DNA Computing

One can imagine the eventual emergence of a

general purpose computer consisting of nothing
more than a single macromolecule conjugated to a
ribosomelike collection of enzymes that act on it.

- Leonard Adleman

Himanshu C. Reddy
B070319EC
 Introduction To DNA
 Ever wondered where we would find the new
material needed to build the next generation of
microprocessors????
 HUMAN BODY (including yours!) ->
DNA computing.
 “Computation using DNA” but not “computation on
DNA”
 Initiated in 1994 by an article written by Dr.
Adleman on solving HDPP using DNA.
 Uniqueness Of DNA
Why is DNA a Unique Computational Element?

 Extremely dense information storage.

 Enormous parallelism.
 Extraordinary energy efficiency.
 Complementary structure.
 Dense Information Storage
 Consider that 1 gm of DNA is compared with
a normal CD.
 A CD can hold 800 MB of data.
 A 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.
 Dense Information Storage
 Just like a string of binary data is encoded with ones
and zeros, a strand of DNA is encoded with four
bases, represented by the letters A, T, C, and G.
 Bases are spaced at a distance of .35 nanometers
along the DNA
 Data density over 18 Mbits/inch.
 Data density is over a million Gbits/sq. inch (2D)
when compared to 7 Gbits/sq. inch in a high
performance HDD.
How Enormous is the Parallelism?
 A test tube of DNA can contain huge numbers
of strands.
 When an operation is done on the test tube,
each of these DNA strands in that tube
undergo the same operation simultaneously.
i.e. Parallel Operations.
 How Extraordinary is the Energy
Efficiency?
 Dr. Adleman, in his experiments, figured that
his DNA computer can run 2x1019 operations
per joule.
 A normal computer using Pentium i7 processor
is able to run 2x105 operations per joule.
 A 2006 Super Computer was able to perform
2x109 operations per joule.
 Complementary Structure
 The bases A and T, and C and G, can bind
together, forming base pairs.
 Every DNA strand has its complement structure.
 DNA and it’s complement bind together
(hybridize) to form a double stranded DNA.
 Presence of complementary structures makes
DNA a unique data structure for computation.
 Error correction is an exploitation of this property.
 Double Stranded DNA

A – Adenine
C – Cytosine
G – Guanine
T – Thymine
 Hamiltonian Path Problem (HPP)
(Travelling Salesman Problem)

 The use of DNA in doing mathematical (logic)

problems was first identified by Dr. Adleman
in 7 point HPP.
 Hamiltonian Path Problem (HPP)
(Travelling Salesman Problem)
 Consider a 4 city HPP.
 Encode this graph in a
DNA.
 Vertices are assigned a
random DNA sequence.
 Edges (flights) are formed
by concatenating the 1st
half of the destination city
and the 2nd half of the
originating city.
 Hamiltonian Path Problem (HPP)
(Travelling Salesman Problem)
 Each city also has a
complementary name.
 Synthesize all the cities
and flights.
 Mix all these sequences in
a common test tube along
with DNA ligase, salt, etc.
 Within a second, you have
a solution for this 4 point
HPP!.. HOW?
 Hamiltonian Path Problem (HPP)
(Travelling Salesman Problem)
 Atlanta-Boston meets the
Boston complement.
- GCAGTCGG

AGCCTGAC
 Now it encounters with
Boston-Chicago.
GCAGTCGGACTGGGCT

AGCCTGAC
 Hamiltonian Path Problem (HPP)
(Travelling Salesman Problem)

 At least one of the many molecules formed is

the Hamiltonian path.
 All the paths were created simultaneously.
 Now the problem is discarding the wrong
paths, and keeping the answer.
 Methods of Extraction
Three pivotal steps in DNA extraction

 Annealing
 Polymerase Chain Reaction
 Gel Electrophoresis
 Annealing
 Annealing, in genetics, means for DNA or RNA to pair
by hydrogen bonds to a complementary sequence, forming a
double-stranded polynucleotide.

 The term is often used to describe the binding of a DNA

probe, or the binding of a primer to a DNA strand during
a polymerase chain reaction (PCR).

 The term is also often used to describe the reformation

(renaturation) of complementary strands that were separated
by heat (thermally denatured).
 Annealing

Single
Stranded
DNA

Double Stranded (Hybrid) DNA

 Polymerase Chain Reaction
 Scientific technique to amplify a single or a
few pieces of DNA across several orders of
magnitude, in a way creating trillions of copies
of the specimen.
 Steps involved in PCR:
- Denaturation
- Annealing
- Elongation
Polymerase Chain Reaction
 Gel Electrophoresis
• Technique used for
separation of DNA using
electric field applied
through a gel matrix.
• Generally used to
measure the length of
the DNA strand
• Can also be used to
preserve DNA before
the initial operations
 Fishing the Necessary Molecule
 Use Annealing and PCR to replicate the DA with the
correct start and end city.
 Put one primer on Atlanta and one on Detroit.
 The right answer is replicated exponentially, while the
wrong paths are replicated linearly or not at all.
 Use Gel Electrophoresis to identify the molecules with
the right length.
 Use the affinity probe separation procedure to weed out
paths without all cities.
 The left out DNA is the required solution.
 What does DNA Computing follow?

 Not based on Deterministic.

 Stochastically driven operations.
 No Brute Force method.
 Uses Generate and Test method.
 Millions of operations done simultaneously.
 Drawbacks of DNA Computing (G&T
Method)
 HPP for higher number of vertices is solved
quicker in Si based computers.
 HPP of 200 vertices would required DNA
weighing more then the Earth.
 Computation time required to solve problems
with DNA computer doesn’t grow
exponentially, but the amount of DNA does.
Different Methods of DNA Computing

 DNA Zymes based Computing

 Enzymes based Computing
 Toehold Exchange Computing
 Algorithmic Self-Assembly

- All these employ the exact function of the three

basic logic gates – AND,OR,NOT
Current Scenario of DNA Computing
 Fredkin and Feynman Gates (Reversible Logic Gates) – Himanshu
Thapliyal and M.B Srinivas.
-Reversible Programmable Logic Array (RPLA).
 Israel scientists at Weizmann Institute of Science, Rehovot, unveiled
a programmable molecular computer that performs 330 trillion
operations, more than 1,00,000 the speed of a normal PC.
-DNA molecules and Enzymes Method is used.
-Next step involved powering a PC with a single DNA
molecule.
 After Adleman’s algorithm, based on it many other efficient
algorithms have been discovered for HPP.
 Japanese researchers successfully stored data on a bacteria’s DNA.
 Promising Future
 DNA Manipulation technology has rapidly improved in recent
years, and future advances may make DNA computers more
efficient.
 Researcher at U.S. Military are experimenting with DNA’s massive
parallelism to crack cryptic codes.
 University of Wisconsin is experimenting with chip-based DNA
computers.
 IBM (International Business Machines) has already started it’s
research on the DNA Microprocessor.
 Research is going on DNA Microchips, which will help to identify
BRCA1 and BRCA2 mutations in human beings (especially
women).
 Conclusions

 Invention of DNA Computing established that

Moore’s Law will never reach it’s end.
 Established a completely new chapter in the
finding of solutions for NP-problems.
 Established a new chapter in the nano-scale
operations.
 References
• Adleman, L.M. Computing with DNA. Scientific American. Vol.
279 (1998). Issue 2. 54-61.
• Adleman, L.M. Molecular Computation of Solutions to
Combinatorial Problems. Science. Vol. 266 (1994). 1021-1024.
• L.Adleman, P.Rothemund, S.Roweis, E.Winfree. On applying
molecular computation to the Data Encryption Standard. 2nd
DIMACS workshop on DNA based computers, Princeton, 1996 .
• Junghuei Chen, John H. Reif, DNA Computing: 9th
International Workshop on DNA Based Computers, DNA9
Madison, WI, USA June 2003, Revised Papers.
 Further Reading
• National Geographic Article, Computer Made
from DNA and Enzymes.
• Himanshu Thapliyal & M. B. Srinavas, An
Extension to DNA Based Fredkin Gate Circuits:
Design of Reversible Sequential Circuits using
Fredkin Gates.
• Will Ryu, DNA Computing, A Premier.
• Lipton R, DNA Solution of Hard Computational
Problems. Science. Vol. 268 (1995). 542-545.
Thank You..