MALAVIYA NATIONAL INSTITUTE OF TECHNOLOGY

DNA COMPUTING

Submitted By
Shubham Aggarwal 2009UCP893

10 April, 2012 Department of Computer Engineering MNIT Jaipur

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Declaration
I, Shubham Aggarwal, declare the following regarding the work presented in this Seminar titled DNA Computing.      

This work is done wholly or mainly while in candidature for a B.Tech Degree. Where any part of this report has previously been submitted for a degree or any other qualification at MNIT Jaipur or any other institution, this has been clearly stated. Where I have consulted the published work of others, this is always clearly attributed. Where I have quoted from the work of others, the source is always given. I have acknowledged all sources of help No part of the report is plagiarized and the report does not suffer from any acts of plagiarism.

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Shubham Aggarwal 2009UCP893 B.ACKNOWLEDGMENT I am really thankful to many of the people who really helped me to create my seminar report. My deepest thank to Mrs. 2 . care and constantly encouraging me with their valuable suggestions and enthused thought me seminar work. Meenakshi Tripathi the guide of my seminar report for guiding and correcting various documents of me with attention. 3rd Year Computer Engineering Deptt.Tech. A special mention needs to be made to our friends who have helped us with their valuable suggestions.

DNA COMPUTING.ABSTRACT In this paper I intend to present the computing technology that has a great future . applications and limitations of dna-computing has been made. The salient features of DNA Computer (one that uses dna computing as its basic method of problem solving) have been mentioned. Finally. An insight into the advantages. The paper begins with a brief description of DNA and its structure. the paper discusses the various stages in its path of development at present and the expectations in the near future 3 . An introduction to DNA COMPUTING and its origin have been given .Various operations performed on DNA is discussed in detail. DNA computing is in its infancy and its implications are only beginning to be explored. disadvantages. 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.

...............2....... 12 4...1 General working aspects ....... Applications of DNA Computing ...............................1 Advantages ....................................................................................................... 10 3........................2.....1 Beginning of DNA computing ............... Structure of DNA:..............................................................Contents 1. 6 Basics of DNA .......................................................................................................................... Bibliography ................................................................ 7 2..............................................2 Drawbacks....... annealing and ligation ................................................................. 9 3.................................. 11 4 Nature of DNA computing...... 16 6......................................... 21 4 ............................................................................................................................................................... 8 3.................................................. FUTURE OF DNA COMPUTER ................................................. 20 9...................................................................................2 Information storage and processing capabilities .............................................................................. Similarities ......... 19 7................ 19 8.............................. 13 5............................................................................ DNA OPERATIONS .......................... 12 4......................................................................... 7 2................................................ 15 5......................................................................................................... 11 3......................................................................................................................................... 5 1............1..................................................................................................1 1......................................................................... Differences .................... 5 Concepts of DNA computing .................................................. DNA Characteristics:........... 18 6....................................................................... 15 5..............................................................................2 2.4 Gel-Electrophoresis........ 18 6........................... Comparison of DNA and Electronic Computers ....... 9 3....... CONCLUSION .......................1 Synthesis ...........3 Hybridization separation .....2 Denaturing................. INTRODUCTION .................................................................

he has chosen Hamiltonian path problem (HPP) known to us as the Traveling salesman problem (TSP) and obtained solution using DNA experiments.1 Beginning of DNA computing DNA computing began in 1994 when Leonard Adleman has first shown that computing can be done using DNA also. A new version of a biomolecular computer developed at the Israel Institute of Technology composed entirely of DNA molecules and enzymes. biological molecules that can store huge amounts of information and are able to perform operations similar to a computer's through the deployment of enzymes. Companies like IBM are attempting to use DNA to produce the next generation of processors. were limited to just 765 simultaneous programs. DNA molecules have already been harnessed to perform complex mathematical problems. without using usual machine but using test tubes etc. in a biological laboratory. It can perform as many as a billion different programs simultaneously. biological catalysts that act like software to execute desired operations. it's important to first understand the basic structure of a DNA molecule. 1. Before discussing how DNA can be used in computers. While this technology is not readily available. INTRODUCTION DNA computing is a nascent technology that seeks to capitalize on the enormous informational capacity of DNA. A DNA-based computer has solved a logic problem that no person could complete by hand. Previous biomolecular computers. setting a new milestone for this infant technology that could someday surpass the electronic digital computer in certain areas. DNA computing is an alternative to the way computers work today. For this. or being mass produced. DNA might one day be integrated into a computer chip to create a so-called Biochip that will push computers even faster. Things would not have gone further if the problem he has chosen is simple 5 . the theory behind it is quite old and the development is on going and catching more speed.1. such as the one built by Institute of Science three years ago.

Graph connectivity and knapsack are classical problems solvable in this 6 . now considered the father of DNA computing. is a professor at the University of Southern California and spawned the field with his paper. The promise of DNA computing is massive parallelism: with a given setup and enough DNA. namely some algorithms based on dynamic programming. Technology is currently available both to select the initial strands and to filter the final solution. which is an NP-Complete problem for which there is no polynomial time algorithm using conventional computer. for which massive parallelism would require large amounts of hardware. Adleman has demonstrated how the massive parallelism of a trillion DNA strands can simultaneously attack different aspects of a computation to crack even the toughest combinatorial problems. The power of the method proposed by Adleman is in the fact that tremendous parallelism can be introduced using DNA operations and that helped Adleman to solve an NP-Complete problem. This approach is interesting due to the massive parallelism available in DNA computers. Also during the same time Charles Bennett’s has done some work on DNA computing. 1.” Since then.2 Concepts of DNA computing A DNA computer is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problem.but as he has taken HPP. Since Adleman’s original experiment researchers have developed several different models to solve other mathematical and computational problems using molecular techniques. These algorithms essentially use a brute force approach to solve hard combinatorial problems.[2] Adleman. ”Molecular Computation of Solutions of Combinatorial Problems. Lipton who showed that formula SAT can be solved on a DNA computer generalized Adelman’s techniques. depending on the problem at hand. not simply more DNA. such as the government’s supposedly uncrackable Data Encryption Standard. one can potentially solve huge problems by parallel search. Also there are classes of algorithms which can be implemented on a DNA computer. it created an exciting and made people to think more about DNA computing. This can be much faster than a conventional computer.

If it is destroyed beyond repair. DNA Characteristics:2. The reason dynamic programming algorithms are suitable for DNA computers are that the sub problems can be solved in parallel. It contains vital information that gets passed on to each successive generation. DNA is one of the nucleic acids. The information in DNA:   guides the cell (along with RNA) in making new proteins that determine all of our biological traits gets passed (copied) from one generation to the next The key to all of these functions is found in the molecular structure of DNA.way. the cell dies. If it is changed slightly. 2. as described by Watson and Crick. . 7 .1 Basics of DNA Deoxyribonucleic acid (DNA) is the master molecule of every cell. These problems are solvable by conventional computers in polynomial time. serious consequences may result. DNA computers using dynamic programming could solve substantially larger instances because their large memory capacity than either conventional computers or previous brute force algorithms on DNA computers. DNA is found in the nucleus of every human cell. information-containing molecules in the cell (ribonucleic acid. is the other nucleic acid). Changes in the DNA of cells in multicellular organisms produce variations in the characteristics of a species. It coordinates the making of itself as well as other molecules (proteins). but only so long as they are small enough to fit in memory. or RNA. Over long periods of time. natural selection acts on these variations to evolve or change the species.

cytosine (C). they are often called bases. the four nucleotides that compose a strand of DNA are as follows: adenine (A). This bond follows a property of complementarity: adenine bonds with thymine (A-T) and vice versa (T-A). Figure 2. It consists of a particular bond of two linear sequences of bases.2. This is known as Watson-Crick complementarity. Structure of DNA:DNA (deoxyribonucleic acid) is a double stranded sequence of four nucleotides.2.’end. and thymine (T).helix) was discovered by James Watson and Francis Crick in 1953. cytosine bonds with guanine (CG) and vice versa (G-C). The chemical structure of DNA (the famous double. The double helix is an anti-parallel (two strands of opposite polarity) bonding of two complementary strands.2: Structure of DNA Each DNA strand has two different ends that determine its polarity: the 3. and the 5.’end. 8 . guanine (G).

The synthesizer is supplied with the four nucleotide bases in solution. Information stored in DNA duplex as CG or AT base pairs. Some operations are specific to certain models of DNA computation. They consist of DNA sequences that have been cloned from many different organisms. The instrument makes millions of copies of the required oligonucleotides and places them in solution in a small vial. 3.3.1: Information storage in DNA 9 .1 Synthesis A desired strand of DNA can be synthesized in lab. DNA OPERATIONS All models of DNA computation apply a specific sequence of biological operations to a set of strands. Longer ’random’ strands are available. which are combined according to a sequence entered by the user. These operations are commonly used by molecular biologists. This is possible for strands up to a certain length. Maximum information density of 2 bits per DNA base location 3’-CAACGTTG-5’ 5’-GTTGCAAC-3’ Figure 3.

Figure 3.2: Process of Ligation 10 . In double-stranded DNA. then this may be repaired by DNA ligase. Annealing is the reverse of melting. Since the hydrogen bonds between strands are much weaker than the covalent bonds within strands. This factor was taken into account when designing sequences to represent computational elements. whereby a solution of single strands is cooled.2 Denaturing. which is an enzyme which helps in joining two DNA strands or pairs of nucleotides. if one of the single strands contains a discontinuity. and allowing complementary strands to bind together. the temperature required to break it is slightly higher than that for an A-T pair. Heating breaks the hydrogen bonds between complementary strands. joined by only two hydrogen bonds.3. annealing and ligation Double-stranded DNA may be dissolved into single strands (or denatured) by heating the solution to a temperature determined by the composition of the strand. Since a G-C pair is joined by three hydrogen bonds. the strands remain undamaged by this process.

3. This is due to the fact that the gel is a dense network of pores through which the molecules must travel.4 Gel-Electrophoresis Gel electrophoresis is an important technique for sorting DNA strands by size.3 Hybridization separation Separation by hybridization is an operation often used in DNA computation. Since DNA molecules carry negative charge. However.3. Smaller molecules therefore migrate faster through the gel. thus sorting them according to size. 3. Electrophoresis is the movement of charged molecules in an electric field. We attach to these oligonucleotides a biotin molecule which binds in turn to a fixed matrix. extract all strands containing the sequence TAGACT). when placed in an electrical field they tend to migrate towards the positive pole.g. each lane corresponds to one particular sample of DNA 11 . Since DNA molecules have the same charge per unit length. they all migrate at the same speed in an aqueous solution. The rate of migration of a molecule in an aqueous solution depends on its shape and electrical charge. At this stage the gel is usually photographed for convenience. One such photograph is depicted in Fig. it is necessary to visualize the results. This is achieved by staining the DNA with the fluorescent dye ethidium bromide and then viewing the gel under ultraviolet light. and a charge applied. strands containing X will anneal to the anchored complementary strands. leaving only strands containing X. These may then be removed from the matrix. polyacrylamide or a combination of the two) the migration rate of a molecule is also affected by its size.. Once the gel has been run (usually overnight).3 Gels are interpreted as follows. If we want to extract single strands containing the sequence X. if electrophoresis is carried out in a gel (usually made of agarose. and involves the extraction from a test tube of any single strands containing a specific short sequence (e. The DNA will be placed in a well cut out of the gel. we first create many copies of its complement. If we pour the contents of the test tube over this matrix. Washing the matrix removes all strands that do not anneal.

the genetic material that encodes for living organisms. DNA is the major information storage molecule in living cells. DNA.[1] Instead of using electrical impulses to represent bits of information. Molecular computing may be a way around this limitation. the DNA computer uses the chemical properties of these molecules by examining the patterns of combination or growth of the molecules or strings. Because biological and mathematical operations have some similarities.Figure 3. DNA can do this through the 12 .4: Gel electrophoresis photograph 4 Nature of DNA computing 4.1 General working aspects Bio-molecular computers work at the molecular level. Our computers. with more and more packed onto their silicon chips are approaching the limits of miniaturization. is stable and predictable in its reactions and can be used to encode information for mathematical systems. and billions of years of evolution have tested and refined both this wonderful Informational molecule and highly specific enzymes that can either duplicate the information in DNA molecules or transmit this information to other DNA molecules.

G (guanine) and T (thymine) as the memory units and recombinant DNA techniques already in existence carry out the fundamental operations. which are biological catalysts that could be called the ’software’. it has been estimated that a gram of DNA can hold as much information as a trillion CDs. This means that DNA computing is a far denser packing of molecular information compared with siliconbased computers. 4. A program on a DNA computer is executed as a series of biochemical operations. In a DNA computer. with one another. used to execute the desired calculation. whose genetic sequences encode certain information.2 Information storage and processing capabilities Nucleic Acids are used because of density. A single bacterium cell measures just a micron square . The input and output are both strands of DNA. DNA computers use deoxyribonucleic acids A (adenine). DNA molecules can store far more information than any existing computer memory chip. The strands have been synthesized by combining the building blocks of DNA. each DNA strand represents one possible answer to the problem that the computer is trying to solve. using techniques developed for biotechnology. 4. computation takes place in test tubes or on a glass slide coated in 24K gold. Their potential power underscores how nature could be capable of crunching number better and faster than the most advanced silicon chips. modifying and cloning the DNA strands. To try to put this in some understandable perspective. called nucleotides. efficiency and speed.manufacture of enzymes. which have the effect of synthesizing. C (cytosine).but holds more than a megabyte of DNA memory and has all the computational structures to sense and respond to its environment.about the same size as a single silicon transistor . extracting.3 Efficiency In both the solid-surface glass-plate approach and the test tube approach. The set of DNA strands is manufactured so that all conceivable answers 13 .

This could make the DNA computer more efficient. DNA Words are linked together to form large combinatorial sets of molecules. biochemical reactions are highly in parallel: a single step of biochemical operations can be set up so that it affects trillions of DNA strands. whereas DNA has four (C. Because a set of strands is tailored to a specific problem. Many restriction enzymes cut the two strands of double-stranded DNA at different positions leaving overhangs of single-stranded DNA. Most electronic computers operate linearly and they manipulate one block of data after another. and a pound of DNA would have more computing power than all the computers ever made. Two pieces of DNA may be rejoined if their terminal overhangs are complementary. G. 14 . it performs an enormous number of operations at a time and requires less energy and space than normal computers. DNA computers just need more DNA. Using these operations.are included. While a DNA computer takes much longer than a normal computer to perform each individual calculation. as well as more easily programmable. Information is stored in DNA as CG or AT base pairs with maximum information density of 2bits per DNA base location. A or T). while electronic computers would require additional hardware. a new set would have to be made for each new problem. Complements are referred to as ’sticky ends’. The only fundamental difference between conventional computers and DNA computers is the capacity of memory units: electronic computers have two positions (on or off). Information on a solid surface is stored in a NON-ADDRESSED array of DNA words of a fixed length (16mers). 1000 liters of water could contain DNA with more memory than all the computers ever made. The study of bacteria has shown that restriction enzymes can be employed to cut DNA at a specific word (W). DNA computers are massively parallel. fragments of DNA may be inserted or deleted from the DNA.

NOR) to transform data. for example. To retrieve data. 15 .a key word.digit sequence. OR. by adding a DNA strand designed so that its sequence sticks to the key word wherever it appears on the DNA. generating longer molecules corresponding to every possible 70. which are manipulated to do processes. To simulate that. 5. the logical statement “X or Y” is true if X is true or if Y is true. it would only be necessary to search for a small part of it . the scientists would pour the DNA strands corresponding to “X” together with those corresponding to “Y”. Vast numbers of these sequences would be mixed together. The logical command “AND” is performed by separating DNA strands according to their sequences.000 AND-OR connections.5. Comparison of DNA and Electronic Computers As we have seen the concepts and characteristics of DNA Computer. To solve it. Vast quantities of information can be stored in a test tube. Manipulation of Data: Electronic computers and DNA computers both store information in strings. A DNA computer should be able to solve a satisfiability problem with 70 variables and 1. The information could be encoded into DNA sequences and the DNA could be stored. Similarities Transformation of Data: Both DNA computers and electronic computers use Boolean logic (AND. and the command “OR” is done by pouring together DNA solutions containing specific sequences. NAND. we can now compare the DNA Computers with Conventional Electronic Computers. For example.1. Computation Ability: All computers manipulate data by addition and subtraction. assign various DNA sequences to represent 0’s and 1’s at the various positions of a 70 digit binary number.

Minimal Storage Requirements: DNA stores memory at a density of about 1 bit per cubic nanometer where conventional storage media requires 1012 cubic nanometers to store 1 bit. mankind’s collective knowledge could theoretically be stored in a small bucket of DNA solution. The first ever-electronic computer took up a large room whereas the first DNA computer (Adleman) was 100 micro liters. made computations equivalent to 109 or better. which is all it took for the reactions to occur. Adleman dubbed his DNA computer the TT-100. or about one-fiftieth of a teaspoon of fluid.2. 16 .000 quarts of fluid. in a bank about a yard square. The chemical bonds that are the building blocks of DNA happen without any outside power source. There is no comparison to the power requirements of conventional computers. for test tube filled with 100 micro liters. Speed: Conventional computers can perform approximately 100 MIPS (millions of instruction per second).5. Minimal Power Requirements: There is no power required for DNA computing while the computation is taking place. arguably over 100 times faster than the fastest computer. The inherent parallelism of DNA computing was staggering. Such a bank would be more capacious than all the memories of all the computers ever made. Differences Size: Conventional computers are about 1 square foot for the desktop and another square foot for the monitor. One new proposal is for a memory bank containing more than a pound of DNA molecules suspended in about 1. In essence. Combining DNA strands as demonstrated by Adleman.

Table: Comparison of a DNA computer and a Conventional Computer DNA Computers Conventional Computers Storage Media Nucleic acids Semiconductors Nature of Operations Parallel Sequential Type of Operations Biochemical Operations Logical Operations Speed of each Operation Slow Ultra-High (one bit per cubic nanometer) One million Gbits per square inch More powerful than any supercomputer Smaller than any computer High Fast (10^12 cubic nanometers to store one bit) 7 Gbits per square inch Memory Capacity Data Density Computational Power Less powerful Computer Size Larger size power requirements Not required Required Cost Cheaper Expensive 17 .

including potential polynomial time solutions to hard computational problems.1 Advantages 1) Perform millions of operations simultaneously. thus effectively doubling our capacity to store information 18 . 6) The differentiation between sub sequences denoting individual bits allows a natural border between encoding sub-strands. as another memory block. especially concerning exploring the limitations of computability and to understanding and manipulating bimolecular chemistry. 4) Efficiently handle massive amounts of working memory. It is even said that DNA can be used in devising the wiring schematics for circuits.6. this can be quite useful in figuring out how to route telephone calls. plane trips.  Contributions to fundamental research within both computer science and the physical sciences.  Applications making use of “classic” DNA computing schemes where the use of massive parallelism holds an advantage over traditional computing schemes. This would involve optimizing the routing of raw materials. the DNA models are much more flexible. 7) Using one template strand as a memory block also allows us to use its compliment. 5) The clear advantage is that we have a distinct memory block that encodes bits.  By the DNA methods. potent. and cost effective 6. including those that make use of informational storage abilities and those that interact with existing and emerging biotechnology. 2) Generate a complete set of potential solutions. Applications of DNA Computing As far as applications are concerned. 3) Conduct large parallel searches. It is also been claimed that DNA can be used to solve optimization problems involving business management.  Applications making use of the “natural” capabilities of DNA. and basically any problem that can be turned into a Hamiltonian problem.

3) This is a rather good encoding. Researchers are working on decreasing error in and damage to the DNA during the computations/reactions.2 Drawbacks 1) Generating solution sets. Princeton. as we increase the size of our memory. including those involving: actual error rates. 7. In the wake of Adleman's solution of the Hamiltonian path problem. a functional DNA "computer" of the type most people are familiar with lies many years in the future. and the ability to perform necessary biooperations conveniently in vitro (for every correct answer there are millions of incorrect paths generated that are worthless). But work continues: in his article Speeding Up Computation via Molecular Biology Lipton shows how 19 . molecular computing is a field with a great deal of potential.. we have to ensure that our sub-strands have distinct complements in order to be able to “set” and “clear” specific bits in our Memory. and the NEC Research Institute in Princeton. there came a host of other articles on computation with DNA. with Dr. With others elsewhere. Currently. with Dr. Currently. Richard Lipton and his graduate students Dan Boneh and Eric Baum. they are developing new branches in this young field. Advancements are being made in cryptography. however. most of them were purely theoretical. may require impractically large amounts of memory (lots and lots of DNA strands are required) 2) Many empirical uncertainties. The Princeton contingent has published papers on models for universal DNA computers. but few suits of practical value. Adleman. even for some relatively simple problems. the generation of optimal encoding techniques. 6. while others have described methods for doing addition and matrix multiplication with these computers. however. FUTURE OF DNA COMPUTER Some centers of research in this area are at the University of Southern California at Los Angeles. NJ.

Because the DNA Computing due to its high degree of parallelism. It has been proved by many research accomplishments that any procedure that can be programmed in a silicon computer can be realized as a DNA computing procedure. a universal computer capable of performing any calculation. 20 . research in DNA computing is gaining some pace and there is a wide scope for the researchers to make use of this powerful computing tool. Tackling problems with DNA computing would be more appropriate when the problems are computationally intractable in nature . The field of DNA computing is truly exciting for the revolution it implies will occur within the next few years. 8. CONCLUSION The research in DNA computing is in a primary level. can overcome the difficulties that may cause the problem intractable on silicon computers. Due to its incredible applications in Cryptography. However using DNA computing principles for solving simple problems may not be suggestible.DNA can be used to construct a Turing machine. High information density of DNA molecules and massive parallelism involved in the DNA reactions make DNA computing a powerful tool. where a computer scientist can mess around with biology equipment and come up with something new and valuable. It also demonstrates the current trend of merging and lack of distinction between the sciences.

[3] W. [2] Diana Rooß “Recent Developments in DNA-Computing’’ Lehrstuhl f¨ur Theoretische Informatik Universit¨atW¨urzburg Am Exerzierplatz 3. Germany. University College. London.com www. London Gower Street.org/wiki/DNA_computing 21 .wikipedia.ieee.. 97072 W¨urzburg.Bibliography [1] Adleman L. Molecular computation of solutions to combinatorial problems. 1994. B. M.howstuffworks. [4] External Links::    www.org en. Langdon “Comparison of DNA chip and Computer Vision Data” Computer Science.

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