DNA CRYPTOGRAPHY

Chapter 1
Introduction

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DNA CRYPTOGRAPHY

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Introduction

1.1 DNA Cryptography
DNA cryptography is a new born cryptographic field emerged with the research of DNA computing, in which DNA is used as information carrier and the modern biological technology is used as implementation tool. The vast parallelism and extraordinary information density inherent in DNA molecules are explored for cryptographic purposes such as encryption, authentication, signature, and so on.

1.2 DNA
DNA is the abbreviation for deoxyribonucleic acid which is the germ plasm of all life styles. DNA is a kind of biological macromolecule and is made of nucleotides. Each nucleotide contains a single base and there are four kinds of bases, which are adenine (A) and thymine (T) or cytosine (C) and guanine (G), corresponding to four kinds of nucleotides. A single-stranded DNA is constructed with orientation: one end is called 5′, and the other end is called 3′. Usually DNA exists as double-stranded molecules in nature. The two complementary DNA strands are held together to form a double-helix structure by hydrogen bonds between the complementary bases of A and T (or C and G).

Fig 1.2.1 Double helix structure of DNA

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DNA CRYPTOGRAPHY 1.3 Amino Acid Codes
Amino Acid Name Alanine Arginine Asparagine Aspartic acid (Aspartate) Cysteine Glutamine Glutamic acid (Glutamate) Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine Asparagine or Aspartic acid (Aspartate) Glutamine or Glutamic acid (Glutamate) Unknown amino acid (any amino acid) Translation stop Gap of indeterminate length Unknown character (any character or symbol not in table) Amino Acid Code Nucleotide Codon

A R N D C Q E G H I L K M F P S T W Y V B Z X * ?

GCT GCC GCA GCG CGT CGC CGA CGG AGA AGG ATT AAC GAT GAC TGT TGC CAA CAG GAA GAG GGT GGC GGA GGG CAT CAC ATT ATC ATA TTA TTG CTT CTC CTA CTG AAA AAG ATG TTT TTC CCT CCC CCA CCG TCT TCC TCA TCG AGT AGC ACT ACC ACA ACG TGG TAT, TAC GTT GTC GTA GTG
Random codon from D and N Random codon from E and Q Random codon

TAA TAG TGA --???

Table 1.3.1 Amino acids and codes 1.4 Primer
A primer is a short synthetic oligonucleotide which is used in many molecular techniques from PCR to DNA sequencing. These primers are designed to have a sequence which is the reverse complement of a region of template or target DNA to which we wish the primer to anneal.

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DNA CRYPTOGRAPHY

Some thoughts on designing primers
1. primers should be 17-28 bases in length; 2. base composition should be 50-60% (G+C); 3. primers should end (3') in a G or C, or CG or GC: this prevents "breathing" of ends and increases efficiency of priming; 4. Tms between 55-80oC are preferred; 5. 3'-ends of primers should not be complementary (ie. base pair), as otherwise primer dimers will be synthesised preferentially to any other product; 6. primer self-complementarity (ability to form 2o structures such as hairpins) should be avoided; 7. runs of three or more Cs or Gs at the 3'-ends of primers may promote mispriming at G or C-rich sequences (because of stability of annealing), and should be avoided.

1.5 Transcription and Translation
Transcription, or RNA synthesis, is the process of creating an equivalent RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA in the presence of the correct enzymes. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, anti-parallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. Translation is the first stage of protein biosynthesis (part of the overall process of gene expression). Translation is the production of proteins by decoding mRNA produced in transcription. Translation occurs in the cytoplasm where the ribosomes are located. Ribosomes are made of a small and large subunit which surrounds the mRNA. In translation, messenger RNA (mRNA) is decoded to produce a specific polypeptide according to the rules specified by the genetic code. This uses an mRNA sequence as a template to guide the synthesis of a chain of amino acids that form a protein. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA are not necessarily translated into an amino acid sequence.

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such as that of a natural language. Encryption is the process of scrambling the plaintext using a known algorithm and a secret key. Here we provide basic terminology used in cryptography. each PCR primer (20-27)-mer nucleotides long is a comparatively perfect selection.DNA CRYPTOGRAPHY 1. Two complementary oligonucleotide primers are annealed to double-stranded target DNA strands.6 Cryptography Data security and cryptography are critical aspects of conventional computing and may also be important to possible DNA database applications. which transforms the encrypted message back to the original form using a key. Such a system is the one-time-pad cipher. The goal is to transmit a message between a sender and receiver such that an eavesdropper is unable to understand it. 1. and is one of the most important inventions in modern biology. The goal of encryption is to prevent decryption by an adversary who does not know the secret key. and lay-ing the basis for future development. An unbreakable cryptosystem is one for which successful cryptanalysis is not possible. establishing corresponding theories. In this study. searching for simple methods of realizing DNA cryptography. Decryption is the reverse process. It gets its name from the fact that the sender and receiver each possess identical notepads ¯lled with random data. The PCR is a very sensitive method. The output is a sequence of characters known as the ciphertext. Plaintext refers to a sequence of characters drawn from a ¯nite alphabet. Each piece of data is used once to encrypt a message by the sender and to decrypt it by the receiver. * The main goal of the research of DNA cryptography is exploring characteristics of DNA molecule and reaction. Thinking about the highly stability of PCR. discovering possible development directions. and a single target DNA molecule can be amplified to 106 after 20 cycles in theory. after which it is destroyed. Thus one can effectively amplify a lot of DNA strands within a very short time. and the necessary target DNA can be amplified after a serial of polymerase enzyme. we selected each PCR primer 20-mer nucleotides NIT KURUKSHETRA 5 . Polymerase Chain Reaction (PCR) is a fast DNA amplification technology based on Watson-Crick complementarity.7 Advantages Of DNA Cryptography The difficult biological problem referred to here is “It is extremely difficult to amplify the message-encoded sequence without knowing the correct PCR two primer pairs”.

1. their security is based on Heinsberg's Uncertainty Principle. 1.9. he must choose two primer sequences from about 10^23 kinds of sequences (the number of combination taking 2 sequences from 420 candidates). so much as P=NP. Quantum cryptography came into being in the 1970s.1 Development Traditional cryptography can be traced back to Caesar cipher 2000 years ago or even earlier.8 Limitations Of DNA Cryptography (i) Lack of the related theoretical basis. Even if an eavesdropper is given the ability to do whatever he wants. 1.9 Comparisons among DNA cryptography. It is impossible for an adversary to obtain a totally NIT KURUKSHETRA 6 . an adversary with infinite power of computation can break them theoretically. Related theory is almost sound. If an adversary without knowing the correct two primer pairs wants to pick out the message encoded sequence by PCR amplification. we believe that this biological problem is difficult and will last a relatively long time.2 Security Only computational security can be achieved for traditional cryptographic schemes except for the one-time pad. Any behavior of eavesdropping will change the cipher so it can be detected. (ii) Difficult to realize and expensive to apply. and has infinite computing re-sources. It is shown that quantum computers have great and striking computational potential. Differently. traditional cryptography and quantum cryptography 1. By and large. It is a special function in PCR amplification that having the correct primer pairs. it is still impossible to break such a scheme. Quantum cryptographic schemes are unbreakable under current theories. that is to say.9. DNA cryptography has only nearly ten years history. All the practical ciphers can be seen as traditional ones. the theory basis is under research and the application costs very much. It would still be extremely difficult to amplify the message-encoded sequence without knowing the correct two primer pairs. and the theory basis has been prepared while implementation is difficult. they have not been plunged into practical use. Although there is uncertainty about the computational power of quantum computers. it is possible that all the traditional schemes except for the one-time pad can be broken by using the future quantum computers.DNA CRYPTOGRAPHY long. So.

authentication. the problem as to what is the extent this kind of security and how long it can be maintained it is still under exploration. only by physical ways can the cipher text of DNA cryptography be transmitted. Using the traditional cryptography we can realize purposes as public and private key encryption. and so on. in view of the development of biological techniques and the requirement of cryptography. thus the attempt to tamper but without being detected in vain.DNA CRYPTOGRAPHY same the quanta with the intercepted one. quantum key agreement schemes have unconditional security. steganography.10 Development directions of DNA cryptography Since DNA cryptography is still in its immature stage. wireless channel and even by a messenger. this making it hard to predict the future. magnetic medium.9. Due to the vast parallelism. such as secure data storage. the data can be transmitted by wire. DNA and other storage medium. cash ticket and identification card. Researches of all the three kinds of cryptography are still in progress. and a great many problems remains to be solved especially for DNA and quantum cryptography. 1. However. Nonetheless. which makes it infeasible to implement publickey encryption and digital signature as easily as traditional one does.3 Application Traditional cryptosystems are the most convenient of which the computation can be executed by electronic. Therefore. quantum as well as DNA computers. we hold the following opinions: NIT KURUKSHETRA 7 . Under the current level of techniques. and the storage can be CDs. exceptional energy efficiency and extraordinary information density inherent in DNA molecules. digital signature. it is too early to predict the future development precisely. But from the above discussions we think it is likely that they exist and develop conjunctively and complement each other rather than one of them falls into disuse thoroughly. 1. the main security basis is the restriction of biological techniques. fiber. identity authentication and digital signature. DNA cryptography can have special advantages in some cryptographic purposes. Quantum cryptosystem is implemented on quantum channels of which main ad-vantage lies in real-time communication. DNA can even be used to produce unforgeable contract. which has nothing to do with the computing power and immunizes DNA cryptographic schemes against attacks using quantum computers. The disadvantage lies in the secure data storage. For the DNA cryptography.

DNA cryptography does not absolutely repulse traditional cryptography and it is possible to construct a hybrid cryptosystem of them. i. and utilizing difficult biological problems that one can utilize but still far from fully understand them as the secure foundation of DNA cryptography to realize novel crypto-system which can resist the attack from quantum com-puters. realizing fast encryption and decryption based on the vast parallelism. Encryption and decryption algorithms hard to be implemented using electronic computers may be feasible using DNA ones with regard to their vast parallel computational ability. The communication model for DNA encryption is also made up of two par-ties. Thus. which obtain the secret key in a secure or authenticated way and then communicate securely with each other in an insecure or unauthenticated channel. More precisely. it must be assumed that an attacker knows the basic biological method the designer used. the advantages inherent in DNA should be fully explored. Since it has not been made sure whether quan-tum computers threaten the hardness of various mathematical hard problems. an attacker should be fully aware of all the details of encryption and decryption except the decryption key. if DNA cryptography is necessary to be developed. It is under this assumption that a cryptosystem can be said secure when any attacker cannot break it. a sender and a receiver. their computational security will be inherited into DNA schemes. these problems being se-curity basis cannot be excluded absolutely. 2) Security requirements :Regardless of the many differences between DNA and traditional cryptography.e.DNA CRYPTOGRAPHY 1) DNA cryptography should be implemented by using modern biological techniques as tools and biological hard problems as main security basis to fully exert the special advantages. such as developing nanoscopic storage based on the tiny volume of DNA. Thereby. If other kinds of cryptosystems are necessary to be researched and developed. they should have properties such as higher security levels and storage density etc. if described by mathematical methods. are easier to be implemented than physical and chemical ones in the present era of electronic computers and the Internet. and has enough knowledge and excellent laboratory devices to repeat the de-signer’s operations. The security requirements should also be founded upon the assumption proposed by Kirchoff that security should depend only on the secrecy of decryption key. which cannot be realized by electronic computers by using mathematical methods. that is. Encryption and decryption are procedures of data transform which. If these schemes withstand attacks by quantum computers. The only thing NIT KURUKSHETRA 8 . they both satisfy the same characteristic of cryptography.

The cur-rent goal or difficulty is to find and make use of the utmost potential. Presently. Modern biology lays particular stress on experiments rather than theories.11 DNA Digital Coding Technology NIT KURUKSHETRA 9 . Scientists can easily operate DNA with the aid of kinds of restriction enzymes only after DNA strands are amplified with amplification technology such as PCR. to establish the theoretical basis and to accumulate the experience. In a DNA cryptosystem. it is still difficult to operate the nanoscopic DNA directly. exceptional energy efficiency and extraordinary information density inherent in DNA. In fact. With the current technology. and sometimes the experiment conditions. If the only requirement is to improve the density of storage. Sound theories have not been founded for both DNA computing and cryptography. 3) For DNA cryptography. 4) Currently. There is no efficient way to measure the hardness of a biological problem and the security level of the corresponding cryptosystems based on the problem. The method is easier to be implemented than encoding message into nucleotides directly while the storage density is somewhat lower. which makes the operations of input/output faster and more convenient. based on which the design of secure and practical DNA cryptosystems is possible. but the related research is in its initial stage. It is more practical to make use of colony property of plentiful DNA for cryptographer. It can be proved that there are vast parallelism.DNA CRYPTOGRAPHY not known by the attacker is the key. store data by DNA chips and read data by hybridization. It is certainly urgent to find such a method similar to computational complexity. the current research target should lie first in security and feasibility. although the related research is just in its initial stage. This motivates the research of DNA computing and cryptography. second in storage density. A sound cryptosystem should be secure as well as easy to be implemented. it is also impossible to store all the worldwide data by using several grams of DNA. For example. the main task for DNA cryptographers is to establish the theory foundations and to accumulate the practical experience. The development of modern biological technology makes it possible to express data by DNA. the most important is to find the sound properties of DNA that can be used to computation and encryption. it is hard to implement DNA cryptography at the present technique level. 1. a key is usually some substances of biological materials or a preparation flow.

that is A to T and C to G according to Watson-Crick complementarity rule. 0123/GATC. 0123/GTAC. (4). 0123/TGCA. two DNA strands are held together complementary in terms of sequence. that is 0(00) to 3(11) and 1(01) to 2(10). Take DNA digital coding into account. 0123/TCGA. 0123/AGCT) which are topologically identical fit the complementary rule of the nucleotide bases. 0123/ACGT. the complementary rule that (~0)=1. whose security on the scheme is mainly based on the difficult biological problems and difficult mathematical problems. To decrease the redundancy of the information coding andimprove the coding efficiency compared to the traditional character DNA coding. The simplest coding patterns to encode the 4 nucleotide bases (A. We will show the way of exchanging message safely just between specific two persons. (2). By using the technology of DNA digital coding. (3). 0123/CATG. This pattern could perfect reflect the biological characteristics of 4 nucleotide bases and have a certain biological significance. which are adenine (A) and thymine (T) or cytosine (C) and guanine (G) in DNA sequence. As we all know. 0123/CTAG. It is suggested that the coding pattern in accordance with the sequence of molecular weight. Obviously. The DNA sequence after preprocessing by DNA digital coding techniques is able to do digital computing and adapt to the existing computer-processing mode. So among these 24 patterns. C. 1. The digital coding of DNA sequence is very convenient for mathematical operation and logical operation and may give a great impact on the DNA bio-computer. the traditional encryption method such as DES or RSA could be used to preprocess to the plaintext in the cryptography scheme. We shall call the NIT KURUKSHETRA 10 . T. The binary digital coding of DNA sequences prevails over the character DNA coding with the following advantages: (1). 2(10). There are four kinds of bases. the most fundamental coding method is binary digital coding. which is anything can be encoded by two state 0 or 1 and a combination of 0 and 1. only 8 kinds of patterns (0123/CTAG. G) is by means of 4 digits: 0(00). and (~1=0) is proposed in this DNA digital coding. 3(11). According to this complementary rule. it should reflect the biological characteristics of 4 nucleotide bases. is the best coding pattern for the nucleotide bases. there are 4!=24 possible coding patterns by this encoding format. we will describe the system design of encryption scheme.DNA CRYPTOGRAPHY In the information science. which facilitates the direct conversion between biological information and encryption information in the cryptographyscheme. 1(01). in a double helix DNA string.12 System Design Of Encryption Scheme Now.

we can get completely different ciphertext from the same plaintext. We will describe the general process of the encryption scheme as follows. The encryption process is: C = EKA (M) The decryption process is: DKB (C) = DKB (EKA (M)) = M It is difficult to obtain M from C unless one has KB. Above all. material. KB and C are not limited to digital data. Bob uses KB to translate the ciphertext C into the plaintext M by a translation D. as well as an decryption key KB that is a pair of PCR primers and Bob’s secret key d. Encryption First of all. Through this preprocess operation. we can get an encryption key KA that is a pair of PCR primers and Bob’s public key e. Using traditional cryptography RSA to preprocess to the plaintext. d). and the intended receiver Bob. We call translation E as encryption process and C as ciphertext. but can be any method. The intended receiver Bob has a pair of keys (e. We call this preprocess operation is pretreatment data process (data pre-treatment). the sender Alice will translate the plaintext M into hexadecimal code by using the built-in computer code. etc. Then hexadecimal code is translated into binary plaintext M_ by using third-party software. Alice uses KA to translate a plaintext M into ciphertext C by a translation E. but can be any physical or chemical or biological or mathematical process such as traditional encryption method. and an intended receiver Bob who owns a decryption key KB (KA = KB or KA ≠ KB). A. KA. Suppose there is a sender Alice who owns an encryption key KA. After a pair of PCR primers is respectively designed and exchanged over a secure communication channel. B. such as DNA sequence. we extend the definition of this encryption scheme as follows. Alice translates the binary plaintext M_ into the binary ciphertext C_ by using Bob’s public key e. E and D are also not limited to mathematical calculations. data. The message-receiver Bob also designs a DNA sequence which is 20-mer oligo nucleotides long as a reverse primer for PCR amplification and transmits it to Alice over a secure channel. which can effectively prevent attack from a possible word as NIT KURUKSHETRA 11 .DNA CRYPTOGRAPHY sender Alice. Finally. Here. an encryption scheme with DNA technologies was proposed in this paper. Key Generation The message-sender Alice designs a DNA sequence which is 20-mer oligo nucleotides long as a forward primer for PCR amplification and transmits it to intended receiver Bob over a secure channel.

he could amplify the secret-message DNA sequence by perform PCR on DNA mixture. Then.12. he could retrieve the plaintext M sended from Alice from the reverse preprocess operation using his secret key d. 1. The last process of this encryption is that Alice generates a certain number of dummies and puts the secrete-message DNA sequence among them. After coding. After mixing the secretemessage DNA sequence with a certain number of dummies. Since the intended receiver Bob had gotten the correct PCR two primer pairs through a secure way. In this scheme. each 20-mer oligo nucleotides long. the secrete-message DNA sequence is prepared. Alice sends the DNA mixture to Bob using an open communication channel.DNA CRYPTOGRAPHY PCR primers. Alice synthesizes the secret-message DNA sequence which is flanked by forward and reverse PCR primers. Thus. This decryption process is not only a mathematic computation. Decryption After the intended receiver Bob gets the DNA mixture.1 Fig. Alice translates the binary ciphertext C_ into the DNA sequence according to the DNA digital coding technology. The pretreatment data flow chart is described in Fig.12. After Bob amplifies the secrete-message DNA sequence. the dummy is generated by sonicating human DNA to roughly 60 to 160 nucleotide pairs (average size) and denaturing it. he can easily find the secrete-message DNA sequence.1 Data pre(post)treatment flow chart NIT KURUKSHETRA 12 . but also a biological process.1. C. It is necessary that each dummy has the same structure as the secretemessage DNA sequence.

DNA CRYPTOGRAPHY In the following part of this section.12. only when both of the primer sequences were correct. we thoroughly discuss details of this encryption scheme with an example shown in fig. In this scheme. that is: 01000111 01000101 01001110 01000101 01000011 01010010 01011001 01010000 01010100 01001111 01000111 01010010 01000001 01010000 01001000 01011001 NIT KURUKSHETRA 13 . Step 2: Data pretreatment. but respectively designed complete cooperation by sender and receiver. Step 1: Key Generation. the amplification was not efficient when one of a primer pair is incorrect. Here we choose “GENECRYPTOGRAPHY” (gene cryptography) as plaintext to encrypt. because even if an adversary somehow caught one of a primer pair. the intended PCR two primer pairs was not independent designed by sender or receiver. The message-sender Alice and the message-receiver Bob respectively design and exchange a pair of PCR primers over a secure communication channel.12.3. 1. 1. The encryption and decryption keys are a pair of PCR primers. The result of the PCR amplification is shown in fig. the amplification could be successful. that is: “47 45 4E 45 43 52 59 50 54 4F 47 52 41 50 48 59”.2. This operation could increase the security of this encryption scheme. We first convert this sentence into hexadecimal code by using the built-in computer code. Then we translate hexadecimal code into binary plaintext M_ by using third-party software.

12. while the most NIT KURUKSHETRA 14 .DNA CRYPTOGRAPHY Fig. Finally.2. The Huffman code is the most economical and would be the best for encrypting text for short-term storage. Step 5: data post-treatment. Both the comma code and the alternating code. Result of the PCR amplification Step 3: Encryption. such as DNA ink or DNA book. After that. Step 4: Decryption. Fig. Alice converts the binary ciphertext C_ into the DNA sequence by using the DNA digital coding technology. the secrete-message DNA is prepared. Then. Alice will encrypt the binary plaintext M_ into the binary ciphertext C_ by using Bob’s public key e.13 The codes The three codes described in detail in this paper are referred to as the Huffman code. symbols or numbers. Bob translates the secret-message DNA sequence into the binary ciphertext C_ by using the DNA digital coding technology. 1. 1. Thus. Alice sends the DNA mixture to Bob using an open communication channel. It should be stated at the outset that none of them fulfill all the criteria listed above. providing that this text lacked any sort of punctuation. Bob can decrypt the binary ciphertext C_ into the binary plaintext M_ by using his secret key e. After the intended receiver Bob gets the DNA mixture.12. After the binary plaintext M_ has been recovered. Flow chart of Encryption scheme system. 1. he can easily pick out the secret-message DNA sequence by using the correct primer pairs.3. Bob can retrieve the plaintext M. After mixing the secrete-message DNA sequence with a certain number of dummies. a secret-message DNA sequence containing an encoded message 64 nucleotides long flanked by forward and reverse PCR primers. “GENECRYPTOGRAPHY” from the binary plaintext M_ by using data posttreatment. the comma code and the alternating code.

Given a suitable start signal. For instance. it is possible to construct very economical codes.g.1 Given the frequencies of occurrence of these letters. Consequently they cannot be included when deriving the Huffman code. and the longest codon is five bases long (representing q and z.e. i. A. at the expense of economy. as the frequency of these characters will be heavily text-dependent. One could counteract this problem by using three instead of four bases (e. shorter than the codons of any of the other codes described in this paper. The unambiguous nature of the Huffman code shown in Table 1 can be seen by encoding any group of letters with it and then decoding them from the beginning of the sequence: there is only one way it can be done. the base sequence CATGTAGTCG can only be read from the beginning as hester – no other interpretation of the message is possible. While of the three codes discussed here. with the most frequent character being given the least number of symbols and the least frequent the most number of symbols. the message generated by a Huffman code is unambiguous. That is. and so would be best suited to the encryption of information for long-term storage. In the code. it does have two disadvantages. the alternating code is also unambiguous. such a code is straightforward to construct (Materials and methods).2 bases.13.1 The Huffman code By varying the number of symbols allotted to a character in a code. there is only one way in which the stream of symbols comprising the message can be read. The Huffman code is the only code discussed in this paper with variable length codons. the most infrequent letters in the English language). the most frequently used letter in the English language). Because of the variable length of the codons. The first is that it does not cater for any symbols or numbers. the Huffman makes the most economical use of DNA. the shortest codon is just one base long (representing e. codes in which the text is encrypted by the minimum number of symbols – it is as short as it can possibly be. C and T). The average codon length is 2. The others all have NIT KURUKSHETRA 15 .DNA CRYPTOGRAPHY uneconomical of the codes. G. 1. no obvious pattern emerges when they are joined together to encode a message.13. The naive investigator might confuse it with natural DNA and therefore not appreciate its significance. C and T for the letters of the English alphabet is shown in Table 1. As well as being compact. have the advantage that they generate base sequences which are obviously artificial. The Huffman code constructed with the four DNA bases A. once the start point has been specified. One of the best ways of constructing an economical code is to use Huffman’s method (Huffman 1952). The second disadvantage of the Huffman code relates to its possible use in long-term storage of information.

which is always the same: e. the comma. and the C’s and W’s can adopt any arrangement (e. but not G. and therefore the comma NIT KURUKSHETRA 16 . G− − − − − G− − − − − G− − − −− G. A and T.13.g.DNA CRYPTOGRAPHY fixed length codons.g. We note that. facilitating the construction of message DNA (‘Criteria for an optimal code’. The repetition of G every six bases must be construed by any careful sequence analyst as a deliberate device. The codons that slot into the gaps in the above framework are made up of the remaining bases C. consecutive 5-base codons are separated by a single base. e. Most (83%) point mutations give nonsense codons.suggested by unrelated work . There are 80 codons in this set. This kind of an arrangement. ATCAC. with the C of the latter always being located in the top strand.1 The Huffman code 1. where W = A or T. These codons are further restricted to three A:T base pairs and two G:C base pairs.2 The comma code In the comma code. Table 1.13. has the advantage that it will generate a set of codons with isothermal melting temperatures.g. WWCWC or WCCWW). in a similar manner to the above. The codons take the general form CWWWC. above). the Huffman code has also been used to construct a ‘perfect’ genetic code comprising variable length codons.

the reading frame is clear. Unlike the comma code.DNA CRYPTOGRAPHY code is good at detecting errors. As well as creating message DNA of an obviously artificial nature. when the commas are included. the alternating structure has the unusual property that. It is very unlikely that the alternating structure formed by strings of these codons would go unremarked – even short stretches (8 base pairs) of alternating purines and pyrimidines have been noted in naturally occurring DNA . three (17%) will produce sense codons (mutation of an A to a T. where R = A or G and Y = C or T (although there is no reason why the purines and pyrimidines should not alternate YRYRYR. which could further complicate the interpretation of the other codes. NIT KURUKSHETRA 17 . there is no automatic reading frame. it might be difficult to orientate oneself with respect to the message. It should also be noted that the base composition of the codons will give. since 67% of single point mutations result in nonsense codons. but less so than the comma code.13. or vice versa) and therefore the remaining 83% of single point mutations will given nonsense codons. Furthermore. message DNA with the unusual property of a 1:1 ratio of A:T to G:C base pairs. in a given piece of message DNA. Of these 18 single point mutations. For example. the number of G:C pairs will be the same as the number of A:T pairs. As in the comma code. Three possible point mutations can occur at each position of the codon GCWWWC (which includes the initial comma). the alternating code has two other advantages of the comma code: it is isothermal.3 The alternating code The alternating code comprises sixty-four 6-base codons of alternating purines and pyrimidines: RYRYRY. But the principal attraction of the comma code is the reading frame established by the regular pattern of repeating G’s. it is not difficult to spot the codon containing the deletion mutation in the following comma-coded sequence: GATCACGATTCCGCTATGACTCAG. 1. and. With the comma code. The other two codes described do not have this advantage. it offers some protection against deletion and insertion mutations. unless a start point is specified. Like the comma code it does not use DNA economically. and it is error-detecting. and therefore there are 18 single point mutations altogether. or be fixed in other arrangements such as YYYRRR or RRYYRY).

DNA CRYPTOGRAPHY Table 1. Although twenty codons is not sufficient to comfortably encrypt text. the 3-base codons AGG. Three others are outlined briefly in this section. showed that twenty 3-base codons could be selected to act in a comma-free manner.2 General features of the codes Table 1. For example. Before experimental data for the nature of the genetic code became available. ACG and GTG are part of a comma free code. As the name suggests. one could not begin reading one base in. there were a number of suggestions as to what form it might take.13. In their original paper on the subject. But.13. in the sequence ACGGTGGTGACGAGG. or the only types of code.13. there is a set of fifty-seven 4-base codons that would be enough to carry out this task. a comma-free code is just a comma code without the commas. at CGG. because CGG does not belong to the set. by restricting oneself to a set of fixed-length codons with particular base combinations. possible.4 Other codes The three codes detailed above are meant to be illustrative rather than exhaustive. the codons in this set can be chosen such that only one reading frame is ever possible – all the others give nonsense. Any combination of these codons will give a sequence which can be read in only one way. One might think that removing the commas would give a code without a reading frame.3 Advantages of the codes 1. They are by no means the only codes. For instance. One of these was the comma-free code. There is nothing particularly wrong with the commaNIT KURUKSHETRA 18 .

the commafree code would be error-detecting to a certain extent. to give a larger codon set (34 = 81 as opposed to 33 = 27). Like the alternating and comma codes. perhaps the most obvious code of all is one similar to the genetic code – a triplet code. In fact. since it is quite economical and establishes an automatic reading frame. the only significant clue to the synthetic nature of message DNA containing text encrypted with a comma-free code would be the absence of runs of four identical bases (e. CTT to encode for ’<’ and AAG for ’>’).g. There are no such absences in natural DNA. Finally. as the comma-free code forbids these. In fact. with error-correcting codons representing symbols with opposite meaning (e. message DNA has already been constructed with a 3-base codon version of this code.DNA CRYPTOGRAPHY free code as a message-encoding scheme. We would probably use a 4-base codon version of this code. One other simple code that should also be mentioned because it produces DNA that is obviously artificial DNA is one that uses only three of the four different bases. However. it ought to be rather good. AAAA).g. Codon assignment in this case may be done in a non-random fashion. however. in a similar manner to the codons of the comma code. such that a degree of error-protection could be achieved. NIT KURUKSHETRA 19 .

DNA CRYPTOGRAPHY Chapter 2 Objective NIT KURUKSHETRA 20 .

Allow users to apply the encoding on textual information. Added to this it is aimed to obtain a clear understanding of the Java cryptography and its native API. Hide the biological complexity involved in basic processing of DNA cryptography. understanding the limitations and configurations needed to perform a new technique (DNA 2.1 Objective The aim of our project is to build a system which fulfills the following objectives : • • • • To implement the basic concepts of DNA Cryptography. To obtain an encoded text as desired.DNA CRYPTOGRAPHY 2. are available in the market this project aims at Although many encoding techniques Cryptography) for encoding text. NIT KURUKSHETRA 21 .2 Product Perspective The main purpose or goal of the project is to implement the basic fundamentals of DNA Cryptography using the Java platform so as to produce an encoding tool capable of applying the elementary encoding transformations to the text.

DNA CRYPTOGRAPHY Chapter 3 System Requirement Analysis NIT KURUKSHETRA 22 .

~ Encoding the text using DNA cryptography and PCR amplifications.DNA CRYPTOGRAPHY 3 System Requirement Analysis: 3.1 Characteristics The important characteristics of the system being developed: FUNCTIONS ~ Loading the text file from source.  HARDWARE SPECIFICATIONS Processor Intel Pentium III or higher Color Monitor 800 x 600 or higher resolution PCR (Polymerase Chain Reaction) Monitor Amplifier Amplifier NIT KURUKSHETRA 23 . INPUT ~ User input text file for encoder ~ Encoded file for the decoder OUTPUT ~ A Transformed encoded text for sending to decoder ~ Original text file at decoder 3.2 System Requirements The following requirements must be fulfilled to run the software on any computer system .

4.0 Programming Language JAVA 5 3.1 Usecase diagram(encoder) NIT KURUKSHETRA 24 .DNA CRYPTOGRAPHY  SOFTWARE SUPPORT Operating System Framework 3.3 Technology Used Windows 9x / XP/ NT / 2000 JVM and JRE installed.1 Encoder Fig 3.4 Use Case Diagram 3.4. NetBeans 6.

4.2 Decoder Fig 3.4.2 Usecase diagram(decoder) NIT KURUKSHETRA 25 .DNA CRYPTOGRAPHY 3.

DNA CRYPTOGRAPHY Chapter 4 Project Overview NIT KURUKSHETRA 26 .

PCR Amplifier is the hardware component that will be used for converting the text into a graphical format which reduces the space consumed.1 Project overview The above figure shows the basic components comprising a typical general-purpose system used for dna cryptography. In dedicated applications sometimes specialized computers are used to achieve the desired level of performance. The functions of each component is as described below. The computer is a general computer that can range from a PC to a supercomputer.DNA CRYPTOGRAPHY 4 Project Overview Network (To Receiver) Text File PCR Computer Amplifier Fig 4. NIT KURUKSHETRA 27 . Text File is a user input that has to be encoded. It consists of specialized modules that perform specific tasks.

DNA CRYPTOGRAPHY Chapter 5 Software Design NIT KURUKSHETRA 28 .

1 Flow Diagram(encoder) NIT KURUKSHETRA 29 . Key generation 2.)) = P. Decryption 5.) = DKB (EKA (P.DNA CRYPTOGRAPHY 5 Software Design 5.2 Flow Diagrams 5. T.T. STEPS: 1.) The decryption process is: DKB (C.1 Methodology OF Encryption Scheme The encryption process is: C. = EKA (P. Encryption 3.T.T.1 Encoder Fig 5.T.2.2.

2.DNA CRYPTOGRAPHY 5.2 Flow Diagram(decoder) NIT KURUKSHETRA 30 .2.2 Decoder Fig 5.

1 Encoder Fig 5.3.1 Class diagram(encoder) NIT KURUKSHETRA 31 .3 Class Diagrams 5.3.DNA CRYPTOGRAPHY 5.

2 Class diagram(decoder) NIT KURUKSHETRA 32 .DNA CRYPTOGRAPHY 5.3.3.2 Decoder Fig 5.

3 KeyGen Fig 5.3.3.3 Class diagram(keyGen) NIT KURUKSHETRA 33 .DNA CRYPTOGRAPHY 5.

DNA CRYPTOGRAPHY Chapter 6 Software Testing NIT KURUKSHETRA 34 .

1 Black-Box Testing Black box testing focuses on the functional requirements of the software. 4. Testing is a process of executing a program with the intent of finding an error. Black Box testing enables the software engineer to derive sets of input conditions that will fully exercise all functional requirements for a program. 2. Rather.2 Testing Objectives 1. Testing is a dynamic method for verification and validation. 6. Black Box Testing is not an alternative to white-box techniques.Black-Box Testing attempts to find errors in the following categories: • Incorrect or missing functions. NIT KURUKSHETRA 35 .1 Testing Methodology Software testing is critical element of software quality assurance and represents the ultimate review of specification.3. it is a complementary approach that is likely to uncover a different class of errors than white-box methods. The above objectives imply a dramatic change in viewpoint. 3. A successful test is one that uncovers an as-yet-undiscovered error.DNA CRYPTOGRAPHY 6 Testing 6. They move counter to the commonly held view that a successful test is one in which no errors are found.3 Testing Technique The techniques followed throughout the testing of the system are as follows: 6. A good test case is one that has a high probability of finding an as-yetundiscovered error. design and coding. That is. 6. where the system to be tested is executed and the behavior of the system is observed. Our objective is to design tests that systematically uncover different classes of errors and do so with a minimum amount of time and effort. It is used to detect errors.

Using white box testing methods the test cases that can derived are:   All independent paths with in a module have been exercised at least once. Tests are designed to answer the following questions:       How is functional validity tested? What classes of input will make good test cases? Is the system particularly sensitive to certain input values? How are the boundaries of a data class isolated? What data rates and data volume can the system tolerate? What effect will specific combinations of data have on system operation? By applying black box techniques. Performance errors. * Unlike White Box Testing. by a count that is greater than one. and  Test cases that tell us something about the presence or absence of classes of errors. 36 NIT KURUKSHETRA .3. Initialization and termination errors. which is performed early in the testing process. the number of additional test cases that must be designed to achieve reasonable testing.2 White-Box Testing White Box Testing knowing the internal workings of a product tests can be conducted to ensure that internal operations are performed according to specifications and all internal components have been adequately exercised. we derive a set of test cases that satisfy the following criteria:  Test cases that reduce. 6. attention is focused on the information domain.DNA CRYPTOGRAPHY • • • • Interface errors. Because Black Box Testing purposely disregards control structure. Exercise all logical decisions on their true and false sides. rather than errors associated only with the specific test at hand. Errors in data structures or external data base access. Black Box Testing tends to be applied during later stages of testing.

3. assume that each statement in a program is assigned a unique statement number and that each function does not modify its parameters or global variables.DNA CRYPTOGRAPHY   Execute all loops at their boundaries and within their operational bounds.3 Control Structure Testing 6. Four different classes of loops:     Simple Loops Nested Loops Concatenated Loops Unstructured Loops 6. NIT KURUKSHETRA 37 .3. If a condition is incorrect then at least one component of the condition is incorrect.3.3 Dataflow Testing The dataflow testing method selects test paths of a program according to the location of definitions and uses of variables in the program. In this testing approach. Therefore types of errors in a condition include the following      Boolean operator error Boolean variable error Boolean parenthesis error Relational operator error Arithmetic expression error 6. Loop testing is a white-box testing technique that focuses exclusively on the validity of loop constructs.3.2 Loop Testing Loops are the corner stone for the vast majority of all algorithms implemented in software. 6. Exercise internal data structures to ensure their validity.1 Condition Testing Condition testing is a test case design method that exercises the logical conditions contained in a program module.3.3.3.

NIT KURUKSHETRA 38 .  Local data structure is examined to ensure that data stored temporarily maintain its integrity.  Boundary conditions are tested to ensure that modules operate properly at boundary limits of processing. Unit testing is essentially for verification of the code produced during the coding phase and hence the goal is to test the internal logic of the module.4 Testing Strategies A strategy for software testing integrates software test case design methods into a well planned series of steps that result in the successful construction of software. the problems of measuring test coverage and selecting test paths for data flow testing are more difficult than the corresponding problems for condition testing. However.interfacing at the same time conducting tests to uncover errors.  The module interface is tested to ensure that information properly flows in and out of program.4.DNA CRYPTOGRAPHY It is useful for selecting test paths of a program containing nested if and loop statement.4. 6. A software testing strategy should be flexible enough to promote a customized testing approach. For example: .  All error-handling paths are tested. Others consider a module for integration and use only after it has been unit tested satisfactorily. 6.We followed a systematic technique for constructing the program structure that is “putting them together”.1 Unit Testing Unit testing focuses verification efforts on the smallest unit of software design. 6. It is white box oriented.  All independent paths are exercised to ensure all statements in a module have been executed at least once. We took unit tested components and build a program that has been dictated by design. This approach is effective for error detection.2 Integration Testing Integration testing focuses on design and construction of the software architecture.

It is intended for all the elements are properly configured and cataloged. Software.4. An important element of validation process is configuration review.DNA CRYPTOGRAPHY 6. and database). people.System testing verifies that all elements mesh properly and that overall system function/performance is achieved..g. 6. hardware. must be combined with other system element (e.3 Validation Testing It is achieved through a series of Black Box tests. Although each test has a different purpose all work to verify that system elements have been properly integrated and perform allocated functions. It is also called AUDIT. once validated. It is a series of different tests whose primary purpose is to fully exercise the computer-based system.4 System Testing The last high-order testing step falls outside the boundary of software engineering and into tile broader context of computer system engineering. NIT KURUKSHETRA 39 .4.

DNA CRYPTOGRAPHY Chapter 7 Project Snapshots NIT KURUKSHETRA 40 .

1 Snapshot(original text) NIT KURUKSHETRA 41 .1 Text file Fig 7.DNA CRYPTOGRAPHY 7.

DNA CRYPTOGRAPHY 7.2 Encoded file Fig 7.2 Snapshot(encoded text) NIT KURUKSHETRA 42 .

3 Snapshot(decoded text) NIT KURUKSHETRA 43 .DNA CRYPTOGRAPHY 7.3 Decoded file Fig 7.

DNA CRYPTOGRAPHY Chapter 8 Conclusion NIT KURUKSHETRA 44 .

This project provided us with an opportunity to analyse and practice all the phases of the Software Development Life Cycle. NIT KURUKSHETRA 45 . This project provides an insight into the various details of the DNA and its use in cryptography purposes.DNA CRYPTOGRAPHY 8 Conclusion The main purpose or goal of the project was to study and implement the basic fundamentals of DNA cryptography on textual information.

DNA CRYPTOGRAPHY Chapter 9 Future Prospects & Enhancements NIT KURUKSHETRA 46 .

 The space complexity can be reduced by practical usage of PCR Amplifier.  Ongoing researches could be used for the future enhancement of this project.  DNA Cryptography can be used to prevent cyber crimes like hacking. and provide secure channel for communication. NIT KURUKSHETRA 47 .DNA CRYPTOGRAPHY 9 Future Prospects and Enhancements  This project can be extended to encrypt other data formats.

DNA CRYPTOGRAPHY APPENDIX Abbreviations DNA RNA PCR C T A G U mRNA tRNA Fullforms Deoxyribose Nucleic Acid Ribose Nucleic Acid Polymer Chain Reaction Cytosine Thymine Adenine Guanine Uracil Messanger Ribose Nucleic Acid Transfer Ribose Nucleic Acid NIT KURUKSHETRA 48 .

Amber . Biotechnology Letters 25: 1125–1130. Fiddes. NIT KURUKSHETRA 49 . Hawkins & Jonathan P. Salah El-Gindi. Cox. Xuncai Zhang An Encryption Scheme Using DNA Technology. A Pseudo DNA Cryptography Method [8] Geoff C. 2003 [3] Java 5. IEEE 2008 [7] Ning Kang. A DNA-based Implementation of YAEA Encryption Algorithm [6] Guangzhao Cui . Borda Monica. Tata McGraw-Hill Publishing Company Limited . A Java Crypto Implementation of DNAProvider Featuring Complexity in Theory and Practice. JAVA2 Complete Reference. IEEE 2008 [5] Sherif T. Smith. Vaida Mircea-Florin . . 2003.0 API Documentation Websites [4] Hodorogea Tatiana. Magdy Saeb . Jonathan P.∗ Some possible codes for encrypting data in DNA. Streletchi Cosmin. Limin Qin . Ceridwyn C. JAVA2 Enterprise Edition 1. Yanfeng Wang .4 Bible .Willey Publishing Inc. Amin .L. Fifth Edition.DNA CRYPTOGRAPHY Bibliography Books & Literature [1] “Herbert Schildt”. 2004 [2] Scott W.