DNA Computers: Doctors in a Cell

Soujanya A Pasumarthi.

Department of Biotechnology, Koneru Lakshimah University, India.

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 biomolecular 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-onaverage NP-complete problem.

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