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HISTORY OF DNA COMPUTING 7. DNA FUNDAMENTALS 8. DNA VS. SILICON 9. THE ADLEMAN‟S EXPERIMENT 10. DNA CRYPTOGRAPHY 11. ORIGINS OF STEGANOGRAPHY 12. DNA STEGANOGRAPHY 13. DNA AUTHENTICATION 14. ADVANTAGES & DISADVANTAGES 15. MODALS & FORMATS OF DNA COMPUTATION 16. PITFALL OF DNA COMPUTING 17. FUTURE OF DNA COMPUTING 18. CONCLUSION 19. REFERENCES
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. Sooner or later the physical speed and miniaturization limits of silicon microprocessors is bound to hit a wall. Chipmakers need a new material to produce faster computing speed with fewer complexities. You won‟t believe where scientists have found this new material. 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 molecules that provide the input can also provide all the necessary operational energy. 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.Scentists and researchers believe that in the foreseeable future DNA computing could scale up to great heights Molecular biologists are beginning to unravel the information-processing tools such as enzymes that evolution has spent billions of years refining. These tools are now been taken in large numbers of DNA molecules and using them as biological computer processors. Dr. Leonard Adleman, a well-known scientist, found a way to exploit the speed and efficiency of the biological reactions to solve the “Hamiltonian path problem”, also known as the “traveling salesman problem”. Based on Dr. Adleman‟s experiment, we will explain DNA computing, its algorithms, how to manage DNA based computing and the advantages and disadvantages of DNA computing.
DNA (Deoxyribose Nucleic Acid) computing, also known as molecular computing is a new approach to massively parallel computation based on groundbreaking work by Adleman. DNA computing was proposed as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the 'NP-complete' or non-deterministic polynomial time complete problems).A DNA computer is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problem, depending on the problem at hand. Technology is currently available both to select the initial strands and to filter the final solution. DNA computing is a new computational paradigm that employs (bio)molecular manipulation to solve computational problems, at the same time exploring natural processes as computational models In 1994, Leonard Adleman at the Laboratory of Molecular Science, Department of Computer Science, University of Southern California surprised the scientific community by using the tools of molecular biology to solve a different computational problem. The main idea was the encoding of data in DNA strands and the use of tools from molecular biology to execute computational operations. Besides the novelty of this approach, molecular computing has the potential to outperform electronic computers. For example, DNA computations may use a billion times less energy than an electronic computer while storing data in a trillion times less space. Moreover, computing with DNA is highly parallel: In principle there could be billions upon trillions of DNA molecules undergoing chemical reactions, that is, performing computations, simultaneously.
The current Silicon technology has following limitations: Circuit integration dimensions Clock frequency Power consumption Heat dissipation.
The problem's complexity that can be afforded by modern processors grows up, but great challenges require computational capabilities that neither most powerful and distributed systems could reach.
The idea that living cells and molecular complexes can be viewed as potential machinic components dates back to the late 1950s, when Richard Feynman delivered his famous paper describing "sub-microscopic" computers. More recently, several people have advocated the realization of massively parallel computation using the techniques and chemistry of molecular biology. DNA computing was grounded in reality at the end of 1994, when Leonard Adleman, announced that he had solved a small instance of a computationally intractable problem using a small vial of DNA. By representing information as sequences of bases in DNA molecules, Adleman showed how to use existing DNA-manipulation techniques to implement a simple, massively parallel random search. He solved the traveling salesman prob-
000. .000.000. can store 1 bit in 1.000 cubic nanometer. (i) The information density of DNA is much greater than that of silicon : 1 bit can be stored in approximately one cubic nanometer. There are two reasons for using molecular biology to solve computational problems. such as videotapes. Others storage media.lem also known as the “Hamiltonian path" problem. (ii) Operations on DNA are massively parallel: 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.
Guanine (G) and Thymine (T). This information is the code used within cells to form proteins and is the building block upon which life is formed. Adenine (A). male. Cytosine (C). 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. These nucleotides will only combine in such a way that C always pairs with G and T always pairs with A. The nucleotides that make up these polymers are named after the nitrogen base that it consists of. These nucleotides consist of one of four nitrogen bases. have a bulbous nose. female or even whether you will be a human or an oak tree.WHAT IS DNA? Before delving into the principles of DNA computing. Figure 1 illustrates two strands of DNA and the bonding priciples of of the 4 types of nucleotides and the Figure 2 illustrates the double helix shape of DNA. The way in which that blueprint is coded is the deciding factor as to whether you will be bald. Strands of DNA are long polymers of millions of linked nucleotides. a five carbon sugar and a phosphate group. All organisms on this planet are made of the same type of genetic blueprint which bind us together. we must have a basic understanding of what DNA actually is. . The two strands of a DNA molecule are antiparallel 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. the mystery of DNA and its construction is slowly being unraveled through mathematical means. With the advances in DNA research in projects such as the Human Genome project (a research effort to characterize the genomes of human and selected model organisms through complete mapping and sequencing of their DNA ) and a host of others. plant). Distinct formulae and patterns have emerged that may have implications well beyond those found in the fields of genetics. These massive amount of combinations allows for the multitude of differences between every living thing on the planet from the large scale (mammal vs. to the small (blue eyes vs. . green eyes).Fig 1 – Graphical representation of inherent Fig 2 – Illustration of double helix shape of bonding properties of DNA  DNA. 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.
Leonard Adleman. a computer scientist at the University of Southern California was the first to pose the theory that the makeup of DNA and it‟s multitude of possible combining nucleotides could have application in brute force computational search techniques. Utilizing DNA for this type of computation can be much faster than utilizing a conventional computer. Basically this means that you can attempt every solution to a given problem until you came across the right one through random calculation.BASICS AND ORIGIN OF DNA COMPUTING DNA computing or molecular computing are terms used to describe utilizing the inherent combinational properties of DNA for massively parallel computation. one can potentially solve huge mathematical problems by parallel search. The idea is that with an appropriate setup and enough DNA. .
and its future looks extremely promising. which encode genetic information for all living things. To give you an idea of the difference in time. a . DNA computing is currently one of the fastest growing fields in both Computer Science and Biology. The promise of DNA computing is massive parallelism: with a given setup and enough DNA. the molecules which encode genetic information for all living things. First and foremost. in computers. for which massive parallelism would require large amounts of hardware. What does this mean. where certain combinations of DNA molecules are interpreted as a particular result to a problem encoded in the original molecules present. It is accomplished in a suspended solution of DNA. This can be much faster than a conventional computer. you ask? Well. essentially while DNA can only carry out computations slowly. where certain combinations of DNA molecules are interpreted as a particular result to a problem encoded in the original molecules present. A highly interdisciplinary study incorporating the research results of computer scientists and biologists. DNA computing is useful because it has a capacity lacked by all current electronics-based computers: its massively parallel nature. in the literal sense. is the use of DNA (Deoxyribose Nucleic Acid) molecules. one can potentially solve huge problems by parallel search. DNA computing is the use of DNA molecules. specifically. in computers. on the order of 10^9 calculations per mL of DNA per second! This capability of multiple co temporal calculations immediately lends itself to several classes of problems which a modern electronic computer could never even approach solving.DNA COMPUTING (DNAC) DNA computing. DNA computers can perform a staggering number of calculations simultaneously. Dr. In the literal sense. not simply more DNA. This is accomplished in a suspended solution of DNA. Leonard Aldeman is a pioneer of DNA computing for his solution to solve Hamiltonian Path Problem using DNA strands. A DNA computer is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problem. Technology is currently available both to select the initial strands and to filter the final solution.
Adleman solved an unremarkable computational problem with a remarkable technique. making them impractical to solve on even the latest super-computer." In Adleman's version of the traveling salesman problem. however. but is more popularly recognized as a variant of the socalled "traveling salesman problem. Leonard M. It's formally known as a directed Hamiltonian Path (HP) problem. The type of problem that Adleman solved is a famous one. Adleman‟s demonstration only involves seven cities. potentially a size limit that may never be reached by the semiconductor industry. Nevertheless. It took Adleman.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! In 1994. It illustrates the possibilities of using DNA to solve a class of problems that is difficult or impossible to solve using traditional computing methods. It demonstrates unique aspects of DNA as a data structure It demonstrates that computing with DNA can work in a massively parallel fashion . As the number of cities increases. It was a problem that a person could solve it in a few moments or an average desktop machine could solve in the blink of an eye. It was a landmark demonstration of computing on the molecular level. his work is significant for a number of reasons. TSPs with a large number of cities quickly become computationally expensive. It's an example of computation at a molecular level. at which point it requires brute force search methods. seven days to find a solution. or "TSP" for short. Why then was this work exceptional? Because he solved the problem with DNA. a hypothetical salesman tries to find a route through a set of cities so that he visits each city only once. the problem becomes more difficult until its solution is beyond analytical analysis altogether. making it in some sense a trivial problem that can easily be solved by inspection.
when Len Adleman of USC announced that he had solved a small instance of a computationally intractable problem using a small vial of DNA. Given a map of mainland Europe. DNA computing was grounded in reality at the end of 1994. we know that we can colour each country one of four colours such that no two countries sharing a border are coloured the same. as are the Travelling Salesman and Bin Packing problems. but one of size 30 may take year. Most of us today. These include quantum. We have made huge advances in miniaturisation since the days of room-sized computers.5 tons. Adleman showed how to use existing DNA-manipulation techniques to implement a simple. several people have advocated the realisation of massively parallel computation using the techniques and chemistry of molecular biology. Some researchers are now looking beyond these boundaries and are investigating entirely new media and computational models.size search space. in the age of smart cards and wearable PCs would find that statement laughable. massively parallel random search. when Richard Feynman delivered his famous paper describing "sub-microscopic" computers. These problems are characterised by an exponential. Today's supercomputers still employ the kind of sequential logic used by the mechanical dinosaurs of the 1930s. optical and DNAbased computers. By representing information as sequences of bases in DNA molecules. It is the last of these developments that this paper concentrates on. what happens if we lose a crayon? Can we still legally colour the map using only three colours? This problem is a member of the large class of notoriously intractable NP-complete problems. .HISTORY OF DNA COMPUTING "Computers in the future may weigh no more than 1. yet the underlying computational framework has remained the same. The idea that living cells and molecular complexes can be viewed as potential machinic components dates back to the late 1950s. The problem of "colouring" has a long history." So said Popular Mechanics in 1949. Scientists at the Universities of Liverpool and Warwick (UK) are currently building a prototype DNA computer to solve a different problem . However. More recently. a problem of size 10 may take a fraction of a second to solve on a PC.
The four kinds of bases are attached to this repetitive sugar-phosphate chain. and two hydrogen bonds exist between A and T. and thymine (T). Deoxyribonucleic Acid. DNA tary base pairs. cytosine(C). The two long chains of a DNA molecule are held together by complementary base pairs. molecules consist of two long chains held together by complemen- Figure 1:. guanine (G). A DNA chain is a long. is the molecular basis of heredity and localized especially in most cell nucleus. unbranched polymer composed of only four type subunits. Three hydrogen bonds form between G and C.DNA Structure .DNA FUNDAMENTALS DNA. These are the deoxyribonucleotides containing the bases adenine (A). The nucleotides are linked together by covalent phosphodiester bonds that join the 5‟ carbon of one deoxyribose group to the 3‟ carbon of the next. The base-pairing mechanism is the basis for DNA replication.
But look what happens after each replication is finished . one naive method would be to set up a search tree. "the inside of a computer is as dumb as hell. Transistor-based computers typically handle operations in a sequential manner. So after 10 iterations. which is what all modern CPUs are. With each additional strand. If forced to behave sequentially. after 30 iterations it increases to 1000 Gbits/sec. Now let's consider how you would solve a nontrivial example of the traveling salesman problem (# of cities > 10) with silicon vs. and modern CPUs incorporate some parallel processing. basically repeats the same "fetch and execute cycle" over and over again. however. But this is only 1000 bits/sec. such as pruning the search tree when one of the branches you are measuring is already longer than the best candidate. the DNA is being replicated at a rate of about 1Mbit/sec. Typically. it fetches an instruction and the appropriate data from main memory. though. in the basic von Neumann architecture computer.DNA VS. the power comes from the memory capacity and parallel processing. DNA loses its appeal. increasing performance of silicon computing means faster clock cycles (and larger data paths). measure each complete branch sequentially. With a von Neumann computer. with its unique data structure and ability to perform many parallel operations. many times in a row. but in general. It does this many. stochastic machines that approach computation in a different way from ordinary computers for the purpose of solving a different class of problems. are non-von Neuman. the replication enzymes can start on the second replicated strand of DNA even before they're finished copying the first one. Improvements could be made with better search algorithms. an impressive achievement. For example. The great Richard Feynman. DNA can be replicated at a rate of about 500 base pairs a second. So already the data rate jumps to 2000 bits/sec. consider that the entire list of routes for a 20 city prob- . allows you to look at a computational problem from a different point of view. let's look at the read and write rate of DNA. which is a snail's pace when compared to the data throughput of an average hard drive. really. For example. and keep the shortest one. First of all. A method you certainly would not use would be to first generate all possible paths and then search the entire list. really fast. A von Neumann machine. but it goes like mad!" DNA computers. and it executes the instruction. This is beyond the sustained data rates of the fastest hard drives. Biologically this is quite fast (10 times faster than human cells) and considering the low error rates. DNA. SILICON DNA. But look what happens if you allow many copies of the replication enzymes to work on DNA in parallel. summed up von Neumann computers by saying.the number of DNA strands increases exponentially (2^n after n iterations). Of course there are multi-processor computers. will doubling the clock speed or doubling your RAM give you better performance? For DNA computing. In bacteria. Why? Well. the data rate increases by 1000 bits/sec. instructions are handled sequentially. in his Lectures on Computation. where the emphasis is on the speed of the CPU and not on the size of the memory.
. However. routes no longer have to be searched through sequentially. it would take two years just to generate all paths (assuming one instruction cycle to generate each city in every path). a relatively small number for biochemistry. Operations can be done all in parallel.lem could theoretically take 45 million GBytes of memory (18! routes with 7 byte words)! Also for a 100 MIPS computer. using DNA computing. this method becomes feasible! 10^15 is just a nano mole of material. Also.
For six. The concepts are the same but the example has been simplified to make it easier to follow and present. The airline I‟m taking has a specific set of connecting flights that restrict which routes I can take (i. He first generated all the possible itineraries and then selected the correct itinerary. Pretty soon you will run out of pen and paper listing all the possible routes.Y. and need to visit four cities: Dallas. This is the advantage of DNA. Starting from L. Miami and then to N. to Chicago.e. The method Adleman used to solve this problem is basically the shotgun approach mentioned previously. or not make it to N. with NY being my final destination. Chicago. but no flight from Miami to Chicago). Suppose that I live in LA.. Dallas. However. Since the enzymes work on many DNA molecules at once. or even eight cities. the problem quickly gets out of hand. you need to fly to Chicago.or perhaps DNA. the problem is still manageable. For this example you obviously don‟t need the help of a computer to find a solution. using the DNA methods demonstrated by Adleman. Assuming a random distribution of connecting routes. Miami. as the number of cities increases. What should my route be if I want to visit each city only once? It should take you only a moment to see that there is only one route. the selection process is massively parallel.A.A.. visit a city twice. Any other choice of cities will force you to miss a destination. and NY. It‟s small and there are combinatorial techniques that can quickly generate many different data strings. the number of itineraries you need to check increases exponentially. So let‟s solve our own directed Hamiltonian Path problem. there is a flight from L.Y. seven.THE ADLEMAN EXPERIMENT There is no better way to understand how something works than by going through an example step by step. . and it becomes a problem for a computer.
Select routes with the correct number of cities. Encode routes by connecting the city sequences for which routes exist. 2. 4. The following operations can be performed with DNA: o o o o o o o o o Synthesis of a desired strand Separation of strands by length Merging: pour two test tubes into one to perform union Extraction: extract those strands containing a given pattern Melting/Annealing: break/bond two DNA molecules with complementary sequences Amplification: use PCR to make copies of DNA strands Cutting: cut DNA with restriction enzymes Ligation: Ligate DNA strands with complementary sticky ends using ligase Detection: Confirm presence/absence of DNA in a given test tube Part I: Generate all possible routes Strategy: Encode city names in short DNA sequences. All of the above steps can be accomplished with standard molecular biology techniques. Generate all possible routes. 3. . the method based on Adleman‟s experiment would be as follows: 1. Select routes that contain each city only once. The key to solving the problem was using DNA to perform the five steps in the above algorithm. Select routes that start with the proper city and end with the final city.Specifically.
CGG) and the first half of the code representing NY (ATG.)... .A -> Chicago -> Dallas -> Miami -> New York would simply be GCTACGCTAGTATCGTACCTACGGATGCCG. For example. The molecules can be made by a machine called a DNA synthesizer or even custom ordered from a third party. For example the route between Miami (CTACGG) and NY (ATGCCG) can be made by taking the second half of the coding for Miami (CGG) and the first half of the coding for NY (ATG). each city can be represented by a "word" of six bases: Los Angeles Chicago Dallas Miami New York GCTACG CTAGTA TCGTAC CTACGG ATGCCG The entire route can be encoded by simply stringing together these DNA sequences that represent specific cities. Itineraries can then be produced from the city encodings by linking them together in proper order. To accomplish this you can take advantage of the fact that DNA hybridizes with its complimentary sequence. or equivalently it could be represented in double stranded form with its complement sequence.DNA can simply be treated as a string of data. For example. So how do we generate this? Synthesizing short single stranded DNA is now a routine process. which not only uniquely represents the route from Miami to NY. you can encode the routes between cities by encoding the compliment of the second half (last three letters) of the departure city and the first half (first three letters) of the arrival city.. but will connect the DNA representing Miami and NY by hybridizing itself to the second half of the code representing Miami (. This gives CGGATG. By taking the complement of this you get. GCCTAC.. For example. the route from L. so encoding the city names is straightforward.
PCR is an iterative process that cycles through a series of copying events using an enzyme called polymerase. say 10^13 copies of each city and each route between cities. we use primers that are complimentary to LA and NY. After many iterations of PCR. Polymerase will copy a section of single stranded DNA starting at the position of a primer. What we want are routes that start with LA and end with NY. By selecting primers that flank the section of DNA you want to amplify. What we end up with after PCR is a test . Part II: Select itineraries that start and end with the correct cities Strategy: Selectively copy and amplify only the section of the DNA that starts with LA and ends with NY by using the Polymerase Chain Reaction. doubling the amount of DNA containing this sequence. a short piece of DNA complimentary to one end of a section of the DNA that you're interested in. For example: We can be confident that we have all possible combinations including the correct one by using an excess of DNA encodings. To accomplish this we can use a technique called Polymerase Chain Reaction (PCR). Finally. the DNA you're working on is amplified exponentially. After Part I. we now have a test tube full of various lengths of DNA that encode possible routes between cities. Remember DNA is a highly compact data format. What we are left with are strands of DNA representing itineraries with a random number of cities and random set of routes. which allows you to produce many copies of a specific sequence of DNA. the DNA strands can be connected together by an enzyme called ligase. the polymerase preferentially amplifies the DNA between these primers. so numbers are on our side. So to selectively amplify the itineraries that start and stop with our cities of interest.For example: Random itineraries can be made by mixing city encodings with the route encodings.
which slows down the DNA at different rates depending on its length. Part III: Select itineraries that contain the correct number of cities. To accomplish this we can use a technique called Gel Electrophoresis. We now want to select those itineraries that are five cities long. Our test tube is now filled with DNA encoded itineraries that start with LA and end with NY. encoding itineraries that start with LA and end with NY. DNA is a negatively charged molecule under most conditions. This is why you use a gel matrix.tube full of double stranded DNA of various lengths. The gel is made up of a polymer that forms a meshwork of linked strands. In this case we would isolate the DNA that was 30 base pairs long (5 cities times 6 base pairs). The DNA now is forced to thread its way through the tiny spaces between these strands. knowing the length of the itinerary gives us the number of cities. . where the number of cities in between LA and NY varies. Since we known that each city is encoded with 6 base pairs of DNA. Strategy: Sort the DNA by length and select the DNA whose length corresponds to 5 cities. with each band corresponding to a certain length. so if placed in an electric field it will be attracted to the positive potential. which is a common procedure used to resolve the size of DNA. The basic principle behind Gel Electrophoresis is to force DNA through a gel matrix by using an electric field. What we typically end up with after running a gel is a series of DNA bands. However since the charge density of DNA is constant (charge per length) long pieces of DNA move as fast as short pieces when suspended in a fluid. We can then simply cut out the band of interest to isolate DNA of a specific length.
and then Chicago'. For example. The order isn‟t important. DNA containing a specific sequence can be purified from a sample of mixed DNA by a technique called affinity purification. using a different city complement for each run. the next run we use Dallas'.beads. If an itinerary is missing a city.beads (where the ' indicates compliment strand) to fish out DNA sequences which contain the encoding for L. Miami'. The beads are then mixed with the DNA. for the first run we use L. This is exactly what we are looking for.A. This is accomplished by attaching the compliment of the sequence in question to a substrate like a magnetic bead.beads.Part IV: Select itineraries that have a complete set of cities Strategy: Successively filter the DNA molecules by city. and finally NY'. visit each city once.beads. Since the DNA we start with contains five cities.beads. So we now affinity purify fives times. DNA. we will be left with strands that encode each city once. (which should be all the DNA because of step 3). These beads can then be retrieved and the DNA isolated.'. . one city at a time. and end in NY. What we are left with are the are itineraries that start in LA. then it will not be "fished out" during one of the runs and will be removed from the candidate pool. which contains the sequence you're after then hybridizes with the complement sequence on the beads. If the answer exists we would retrieve it at this step.A.
Public key encryption splits the key up into a public key for encryption and a secret key for decryption. Bob generates a pair of keys and tells everyone his public key. It's not possible to determine the secret key from the public key. Anyone can use Bob's public key to send him an encrypted message. The potential eavesdropper.  . They argue that current practical applications of cryptographic systems based on one-time pads is limited to the confines of conventional electronic media whereas as small amount of DNA can suffice for a huge one time pad for use in public key infrastructure (PKI). will have an incredible amount of work to perform to attempt decryption of their transmission than either Alice or Bob. This scheme allows Alice and Bob to communicate in secret without having to physically meet as in symmetric encryption methods. Eve. while only he knows his secret key. but only Bob knows the secret key to decrypt it.  To put this into terms of the common Alice and Bob description of secure data transmission and reception. and Alice will use it to send an encrypted message to him.DNA CRYPTOGRAPHY ‘DNA-based Cryptography‟ which puts an argument forward that the high level computation- al ability and incredibly compact information storage media of DNA computing has the possibility of DNA based cryptography based on one time pads. they are basing their argument of DNA cryptography on Bob providing Alice his public key.
Injecting DNA cryptography into the common PKI scenario. This puts the idea of this form of DNA computing at great risk in the field of cryptography. albeit highly parallelized. Public Key Encryption illustrated.Fig 5. It can easily be argued that DNA computing is just classical computing. the researchers from Duke argue that we have the ability to follow the same inherent pattern of PKI but using the inherent massively parallel computing properties of DNA bonding to perform the encryption and decryption of the public and private keys. the obstacles of utilizing this kind of technology outside of a lab are extremely high. thus with a large enough key. . As well. one should be able to thwart any DNA computer that can be built.
Throughout our history there have been many other forms of steganography used to hide messages such as the use of null ciphers. It has been reported that the Al Queda network of terrorists may have used steganographic means to hide their communications in organizing the September 11th attacks on the United States of America. within other text or graphics that are electronically transmitted. . One of the early Grecian methods of steganography was to shave the head of a messenger. More recently. tattoo the message to be hidden . The ability to transfer text and images is now instantaneous and accessible by individuals virtually everywhere on the planet. In World War II for example. usually unencrypted.ORIGINS OF STEGANOGRAPHY Steganography is a variety of encryption that completely hides text or graphics. German cryptographers devised a method of using microdots to conceal messages within messages themselves. computer technology and the Internet have provided a medium for steganography that has been unseen in the past. The term steganography derives from the Greek words steganos meaning hidden and graphein meaning to write. invisible inks and others. Readily available software applications such as the freeware application JPHide and JPSeek will encrypt messages with the common JPG format of graphic files. Messages can now be hidden in the inconspicuous advertising banners of web pages and the music files we listen to. Other applications give the user the ability to hide data within other graphic formats such as GIF or BMP and audio formats such as MP3.
 Utilizing these methods.DNA STEGANOGRAPHY Experiments in DNA Steganography have been conducted by Carter Bancroft and his team at the Mt. Once the strand is determined via identifying the markers. Sinai School of Medicine to encrypt hidden messages within microdots. The mixture is then dried on to paper that can be cutup into microdots with each dot containing billions of strands of DNA. Not only is the microdot difficult to detect on the plain message medium but only one strand of those billions within the microdot contains the message. Bancroft and his team were successfully able to encode and decode the famous message „June 6 Invasion: Normandy‟ within a microdot placed in the full stops on a posted typed letter. The key to decrypting the message lies in knowing which markers on each end of the DNA are the correct ones which mean there must be some sort of shared secret that is transmitted previously for this type of transmission to work successfully. the recipient uses polymerase chain reaction to multiply only the DNA which contains the message and applies the simple code to finally decode the true message. . The principles used in this experiment used a simple code to convert the letters of the alphabet into combinations of the four bases which make up DNA and create a strand of DNA based on that code. The encoded piece of DNA is then placed into a normal piece of human DNA which is then mixed with DNA strands of similar length. A piece of DNA spelling out the message to be hidden is synthetically created which contains the secret encrypted message in the middle plus short marker sequences at the ends of the message.
Structure of secret message DNA strand illustrating marker sequences. key used to encode message in DNA. this methodology would allow engineers to place DNA authentication stamps within organisms they are working with to easily detect counterfeits or copyright infringements. b. . Gel analysis of DNA strand. Sequence of cloned product of PCR amplification and resulting encoded message.  The DNA microdot team does see this technology having applications in another field however – that of authentication. DNA Steganography. c. d. a.Fig 6. With the amount of plant and animal genetic engineering that is taking place today and will continue to do so in the future.
the possibility of counterfeiting this merchandise is difficult to say the least. sports collectibles and limited edition art markets such as original animation cells distributed by the Hanna Barbara group of artists. databasing . DNA-tagging is much cheaper in comparison and ultimately more difficult to thwart. As it is estimated that the human genome is roughly 3 billion base pairs in size. For the Sydney games. and the samples taken were from a random athlete from a Olympic team of hundreds. A hand held scanner is then used to scan the inked area of the clothing to determine if a piece of merchandise is authentic or not. a Canadian company named DNA Technologies was able to showcase its DNA-tagging abilities on the world stage in the summer of 2000. DNA inks were applied too nearly 50 million items at a cost of about five cents each. . including licensing.DNA AUTHENTICATION It is worth mentioning that DNA authentication is currently at work in the marketplace today albeit not in the genetic engineering form envisioned by Bancroft and his team. There are possibilities of this type of technology to be used in the arenas of currency and other such brandable items where existing authentication methods such as holograms are proving ineffective and costly. All Olympic merchandise from shirts and hats to pins and coffee mugs were tagged with special ink that contained DNA taken from an unnamed Australian athlete. In the case of the clothing used in the Sydney Olympic Games. and back-end support. Forms of DNA authentication have already been used for such items as the official clothing from the Sydney Olympic Games. DNA was taken via saliva samples from the athlete and mixed into existing ink compounds which was in turn used in the regular merchandise manufacturing process.
arrived at in a much shorter time than with a conventional computer. Their capacity for memory storage is tremendous. their computational power is incomparable to anything in existence. DNA computing is useful because it has a capacity lacked by all current electronics-based computers: its massively parallel nature. DNA computers do have their disadvantages. though it will certainly be a very good one. What does this mean. 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. They are not programmable and the average dunce can not sit down at a familiar keyboard and get to work. they are inexpensive to build. computers will be a combination of the current models and DNA. on the order of 10^9 calculations per mL of DNA per second! This capability of multiple co temporal calculations immediately lends itself to several classes of problems which a modern electronic computer could never even approach solving. you ask? Well. using the most attractive features of both to create a vastly improved total product. essentially while DNA can only carry out computations slowly. First and foremost. DNA computers could not (at this point) replace traditional computers. research is ongoing in doing Boolean logic with DNA and designing universal (programmable) DNA computers. To give you an idea of the difference in time. Many of the DNA molecules could be reused with a little splicing. Then. being made of common biological materials. 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! However. However. specifically. it took about a week to fish the solution molecules out from the rest of the possible path molecules that had formed. Also. Some think that in the future.ADVANTAGES AND DISADVANTAGES The advantages presented by a DNA computer are amazing. Although Adleman's first application of the computer took only milliseconds to produce a solution. There is also no guarantee that the solution produced will necessarily be the absolute best solution. DNA computers can perform a staggering number of calculations simultaneously. so the whole computer is really materialistically very efficient.
made computations 9 equivalent to 10 or better. genetic programming and algorithms.but it certainly might be used in the study of logic. or a DNA-like biopolymer. Perhaps it won‟t be used to play Quake IV or surf the web -. . Minimal Power Requirements . language systems. Advantages Speed – Conventional computers can perform approximately 100 MIPS (millions of instruction per second). There is no comparison to the power requirements of conventional computers.things that traditional computers are good at -.There is no power required for DNA computing while the computation is taking place. Minimal Storage Requirements – DNA stores memory at a density of about 1 bit per cubic 12 nanometer where conventional storage media requires 10 cubic nanometers to store 1 bit. as a computing substrate along with set of designer enzymes. The chemical bonds that are the building blocks of DNA happen without any outside power source. Combining DNA strands as demonstrated by Adleman. In essence. 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. Considering all the attention that DNA has garnered. encryption. automata. mankinds collective knowledge could theoretically be stored in a small bucket of DNA solution. It certainly has been the molecule of this century and most likely the next one. the genetic code of life itself. The inherent parallelism of DNA computing was staggering. and lots of other interesting things that haven't even been invented yet. arguably over 100 times faster than the fastest computer.And of course we are talking about DNA here.
It is a common feature of all the proposed implementations that the biological operations to be used are assumed to be error-free.MODELS AND FORMATS OF DNA COMPUTATION In the two years that followed. However. Especially for a large problem. The other model is by splicing operation proposed by Head and vigrously followed by many researchers using formal language theory. this model is particularly effective for algorithmic description. There are two general formats in which complex combinatorial sets of DNA molecules may be manipulated. It is shown that the generative power of finite extended splicing systems is equal to that of Turing Machines. Thus. A Facilitated sample handling. Ã Decreased losses during sample handling A Reduction of interference between oligonucleotides A Solid-phase chemistry permits facile purification of the DNA molecules at every step of the process. An operation central to and frequently employed in most models is the extraction of DNA strands containing a certain sequence (known as removal by DNA hybridization). . Also there is a proposal about the tendency of DNA structures to selfassemble as a computational tool. These steps are readily automated. there are some impediments to effective computation by these models. They are addition of a solution to the support and removal (washing) to a solution from the support. the Subgraph isomorphism problem. or even thousands resulting a high probability of incorrect hybridization. the sticker mode has a memory that can both read and written to. Unlike previous models. With the DNA molecules attached to a support. Afterwords. Like previous models. They show that the self-assembly of complex branches known as double cross-overs into two-dimensional sheets or three-dimensional solids is a computationally powerful model. a novel error-resistant model of DNA computation has been proposed by Alan Gibbons and his team that obviates the need for hybridization extraction within the main body of the computation. Â¢ in solution ( solution-phase format) Â¢ attached to a surface (solid-phase format) The solid-phase format possesses many important advantages over the solution-phase format. the number of extractions required may run into hundreds. a lot of theoretical work has been done on generalizing Adleman's approach in order to define a general-purpose DNA-based molecular computer that could also be implemented by an in vitro system. The most important problem with this method is that extraction is not 100% efficient and may at times inadvertently remove strands that do not contain the specified sequence. and the Maximum clique and maximum independent set problem. the experimental manipulations are very simple. Paun and others introduced the so-called sticker model. It is sufficiently strong to solve any of the problems in the class NC and the authors have given DNA algorithms for 3-vertex-colorability problem. Lipton generalized Adleman's model and showed how his model can encompass solutions to other NP-complete problems. Hamiltonian Path Problem. and employs reusable DNA. Permutations Problem.
However. If this is increased to 100 variables. if enhanced to 50 or 100 cities. the function of 2n is exponential whether it counts time or molecules. It has been estimated that Adleman's Hamiltonian path problem. The fundamental problem is that. The minimum amount of required DNA for Lipton's SAT method needs a few grams of DNA molecules for 70 variables.PITFALLS OF DNA COMPUTING The idea of using DNA to solve computational problems is certainly intriguing and elegant. Many enhancive ideas have been published but all of them suffer under this fundamental problem. the minimum DNA requirement of millions of kilograms. and DNA does provide a massive parallelism far beyond what is available on existing siliconbased computers. there are many technological hurdles to overcome. would require tons of DNA.Thus raw idea of brute-force enumeration is not going to work beyond modest problem sizes. Hopefully the future molecular computation methods may bring forth new revolutionary ideas to overcome this very fundamental as well as significant hurdle . Thus it is imperative to bring forth new revolutionary ideas to make this notion of DNA-based computing to work realistically. We give below one of the huge fundamental problem to be solved to attain the goal of designing universally programmable molecular computer. Only time and investment will tell where the initial ideas for DNA computing from those experts will lead.
Lipton. Currently. molecular computing is a field with a great deal of potential. they are developing new branches in this young field. there came a host of other articles on computation with DNA. In the wake of Adleman's solution of the Hamiltonian path problem. Adleman. and others will come to replace traditional silicon-based machines. Advancements are being made in cryptography. The Princeton contingent has published papers on models for universal DNA computers. Richard Lipton and his graduate students Dan Boneh and Eric Baum. Princeton. NJ. but few results of practical value. and the NEC Research Institute in Princeton. .THE FUTURE OF DNA COMPTUING Some centers of research in this area are at the University of Southern California at Los Angeles. With others elsewhere. Currently. But work continues: in his article Speeding Up Computation via Molecular Biology Lipton shows how DNA can be used to construct a Turing machine. while others have described methods for doing addition and matrix multiplication with these computers. While it currently exists only in theory. a functional DNA "computer" of the type most people are familiar with lies many years in the future. with Dr. where a computer scientist can mess around with biology equipment and come up with something new and valuable. however. Researchers are working on decreasing error in and damage to the DNA during the computations/reactions. 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. it's possible that in the years to come computers based on the work of Adleman. most of them were purely theoretical. a universal computer capable of performing any calculation. with Dr.
And of course we are talking about DNA here. It certainly has been the molecule of this century and most likely the next one. . Production technology of MEMS is advancing rapidly. it certainly will not be done with the procedure described above. look at sequencing.CONCLUSION So will DNA ever be used to solve a traveling salesman problem with a higher number of cities than can be done with traditional computers? Well. This first demonstration of DNA computing used a rather unsophisticated algorithm. allowing for novel integrated small scale DNA processing devices. considering that the record is a whopping 13. but as the formalism of DNA computing becomes refined.509 cities. automation. 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.D thesis takes Celera just one day. Just look at the number of advances in DNA-related technology that happened in the last five years. but because they used some very efficient branching rules." where DNA strands are attached to a silicon substrate in large arrays (for example Affymetrix's genechip). improvements in biotechnology are happening at a rate similar to the advances made in the semiconductor industry. new algorithms perhaps will one day allow DNA to overtake conventional computation and set a new record. using three Digital AlphaServer 4100s (a total of 12 processors) and a cluster of 32 Pentium-II PCs. what once took a graduate student 5 years to do for a Ph. the genetic code of life itself. On the side of the "hardware" (or should I say "wetware"). The future of DNA manipulation is speed. It took this group only three months. this isn't surprising. Considering all the attention that DNA has garnered. or a DNA-like biopolymer. The solution was possible not because of brute force computing power. Today we have not one but several companies making "DNA chips. With the amount of government funded research dollars flowing into genetic-related R&D and with the large potential payoffs from the lucrative pharmaceutical and medical-related markets. The Human Genome Project is producing rapid innovations in sequencing technology. and miniaturization. as a computing substrate along with set of designer enzymes. For instance.
encryption. but the obstacles that face the field such as the extrapolation and practical computational environments required are daunting. The beauty of both these DNA research trends is found in the possibility of mankinds utilization of its very life building blocks to solve its most difficult problems. and lots of other interesting things that haven't even been invented yet.a strong argument for continued research. genetic programming and algorithms. Is DNA computing viable – perhaps.chemistry and medicine. The field of DNA computing is still in its infancy and the applications for this technology are still not fully understood. DNA authentication methods on the other hand have shown great promise in the marketplace of today and it is hoped that its applications will continue to expand. . DNA computing research has resulted in significant progress towards the ability to create molecules with the desired properties . automata. This ability could have important applications in biology .things that traditional computers are good at -. language systems.but it certainly might be used in the study of logic.Perhaps it won‟t be used to play Quake IV or surf the web -.
msci.. Gilbert. Reinhold (1961)  Leonard Adleman.wi. Error-resistant Implementation of DNA Computations.memphis.html  http://www. W. Johnson. Science 266. 1998). Princeton University. 282-296. There's Plenty of Room at the Bottom. ed.leidenuniv. American Mathematical Society (1996) (To appear)  Michael R. III (#48). Feynman.nl/~jdassen/dna.edu/~garzonm/bmc. Alan Gibbons and David Hodgson. Miniaturization. Genetic Programming 2 (WisconsinMadison. IEEE International Conference on Evolutionary Computation (Indianapolis. June 1999)  Other: Genetic Programming 1 (Stanford.html . Garey and David S. V(MIT. 1997)  Richard P. 1021-1024 (1994)  Martyn Amos. Computers and Intractability: A Guide to the Theory of NP-Completeness. 1997). II (#44). IV (Special Issue of Biosystems). Molecular computation of solutions to combinatorial problems. In D.edu/winfree/DNA.html  http://dope. Freeman and Company (1979)  http://www. In Proceedings of the Second Annual Meeting on DNA Based Computers. H.caltech.REFERENCES  DIMACS Proceedings: DNA Based Computers I (#27).
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