DNA Computers

Doctors in a Cell
A FULL PAPER ON GENETIC ENGINEERING

CONTENTS

• ABSTRACT
• DNA COMPUTING
• HOW DO THEY WORK ?
• MOLECULES IN DNA COMPUTING DEVICE
• DNA COMPUTER MAKES ITS OWN ENERGY
• DOCTORS IN A CELL
• DNA IDENTIFY MUTATING CELLS
• DNA COMPUTER TARGET CANCER
• CONCLUSION
• REFERENCES

DNA COMPUTERS
Doctors in a Cell

ABSTRACT :

Think of DNA as software and enzymes as hardware, put them together in a

test tube. The way in which these molecules undergo chemical reactions with each other
allows simple operations to be performed as a byproduct of the reaction. DNA
Computers use deoxyribonucleic acids …A (Adenine), C (cytosine), G (guanine) and T
(Thymine) … as a memory units, and recombinant DNA techniques already in existence
carry out the fundamental operations.

DNA Computing devices could perhaps most importantly revolutionize the

pharmaceutical and biomedical fields. Some scientists predict a future where our bodies
are patrolled by tiny DNA computers that monitor our wellbeing and release the right
drugs to repair damaged or unhealthy tissue as “Doctors in a Cell”, operating inside
living cells and sensing anomalies in the host. DNA computer can detect the presence of
diagnostic markers for cancer and release a suitable cancer treatment molecule.

Research is going on hope to some day inject tiny computers in to humans to

zap viruses fix good cells gone bad and otherwise keep us healthy as “Doctors inside the
Cell”.

DNA COMPUTING :

DNA computing is a form of computing which uses DNA and biochemistry

and molecular biology instead of the traditional silicon based computer technologies.
DNA computing or more generally molecular computing is a fast developing
interdisciplinary area.

Eventhough biologically inspired computing technologies may only prove to

be useful for very specialized problems, their potential is still impressive. For example,
compared to conventional computers, DNA used as a computing medium may prove to
be a billion times more energy efficient and to have a trillion times more data storage
capacity.

DNA computing is massively parallel, compute with extreme high energy -

efficiency ad store enormous quantities of information. DNA itself provides the added
benefits of being a cheap, energy, efficient resource. The computing device is so small
that 3 trillion such devices can reside in one micro liter of solution, a fact that won it the
Guinness World Record for the world’s smallest biological computing device.

Think of DNA as software, and enzymes as hardware, put them together in

a test tube. The way in which these molecules undergo chemical reactions with each
other allows simple operations to be performed as a by product of the reactions. The
scientists till the devices what to do by controlling the composition of DNA software
molecules. Its a completely different approach to pushing electrons around a dry
circuit in a conventional computer. To the naked eye, the DNA computer looks like
clear water solution in a test tube. There is no mechanical device. A trillion bio-
molecular devices could fit into a single drop of water. Instead of showing upon a
computer screen, results are analysed using a technique that allows scientists to see the
length of the DNA output molecule.

HOW DO THEY WORK ? :

DNA computer uses the chemical properties of DNA molecules by examining

the patterns of combination or growth of the molecules or strings. DNA can do this
through the manufacture of enzymes, which are biological catalysts that could be called
the ‘software’ used to execute the desired calculation.

DNA computers use deoxyribonucleic acids - A (adenine), C (cytosine), G

(guanine) and T (thymine) as the memory units, and recombinant DNA techniques
already in existence carry out the fundamental operations. In a DNA computer,
computation takes place in test tube or on a glass slide coated in 24K gold. The input and
output are both strands of DNA, whole genetic sequences encode certain information. A
progress on a DNA computer is executed as a series of biochemical operations, which
have the effect of synthesizing, extracting, modifying and cloning the DNA strands.
Their potential power underscores how nature could be capable of crunching number
better and faster than the most advanced silicon chips.

The only fundamental difference between conventional computers and DNA

computers is the capacity of memory units : Electronic computers have two positions (on
or off), where as DNA has four (C, G, A or T). Different restriction enzymes cut the
two strands of double stranded DNA have been employed in computing.

By forcing DNA molecules to generate different chemical states, which can

then be examined to determine an answer to a problem by combination of molecules into
strands or the separation of strands, the answer is obtained.
MOLECULES IN DNA COMPUTING DEVICE :

Self contained, programmable computing device uses only three types of

molecules.

1. DNA input molecules, encoding the data and providing the fuel for the
computation.
2. DNA software molecules, encoding the rules of computation.
3. A hardware molecule, a DNA cutting enzymes

DNA COMPUTER MAKES ITS OWN ENERGY :

These devices uses DNA molecules as both input data and as a fuel source
without external energy supply. Thus DNA molecules serve as input, output and
software. The restriction enzyme FOKI serves as the hardware, aiding the cleavage of
the input DNA molecule and releases the energy to drive the device. Combining as input
data and an energy supply for the computation in the same physical entity is unthinkable
in the realm of electronic computers.

DOCTORS IN A CELL :

DNA computing devices could perhaps most importantly revolutionize the

pharmaceutical and biomedical fields. DNA computers control chemical and biological
systems in a way that is analogous to the way we use electronic computers to control
electrical and mechanical systems. Some scientists predict a future, where our bodies are
patrolled by tiny DNA computers that monitor our well being and release the right drugs
to repair damaged or unhealthy tissue. Autonomous bio-molecular computers may be
able to work as “doctors in a cell” operating inside living cells and sensing anomalies in
the host.

DNA IDENTIFY MUTATING CELLS :

When inserted into a biological environment, the designer molecule begins to

sense ribonucleic acid (RNA), a similar molecule crucial to the replication of DNA, the
chemical building block of genes. In particular it is attracted to abnormal forms of RNA
that are associated with lung or other type of cancer. The attraction occurs, because the
sequence of the enzymes on the DNA strand corresponds to complimentary sequences
found on RNA from malignant cells. Once detected, the designer molecule can then
release chemicals to inhibit growth of malignant cells or even kill them.

DNA COMPUTER TARGET CANCER :

DNA Computer can detect the presence of diagnostic markers for cancer and
release a suitable cancer treatment molecule. So far, the molecular computer has only
been trailed in test tubes, but ultimately it could find a use inside the body.

Our medical computer might one day be administered as a drug and

distributed through out the body by the blood stream to detect disease markets
autonomously and independently in every cell. In this way a single cancer cell could be
detected and destroyed before the tumor develops. Even in a late stage cancer, this kind
of treatment could reach every secondary growth, however small and effectively
terminate the disease.

This molecular computer consists of three modules : Input, computation and output.

- The input module consists of single strands of DNA that contain stretches of bases
that pair with and so identify certain stretches of messenger RNA.
- The computation module processes a series of input modules to determine whether
the balance of certain types of messenger RNA indicates the presence of cancer
cells.
- The output module administers a drug in the form of another DNA strand when
cancer cells are indicates.

A second type of DNA computer that is programmed to release a DNA strand

that inhibits the first computers drug molecule if cancer cells are not present must also be
administered. The method has the potential to detect multiple disease conditions at once.

In situ detection and analysis of molecular signals in living organisms is not

possible with electronic computers. With today’s computer chips, energy consumption
and the heat produced as a by product can cause malfunctions. But the chemical
reactions that make DNA computer work require little energy.
CONCLUSION :
Our work does not attempt to compete with electronic computers head on, but rather to
design molecular scale computing devices, which might have applications in areas not
assessable to electronic computer such as “smart components” in biochemical reactions.
Research is going on, hope to some day inject tiny computers into humans to zap viruses,
fix good cells gone bad and otherwise keep us healthy as doctors inside the cell.

REFERENCES :

¨ Leonard M. Adleman (1994-11-11) “Molecular Computation Of Solutions To

Combinatorial Problems”. · Science (journal) 266 (11): 1021–1024. — The first
DNA computing paper. Describes a solution for the directed · Hamiltonian path
problem.

¨ Martyn Amos (June 2005). · Theoretical and Experimental DNA Computation.

Springer. · ISBN 3-540-65773-8. — The first general text to cover the whole field.

¨ Dan Boneh, Christopher Dunworth, · Richard J. Lipton, and Jiri Sgall (1996). “· On
the Computational Power of DNA”. DAMATH: Discrete Applied Mathematics and
 Combinatorial Operations Research and Computer Science 71. — Describes a
solution for the · boolean satisfiability problem.

¨ Gheorge Paun, Grzegorz Rozenberg, ·Arto Salomaa (October 1998). DNA Computing
New Computing Paradigms. Springer-Verlag. ISBN 3-540-64196-3. — The book
starts with an introduction to DNA-related matters, the basics of biochemistry and
language and computation theory, and progresses to the advanced mathematical theory
of DNA computing.

¨ Lila Kari, Greg Gloor, Sheng Yu (January 2000). “· Using DNA to solve the Bounded
Post Correspondence Problem”. Theoretical Computer Science 231 (2): 192–203.
Describes a solution for the bounded · Post correspondence problem, a hard-on-
average NP-complete problem.

¨ JB. Waldner (January 2007). Nanocomputers and Swarm Intelligence. ISTE, 189
ISBN 2746215160.