DNA COMPUTING ABSTRACT
In this era where computational processes come to the rescue of Biological conundrums -the underlying dogma of Bioinformatics, this paper aspires to explore the vice-versa. The prime contention of the paper is to assert that DNA, the genetic material of all living organisms can be exploited as a computational tool.
Chipmakers need a new material to produce faster computing speed with fewer complexities. DNA, the material our genes are made of, is being used to build the next generation of microprocessors. Scientists are using this genetic material to create nano-computers that might take the place of silicon computers in the next decade.
A nascent technology that uses DNA molecules to build computers that are faster than the world’s most powerful human-built computers is called DNA computing. Molecular biologists are beginning to unravel the information processing tools such as enzymes, copying tools, proofreading mechanisms and so on, that evolution has spent millions of years refining. Now we are taking those tools in large numbers molecules and using them as biological computer processors.
DNA computing has a great deal of advantage over conventional silicon-based computing. DNA computers can store billions of times more data than your personal computer. DNA computers have the ability to work in a massively parallel fashion, performing many calculations simultaneously. DNA computing has made a remarkable progress in almost every field. It has found application in fields like biomedical, pharmaceutical, information security, cracking secret codes, etc.
Scientists see such DNA computers as future competitors for their more conve-
ntional cousins because miniaturization is reaching its limits and DNA has the potential to be
much faster than conventional computers.
1. Introduction
Man’s thirst for knowledge has driven the information revolution. Human brain, a master processor, processes the information about the internal and external environment and sends signals to take appropriate actions. In nature, such controls exist at every level. Even the smallest of the cells has a nucleus, which controls the cell. Where does this power actually come from? It lies in the DNA. The ability to harness this computational power shall determine the fate of next generation of computing.
DNA computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA, biological molecules that can store huge amounts of information and are able to perform operations similar to that of a computer, through the deployment of enzymes, biological catalysts that act like software to execute desired operations. The appeal of DNA computing lies in the fact that DNA molecules can store far more information than any existing conventional computer chip. Also, utilizing DNA for complex computation can be much faster than utilizing a conventional computer, for which massive parallelism would require large amounts of hardware, not simply more DNA.
The concepts of utilizing DNA computing in the field of data encryption and DNA authentication methods for thwarting the counterfeiting industry are subjects that have been surfacing in the media of late. Researchers have been looking at alternatives to the traditional microprocessor design. One of the most interesting and emerging technology is DNA computers. The computing power of a teardrop-sized DNA computer, will be more powerful than the world’s most powerful supercomputer.
The massive parallelism involved in DNA interaction vindicates the idea and hence the idea of using DNA as a computational tool for parallel processing.
2. What is DNA?
Before delving into the principles of DNA computing, we must have a basic understanding of what DNA actually is. All organisms on this planet are made of the same type of genetic blueprint which bind us together. The way in which that blueprint is
coded is the deciding factor as to whether you will be bald, have a bulbous nose, male, female or even whether you will be a human or an oak tree.
Within the cells of any organism is a substance called Deoxyribonucleic Acid (DNA) which is a double-stranded helix of nucleotides which carries the genetic information of a cell. This information is the code used within cells to form proteins and is the building block upon which life is formed.
Strands of DNA are long polymers of millions of linked nucleotides. These nucleotides consist of one of four nitrogen bases, a five carbon sugar and a phosphate group. The nucleotides that make up these polymers are named after the nitrogen base that it consists of; Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). These nucleotides will only combine in such a way that C always pairs with G and T always pairs with A. The two strands of a DNA molecule are anti parallel where each strand runs in an opposite direction .
The combination of these 4 nucleotides in the estimated million long polymer strands can result in billions of combinations within a single DNA double-helix.These massive amount of combinations allows for the multitude of differences between every living thing on the planet from the large scale(mammal vs. plant), to the small(blue eyes vs. green eyes). What does all this chemistry and biology have to do with security you might ask? To answer that question we must first look at how biological science can be applied to mathematical computation in a field known as DNA computing.
Graphical representation of inherent bonding properties of DNA Illustration of double helix shape of DNA.
The bases (nucleotides) are spaced every 0.35 nanometers along the DNA molecule, giving it a remarkable data density of nearly 18Mbits per inch. These nucleotides will only combine in such a way that C always pairs with G and T always pairs with A. This complementarity makes DNA a unique data structure for computation and can be exploited in many ways.For example if one strand of DNA is of the sequence
AGTCAT
The other must be of the sequence
TCAGTA
i.e
A G T C A T
| | | | | |
T C A G T A
Because A always pairs T, and G with C.
This is called the complementarity of the DNA. One strand is always the complement of the other strand. Thus if two complementary single stranded DNA molecules come together they bind to form double stranded helical molecule.
POLYMERASE, LIGASE
These are enzymes that are vital for DNA replication and slick together the DNA molecules when they come into close proximity in a linear fashion.
3. A Successor to Silicon
Silicon microprocessors have been the heart of computing world for more than forty years. Computer chip manufacturers are furiously racing to make the next microprocessor that will topple speed records and in the process are cramming more and more electronic devices onto the microprocessor. Many have predicted that Moore’s law (which states that the microprocessors would double in complexity every two years) will soon reach its end, because of the physical speed and miniaturization limits of silicon microprocessors.
DNA computers have the potential to take computing to new levels, picking up where Moore’s law leave off. DNA computers could surpass their silicon-based predecessors. The several advantages of DNA over silicon are:
As long as there are cellular organisms, there will be a supply of DNA. The large supply of DNA makes it a cheap resource. Unlike the toxic materials used to make traditional microprocessors, DNA biochips can be made cleanly. DNA computers are many times smaller than today’s computers.
DNA molecules have a potential to store extensively large amount of information. It has been estimated that a gram of dried DNA can hold as much information as a trillion CD’s. More than 10 trillion DNA molecules can fit into an area of 1 cubic centimeter. With this small amount if DNA a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations at a time.
In a biochemical reaction taking place in a tiny surface area, a very large number of DNA molecules can operate in concert, creating a parallel processing system that mimics the ability of the most powerful supercomputer. DNA computers have the ability to perform many calculations simultaneously; specifically, on the order of 10^9 calculations per ml of DNA per second! A calculation that would take 10^22 modern computers working in parallel to complete in the span of one human’s life would take one DNA computer only 1 year to polish off!
4. Applications
DNA logic gates are the first step towards creating a computer that has a structure similar to that of an electronic PC. Instead of using electrical signals to perform logical operations, these DNA logic gates rely on DNA code. They detect fragments of genetic material as input, splice together these fragments and form a single output. Recent works have shown how these gates can be employed to carry out fundamental computational operations, addition of two numbers expressed in binary. This invention of DNA logic gates and their uses are a breakthrough in DNA computing.
A group of researchers at Princeton University in early 2000 demonstrated an RNA computer similar to Adleman’s, which had the ability to solve a chess problem involving how many ways there are to place knights on a chessboard so that none can take the others.
While a desktop PC is designed to perform one calculation very fast, DNA strands produce billions of potential answers simultaneously. This makes the DNA computer suitable for solving "fuzzy logic" problems that have many possible solutions rather than the either/or logic of binary computers. In the future, some speculate, there may be hybrid machines that use traditional silicon for normal processing tasks but have DNA co-processors that can take over specific tasks they would be more suitable for.
DNA computing is in its infancy, and its implications are only beginning to be explored. But DNA computing devices could revolutionize the pharmaceutical and biomedical fields. 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. They could act as ‘Doctors in a cell’.
DNA computing can be used by national governments for cracking secret codes, or by airlines wanting to map more efficient routes. The concept of using DNA computing in the fields of cryptography, steganography and authentication has been identified as a possible technology that may bring forward a new hope for unbreakable algorithms in the world of information security.
5. Scope and recent updates
Scientists have taken DNA from the free-floating world of the test tube and anchored it securely to a surface of glass and gold. University of Wiscosnin-Madison researchers have developed a thin, gold-coated plate of glass about an inch square. They believe it is the optimum working surface on which they can attach trillions of strands of DNA. Putting DNA computing on a solid surface greatly simplifies the complex and repetitive steps previously used in rudimentary DNA computers. Importantly it takes DNA out of the test tube and puts it on a solid surface, making the technology simpler, more accessible and more amenable to the development of large DNA computers capable of tackling the kind of complex problems that conventional computers now handle routinely. Researchers believe that by the year 2010 the first DNA chip will be commercially available.
Advantages
The advantage of DNA approach is that it works in parallel, processing all possible answers simultaneously.
DNA computing is an example of computing at a molecular level, potential a size limit that may never be reached by the semiconductor industry.
It can be used to solve a class of problems that are difficult or impossible to solve using traditional computing methods.
There is no power required for DNA computing while the computation is taking place. The chemical bonds that are the building blocks of DNA happen without any outside power source. It’s energy-efficiency is more than a million times that of a PC.
Disadvantages
DNA computers require human assistance.
Technological challenges remain before DNA computing. Researchers need to develop techniques to reduce number of computational errors produced by unwanted chemical reactions with the DNA strands. They need to eliminate, combine, or accelerate the steps in processing the DNA.
The extrapolation and practical computational environment required are daunting. The ‘test tube’ environment used for DNA computing is far from practical for everyday use.
CONCLUSION
DNA computers have tremendous potential to compete with electronic computers, which boasts of superior speeds in computation.. A new face in the field of computation is introduced and the possibility of using DNA as a computational tool is high-lightened and described that even a molecular biology laboratory can be made to perform computational operations just like the dry lab or the computer lab, broadening the horizon of computational sciences. Scientists and mathematicians around the world are now looking at the application of DNA computers to a whole range of “intractable” computing problems.
DNA computing can be viewed as a manifestation of an emerging new area of science made possible by our rapidly developing ability to control the molecular world.
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