (precursor Feynman)
First important experiment 1994: Leonard Adleman
Molecular level (just greater than 10-9 meter)
Massive parallelism.
In a liter of water, with only 5 grams of DNA we get
around 1021 bases !
Each DNA strand represents a processor !
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 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.
A bit of biology
The DNA is a double stranded molecule.
Each strand is based on 4 bases:
 Adenine (A)
 Thymine (T)
 Cytosine (C)
 Guanine (G)
Those bases are linked through a sugar (desoxyribose)
IMPORTANT:
 The linkage between bases has a direction.
 There are complementarities between bases (Watson-Crick).
(A) (T)
(C)(G)
DNA manipulations:
If we want to use DNA as an information bulk, we
must be able to manipulate it .
However we are talking of handling molecules…
ENZYMES = Natural CATALYSERS.
So instead of using physical processes, we would
have to use natural ones, more effective:
for lengthening: polymerases…
for cutting: nucleases (exo/endo-nucleases)…
for linking: ligases…
Serialization: 1985: Kary Mullis  PCR
Thank this reaction we get millions of identical strands, and we are
allowed to think of massive parallel computing.
And what now ?
Situation:
Molecular level.
Lots of “agents”. (strands)
Tools provided by nature. (enzymes)
How can we use all this? If there is a utility …
Coding the information:
1994: THE Adleman’s experiment.
Given a directed graph can we find an hamiltonian
path (more complex than the TSP).
In this experiment there are 2 keywords:
massive parallelism (all possibilities are generated)
complementarity (to encode the information)
 This experiment proved that DNA computing wasn’t just a theoretical
study but could be applied to real problems like cryptanalysis
(breaking DES ).
Adleman experiment:
Input: A directed graph G with n vertices, and designated
vertices vin and vout.
Step 1: Generate paths in G randomly in large quantities.
Step 2: Reject all paths that
 do not begin with vin and
 do not end in v .
out

Step 3: Reject all paths that do not involve exactly n vertices.

Step 4: For each of the n vertices v:
 reject all paths that do not involve v.
Output: YES, if any path remains; NO, otherwise.
Example
Step 1
Each node of the graph was encoded as a random 20-
base strand of DNA.
For each edge of the graph, a different 20-base
oligonucleotide was generated that contains the
second half of the source code plus the first half of the
target node.
Step 1
City DNA Name Complement
ATLANTA ACTTGCAG TGAACGTC
BOSTON TCGGACTG AGCCTGAC
CHICAGO GGCTATGT CCGATACA
DETROIT CCGAGCAA GGCTCGTT

City DNA Flight Number

Atlanta - Boston GCAGTCGG
Atlanta - Detroit GCAGCCGA
Boston - Chicago ACTGGGCT
Boston - Detroit ACTGCCGA
Boston - Atlanta ACTGACTT
Chicago - Detroit ATGTCCGA
Step 2
the product of step 1 was amplified by PCR using
oligonucleotide primers representing  vin and vout and
ligase enzyme.
This amplified and thus retained only those molecules
encoding paths that begin with vin and end with vout.
~1014 computations are carried out in a single second.
Step 3
Product of step 2 is run on agarose gel and the 140bp
(since 7 vertices) band was excised and soaked in
doubly distilled H2O to extract DNA.
This product is PCR amplified and gel purified several
times to enhance its purity.
Step 4
It was accomplished by successive use of affinity
purification for each node other than the start and end
nodes.
The solution strand has to be filtered from the test
tube:
GCAG TCGG ACTG GGCT ATGT CCGA
Atlanta → Boston → Chicago → Detroit
Conclusion on HDPP
We see in a graph with n vertices, there are a possible (n-1)!
permutations of the vertices between beginning and
ending vertex.
To explore each permutation, a traditional computer must
perform O(n!) operations to explore all possible cycles.
However, the DNA computing model only requires the
representative oligos. Once placed in solution, those oligos
will anneal in parallel, providing all possible paths in the
graph at roughly the same time. That is equivalent to O(1)
operations, or constant time. In addition, no more space
than what was originally provided is needed to contain the
constructed paths.
Disadvantages
 Generating solution sets, even for some relatively simple problems,
may require impractically large amounts of memory (lots and lots of
DNA strands are required)
 Many empirical uncertainties, including those involving: actual error
rates, the generation of optimal encoding techniques, and the ability to
perform necessary bio-operations conveniently in vitro (for every
correct answer there are millions of incorrect paths generated that are
worthless).
 DNA computers could not (at this point) replace traditional
computers. They are not programmable and the average dunce can not
sit down at a familiar keyboard and get to work.
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!!!