DNA COMPUTERS

1.INTRODUCTION

What is a DNA Computer?

DNA computers can be defined as the use of biological molecules,

primarily DNA (or RNA), to solve computational problems that are adapted
to this new biological format.

Basics of DNA Computing

1. DNA computing is utilizing the property of DNA for massively parallel

computation.

2. With an appropriate setup and enough DNA, one can potentially solve huge
problems by parallel search.

3. Utilizing DNA for this type of computation can be much faster than utilizing a
conventional computer.

4. Leonard Adleman proposed that the makeup of DNA and its multitude of
possible combining nucleotides could have application in computational research
techniques.

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2.UNIQUENESS OF DNA

1. Can store information at the nanoscale

– 1 gram can store as much information as would

fit on 1 trillion CD's.

 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.

2. Can be synthesized quickly and cheaply.

– 1017 copies of a short sequence costs less than
CAN$50.
3. Can be copied, or sorted by length.
4. Enormous 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.
5. Extraordinary energy efficiency.

–Adleman figured his computer was running

2 x 1019 operations per joule.

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3.ADLEMAN’s SOLUTION OF THE HAMILTONIAN

DIRECTED PATH PROBLEM (HDPP).

I believe things like DNA computing will eventually

lead the way to a “molecular revolution,” which
ultimately will have a very dramatic effect on the world. – L. Adleman

Traveling Salesman Problem:

Find a path from city 1 to city 7 going through all the cities only once.

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The following algorithm solves the Hamiltonian Path

problem.

1. Generate random paths through the graph.

2. Keep only those paths that begin with the start city (1) and conclude with the end city

(7).

3. If the graph has n cities, keep only those paths with n cities. (n=7).

4. Keep only those paths that enter all cities at least once.

5. Any remaining paths are solutions.

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Encode Graph into DNA sequences

Step 1 : Represent each city by a single DNA strand 20

nucleotides long randomly chosen.

The molecules can be made by a machine called DNA Synthesizer.

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Represent the route between any two cities by a single DNA

strand 20 nucleotides long.

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Step 2: Select paths that start and end with the correct cities.

1. Millions of strands of DNA representing every city and every possible route between
any two cities are placed in a test tube where the strands combine.

2. We select only strings that have City 1 at one end and City 7 at the other by using
Polymerase Chain Reaction (PCR).

The polymerase chain reaction (PCR) is a biochemistry and molecular biology

technique for exponentially amplifying DNA, via enzymatic replication, without using a
living organism (such as E. coli or yeast). As PCR is an in vitro technique, it can be
performed without restrictions on the form of DNA, and it can be extensively modified to
perform a wide array of genetic manipulations.

PCR is commonly used in medical and biological research labs for a variety of tasks,
such as the detection of hereditary diseases, the identification of genetic fingerprints, the
diagnosis of infectious diseases, the cloning of genes, paternity testing, and DNA
computing.

PCR was invented by Kary Mullis. At the time he thought up PCR in 1983, Mullis was
working in Emeryville, California for Cetus Corporation, one of the first biotechnology
companies.

3.

What we end up with after PCR is a test tube full of double stranded DNA of various
lengths.

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Step 3: Select paths that contain the correct number of cities.

We now want to select those paths that are seven cities long.

To accomplish this we can use a technique called Gel Electrophoresis.

Gel Electrophoresis

Gel electrophoresis is a group of techniques used to separate molecules based on

physical characteristics such as size, shape, or isoelectric point. Gel electrophoresis is
usually performed for analytical purposes, but may be used as a preparative technique to
partially purify molecules prior to use of other methods such as mass spectrometry, PCR,
cloning, DNA sequencing, or immuno-blotting for further characterization.

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DNA electrophoresis apparatus. An agarose gel is placed in this buffer-filled box

and electrical current is applied via the power supply to the rear. The negative terminal is
at the far end (black wire), so DNA migrates towards the camera.

Separation of large (macro) molecules depends upon two forces: charge and mass. When
a biological sample, such as proteins or DNA, is mixed in a buffer solution and applied to
a gel, these two forces act together. The electrical current from one electrode repels the
molecules while the other electrode simultaneously attracts the molecules. The frictional
force of the gel material acts as a "molecular sieve," separating the molecules by size.
During electrophoresis, macromolecules are forced to move through the pores when the
electrical current is applied. Their rate of migration through the electric field depends on
the strength of the field, size and shape of the molecules, relative hydrophobicity of the
samples, and on the ionic strength and temperature of the buffer in which the molecules
are moving. After staining, the separated macromolecules in each lane can be seen in a
series of bands spread from one end of the gel to the other.

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Step 4: select paths that have a complete set of cities.

Now we filter the DNA molecules by city, one city at a time. Since the DNA
we start with contains seven cities, we will be left with strands that encode
each city once.
• DNA containing a specific sequence can be purified from a sample of mixed
DNA by a technique called Affinity Purification.
• An iron bead is attached to a fragment complementary to a substring.
• A magnetic field is the used to pull out all of the DNA fragments containing such a
sequence.

Reading out the answer

To find the answer we can sequence the DNA strands or use a method called
Graduated PCR.

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4.INFORMATION STORAGE IN DNA

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.
Nucleic Acids are used because of density, efficiency and speed. DNA molecules can
store far more information than any existing computer memory chip.

A single bacterium cell measures just a micron square - about the same size as a single
silicon transistor - but holds more than a megabyte of DNA memory and has all the
computational structures to sense and respond to its environment.

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5.EFFICIENCY OF DNA COMPUTERS

While traditional computers represent information as a sequence of 0s and 1s, DNA

computers encode the information directly in their chemical sequence. The density of
information that can be stored on DNA is 1 bit per cubic nanometer which is a trillionth
of the space required of conventional computers with a density of 1 bit per 1012 cubic
nanometers. Also, DNA computers are efficient according to Adleman. 1 joule is
sufficient for 2 * 1019 operations where an operation is defined to be the ligation of two
DNA molecules. Computers have an efficiency of about 109 operations per joule.

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However, as others have pointed out , Adleman did not include the cost of extracting the
information, the PCR that was needed to amplify the initial DNA, and so forth. One way
that DNA may be used is to store information. Searching for information would only
require the synthesis of a small probe complementary to the region of interest, and then to
locate where the probe bound to the DNA. DNA in a test tube could hold a million times
more information than is thought to be stored in the human brain.
Because the biochemical operations involved are subject to errors , rigorous tests of the
accuracy is needed.
Every a set of strands is tailored to a specific problem, so we need a new set each new
problem.
While a DNA computer takes much longer than a normal computer to perform each
individual calculation, it performs an enourmous number of operations at a time and
requires less energy and space than normal computers.

6.ADVANTAGES OF DNA COMPUTERS

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.

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DNA computers show promise because they do not have the limitations of silicon-based
chips. For one, DNA based chip manufacturers will always have an ample supply of raw
materials as DNA exists in all living things; this means generally lower overhead costs.
Secondly, the DNA chip manufacture does not produce toxic by-products. Last but not
the least, DNA computers will be much smaller than silicon-based computers as one
pound of DNA chips can hold all the information stored in all the computers in the world.
With the use of DNA logic gates, a DNA computer the size of a teardrop will be more
powerful than today's most powerful supercomputer. A DNA chip less than the size of a
dime will have the capacity to perform 10 trillion
parallel calculations at one time as well as hold ten terabytes of data. The capacity to

perform parallel calculations, much more trillions of parallel calculations, is something

silicon-based computers are not able to do. As such, a complex mathematical problem

that could take silicon-based computers thousands of years to solve can be done by DNA

Computers in hours. For this reason, the first use of DNA computers will most probably

be cracking of codes, route planning and complex simulations for the government.

7.DISADVANTAGES OF DNA COMPUTERS

High cost is time.

Occasionally slower-Simple problems are solved much faster on electronic

computers. It can take longer to sort out the answer to a problem than it took to solve the
problem.
n-Reliability- There is sometime errors in the pairing of DNA strands .

Although Adleman's first application of the computer took only milliseconds to produce a
solution, it took about a week to fish the solution molecules out from the rest of the

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possible path molecules that had formed. To make these computers more realistically
viable, the DNA splicing and selection equipment needs to be refined for this purpose
and better methods for fishing developed. There is also no guarantee that the solution
produced will necessarily be the absolute best solution, though it will certainly be a very
good one, arrived at in a much shorter time than with a conventional computer. 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. Some think that in the future, computers will be a combination of the current
models and DNA, using the most attractive features of both to create a vastly improved
total product. However, research is ongoing in doing Boolean logic with DNA and
designing universal (programmable) DNA computers.

And of course we are talking about DNA here, the genetic code of life itself. It certainly
has been the molecule of this century and most likely the next one. Considering all the
attention that DNA has garnered, it isn’t too hard to imagine that one day we might have
the tools and talent to produce a small integrated desktop machine that uses DNA, or a
DNA-like biopolymer, as a computing substrate along with set of designer enzymes.
Perhaps it won’t be used to play Quake IV or surf the web -- things that traditional
computers are good at -- but it certainly might be used in the study of logic, encryption,
genetic programming and algorithms, automata, language systems, and lots of other
interesting things that haven't even been invented yet.

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8.FUTURE OF DNA COMPUTERS

The most logical applications will be in:

Biology, Chemistry, Medicine

1.Enabling a computing system to read and decode natural DNA directly.

Such a computer also might be able to perform DNA fingerprinting –matching a sample
of DNA, such as that in blood found at a crime scene, with the person from whom it
came.

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2.Another promising direction is the molecular self-assembly of DNA to build complex

molecular structures, which could have an impact on other fields, such as
Nanotechnology.

Military
Researchers from Stanford and Princeton Universities, have outlined a way for a DNA
computer to crack messages coded with the U.S. government's own Data Encryption
Standard, which is used to protect a wide range of data, including telephone
conversations on classified topics and data transmissions between banks and the Federal
Reserve.

Some centers of research in this area are at the University of Southern California at Los
Angeles, with Dr. Adleman, Princeton, with Dr. Richard Lipton and his graduate students
Dan Boneh and Eric Baum, and the NEC Research Institute in Princeton, NJ. With
others elsewhere, they are developing new branches in this young field. Advancements
are being made in cryptography. Researchers are working on decreasing error in and
damage to the DNA during the computations/reactions. The Princeton contingent has
published papers on models for universal DNA computers, while others have described
methods for doing addition and matrix multiplication with these computers.

Currently, molecular computing is a field with a great deal of potential, but few results of
practical value. In the wake of Adleman's solution of the Hamiltonian path problem, there
came a host of other articles on computation with DNA; however, most of them were
purely theoretical. Currently, a functional DNA "computer" of the type most people are
familiar with lies many years in the future. But work continues: in his article Speeding
Up Computation via Molecular Biology Lipton shows how DNA can be used to construct
a Turing machine, a universal computer capable of performing any calculation. While it
currently exists only in theory, it's possible that in the years to come computers based on
the work of Adleman, Lipton, and others will come to replace traditional silicon-based
machines.

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The field of DNA computing is truly exciting for the revolution it implies will occur
within the next few years. It also demonstrates the current trend of merging and lack of
distinction between the sciences, where a computer scientist can mess around with
biology equipment and come up with something new and valuable.

9.CONCLUSION

The 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.
The field of DNA computing is still in its infancy and the applications for this technology
are still not fully understood.
Is DNA computing viable – perhaps, but the obstacles that face the field such as the
extrapolation and practical computational environments required are daunting.
However DNA computers won’t flourish soon in our daily environment due to the
technologic issues. NA computing has lead to a very important theoretical research.
The paradigm of DNA computing has lead to a very important theoretical research.

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10. BIBLIOGRAPHY

http://www.ieee.org

http://en.wikipedia.org/wiki/dnacomputers

Mind Sports Worldwide (Feb/2000)

http://www.msoworld.com/mindzine/news/chess/web_
round/web_round12.html

Scientific Guide to DNA Computers:

http://dna2z.com/dnacpu/dna2.html

Arstechnica Review(4/2000):

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http://arstechnica.com/reviews/2q00/dna/dna-2.html

Leonard Adleman’s Home Page:

http://www-scf.usc.edu/~pwkr/adleman-home.html

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