Chapter 1






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



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 * ?

Random codon from D and N Random codon from E and Q Random codon


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.




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.



Each piece of data is used once to encrypt a message by the sender and to decrypt it by the receiver. which transforms the encrypted message back to the original form using a key. 1. searching for simple methods of realizing DNA cryptography. and a single target DNA molecule can be amplified to 106 after 20 cycles in theory. Thus one can effectively amplify a lot of DNA strands within a very short time. The goal of encryption is to prevent decryption by an adversary who does not know the secret key. The output is a sequence of characters known as the ciphertext. Two complementary oligonucleotide primers are annealed to double-stranded target DNA strands. such as that of a natural language. Polymerase Chain Reaction (PCR) is a fast DNA amplification technology based on Watson-Crick complementarity. and is one of the most important inventions in modern biology. discovering possible development directions. It gets its name from the fact that the sender and receiver each possess identical notepads ¯lled with random data. Encryption is the process of scrambling the plaintext using a known algorithm and a secret key. Such a system is the one-time-pad cipher. we selected each PCR primer 20-mer nucleotides NIT KURUKSHETRA 5 . after which it is destroyed. establishing corresponding theories. In this study. * The main goal of the research of DNA cryptography is exploring characteristics of DNA molecule and reaction. The goal is to transmit a message between a sender and receiver such that an eavesdropper is unable to understand it. and the necessary target DNA can be amplified after a serial of polymerase enzyme. Thinking about the highly stability of PCR. Plaintext refers to a sequence of characters drawn from a ¯nite alphabet. Here we provide basic terminology used in cryptography. An unbreakable cryptosystem is one for which successful cryptanalysis is not possible. Decryption is the reverse process.6 Cryptography Data security and cryptography are critical aspects of conventional computing and may also be important to possible DNA database applications. and lay-ing the basis for future development.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”. The PCR is a very sensitive method. each PCR primer (20-27)-mer nucleotides long is a comparatively perfect selection.DNA CRYPTOGRAPHY 1.

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

only by physical ways can the cipher text of DNA cryptography be transmitted. Therefore. 1.9. cash ticket and identification card. we hold the following opinions: NIT KURUKSHETRA 7 . and so on. However.DNA CRYPTOGRAPHY same the quanta with the intercepted one. the problem as to what is the extent this kind of security and how long it can be maintained it is still under exploration. exceptional energy efficiency and extraordinary information density inherent in DNA molecules.3 Application Traditional cryptosystems are the most convenient of which the computation can be executed by electronic. the main security basis is the restriction of biological techniques. The disadvantage lies in the secure data storage. which makes it infeasible to implement publickey encryption and digital signature as easily as traditional one does. Due to the vast parallelism. it is too early to predict the future development precisely. and the storage can be CDs. 1. thus the attempt to tamper but without being detected in vain. quantum as well as DNA computers. such as secure data storage. steganography. this making it hard to predict the future. Using the traditional cryptography we can realize purposes as public and private key encryption. the data can be transmitted by wire. magnetic medium.10 Development directions of DNA cryptography Since DNA cryptography is still in its immature stage. wireless channel and even by a messenger. For the DNA cryptography. authentication. DNA can even be used to produce unforgeable contract. quantum key agreement schemes have unconditional security. digital signature. DNA cryptography can have special advantages in some cryptographic purposes. which has nothing to do with the computing power and immunizes DNA cryptographic schemes against attacks using quantum computers. DNA and other storage medium. Nonetheless. Quantum cryptosystem is implemented on quantum channels of which main ad-vantage lies in real-time communication. 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. Researches of all the three kinds of cryptography are still in progress. identity authentication and digital signature. in view of the development of biological techniques and the requirement of cryptography. fiber. Under the current level of techniques. and a great many problems remains to be solved especially for DNA and quantum cryptography.

their computational security will be inherited into DNA schemes. Since it has not been made sure whether quan-tum computers threaten the hardness of various mathematical hard problems. if described by mathematical methods. the advantages inherent in DNA should be fully explored. it must be assumed that an attacker knows the basic biological method the designer used. 2) Security requirements :Regardless of the many differences between DNA and traditional cryptography. an attacker should be fully aware of all the details of encryption and decryption except the decryption key. i.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. realizing fast encryption and decryption based on the vast parallelism. that is. 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. these problems being se-curity basis cannot be excluded absolutely. they both satisfy the same characteristic of cryptography.e. 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. 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. which cannot be realized by electronic computers by using mathematical methods. The only thing NIT KURUKSHETRA 8 . a sender and a receiver. If these schemes withstand attacks by quantum computers. The communication model for DNA encryption is also made up of two par-ties. It is under this assumption that a cryptosystem can be said secure when any attacker cannot break it. 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 security requirements should also be founded upon the assumption proposed by Kirchoff that security should depend only on the secrecy of decryption key. DNA cryptography does not absolutely repulse traditional cryptography and it is possible to construct a hybrid cryptosystem of them. More precisely. If other kinds of cryptosystems are necessary to be researched and developed. Thereby. they should have properties such as higher security levels and storage density etc. such as developing nanoscopic storage based on the tiny volume of DNA. Encryption and decryption are procedures of data transform which. if DNA cryptography is necessary to be developed.

Sound theories have not been founded for both DNA computing and cryptography. second in storage density. In a DNA cryptosystem. For example. The development of modern biological technology makes it possible to express data by DNA. This motivates the research of DNA computing and cryptography. In fact. exceptional energy efficiency and extraordinary information density inherent in DNA. 1. With the current technology. based on which the design of secure and practical DNA cryptosystems is possible. The cur-rent goal or difficulty is to find and make use of the utmost potential. a key is usually some substances of biological materials or a preparation flow.11 DNA Digital Coding Technology NIT KURUKSHETRA 9 . although the related research is just in its initial stage. store data by DNA chips and read data by hybridization. Modern biology lays particular stress on experiments rather than theories. 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.DNA CRYPTOGRAPHY not known by the attacker is the key. 4) Currently. The method is easier to be implemented than encoding message into nucleotides directly while the storage density is somewhat lower. it is still difficult to operate the nanoscopic DNA directly. If the only requirement is to improve the density of storage. the main task for DNA cryptographers is to establish the theory foundations and to accumulate the practical experience. It is more practical to make use of colony property of plentiful DNA for cryptographer. which makes the operations of input/output faster and more convenient. and sometimes the experiment conditions. it is also impossible to store all the worldwide data by using several grams of DNA. 3) For DNA cryptography. A sound cryptosystem should be secure as well as easy to be implemented. Presently. It is certainly urgent to find such a method similar to computational complexity. but the related research is in its initial stage. It can be proved that there are vast parallelism. to establish the theoretical basis and to accumulate the experience. the current research target should lie first in security and feasibility. the most important is to find the sound properties of DNA that can be used to computation and encryption. 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. it is hard to implement DNA cryptography at the present technique level.

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

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

12. The last process of this encryption is that Alice generates a certain number of dummies and puts the secrete-message DNA sequence among them.1 Fig. In this scheme. Alice synthesizes the secret-message DNA sequence which is flanked by forward and reverse PCR primers. the secrete-message DNA sequence is prepared.DNA CRYPTOGRAPHY PCR primers. After coding. Then. Alice sends the DNA mixture to Bob using an open communication channel. the dummy is generated by sonicating human DNA to roughly 60 to 160 nucleotide pairs (average size) and denaturing it.1. Since the intended receiver Bob had gotten the correct PCR two primer pairs through a secure way. The pretreatment data flow chart is described in Fig. but also a biological process.12.1 Data pre(post)treatment flow chart NIT KURUKSHETRA 12 . Decryption After the intended receiver Bob gets the DNA mixture. 1. he could amplify the secret-message DNA sequence by perform PCR on DNA mixture. Thus. Alice translates the binary ciphertext C_ into the DNA sequence according to the DNA digital coding technology. he can easily find the secrete-message DNA sequence. It is necessary that each dummy has the same structure as the secretemessage DNA sequence. After mixing the secretemessage DNA sequence with a certain number of dummies. After Bob amplifies the secrete-message DNA sequence. he could retrieve the plaintext M sended from Alice from the reverse preprocess operation using his secret key d. C. This decryption process is not only a mathematic computation. each 20-mer oligo nucleotides long.

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

Bob translates the secret-message DNA sequence into the binary ciphertext C_ by using the DNA digital coding technology. Then. 1. Step 5: data post-treatment. Step 4: Decryption. Both the comma code and the alternating code. the comma code and the alternating code. Thus. providing that this text lacked any sort of punctuation. he can easily pick out the secret-message DNA sequence by using the correct primer pairs. Flow chart of Encryption scheme system. a secret-message DNA sequence containing an encoded message 64 nucleotides long flanked by forward and reverse PCR primers. The Huffman code is the most economical and would be the best for encrypting text for short-term storage. Result of the PCR amplification Step 3: Encryption.12. After the binary plaintext M_ has been recovered. 1.2.DNA CRYPTOGRAPHY Fig. Alice sends the DNA mixture to Bob using an open communication channel. while the most NIT KURUKSHETRA 14 . such as DNA ink or DNA book. 1. symbols or numbers. Bob can retrieve the plaintext M. the secrete-message DNA is prepared. After mixing the secrete-message DNA sequence with a certain number of dummies. After the intended receiver Bob gets the DNA mixture. It should be stated at the outset that none of them fulfill all the criteria listed above. Finally. Alice converts the binary ciphertext C_ into the DNA sequence by using the DNA digital coding technology.12. Bob can decrypt the binary ciphertext C_ into the binary plaintext M_ by using his secret key e. “GENECRYPTOGRAPHY” from the binary plaintext M_ by using data posttreatment.3. Alice will encrypt the binary plaintext M_ into the binary ciphertext C_ by using Bob’s public key e. Fig. After that.13 The codes The three codes described in detail in this paper are referred to as the Huffman code.

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

A and T. G− − − − − G− − − − − G− − − −− G. in a similar manner to the above. the comma.2 The comma code In the comma code. but not G. which is always the same: e.suggested by unrelated work . This kind of an arrangement. Table 1. with the C of the latter always being located in the top strand. We note that. These codons are further restricted to three A:T base pairs and two G:C base pairs. the Huffman code has also been used to construct a ‘perfect’ genetic code comprising variable length codons.g. e.g.g. and therefore the comma NIT KURUKSHETRA 16 . facilitating the construction of message DNA (‘Criteria for an optimal code’. and the C’s and W’s can adopt any arrangement (e. WWCWC or WCCWW). where W = A or T.DNA CRYPTOGRAPHY fixed length codons.13. above). There are 80 codons in this set. The repetition of G every six bases must be construed by any careful sequence analyst as a deliberate device.13.1 The Huffman code 1. The codons take the general form CWWWC. has the advantage that it will generate a set of codons with isothermal melting temperatures. consecutive 5-base codons are separated by a single base. ATCAC. The codons that slot into the gaps in the above framework are made up of the remaining bases C. Most (83%) point mutations give nonsense codons.

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

Any combination of these codons will give a sequence which can be read in only one way. For instance. But. possible. the codons in this set can be chosen such that only one reading frame is ever possible – all the others give nonsense.13. For example. showed that twenty 3-base codons could be selected to act in a comma-free manner. One might think that removing the commas would give a code without a reading frame. in the sequence ACGGTGGTGACGAGG. ACG and GTG are part of a comma free code. They are by no means the only codes.3 Advantages of the codes 1.2 General features of the codes Table 1. there is a set of fifty-seven 4-base codons that would be enough to carry out this task. One of these was the comma-free code.4 Other codes The three codes detailed above are meant to be illustrative rather than exhaustive. Although twenty codons is not sufficient to comfortably encrypt text. a comma-free code is just a comma code without the commas. There is nothing particularly wrong with the commaNIT KURUKSHETRA 18 . because CGG does not belong to the set. one could not begin reading one base in. As the name suggests. by restricting oneself to a set of fixed-length codons with particular base combinations.13. the 3-base codons AGG. In their original paper on the subject. Before experimental data for the nature of the genetic code became available. at CGG.DNA CRYPTOGRAPHY Table 1. there were a number of suggestions as to what form it might take. or the only types of code.13. Three others are outlined briefly in this section.

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


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. NIT KURUKSHETRA 21 . Added to this it is aimed to obtain a clear understanding of the Java cryptography and its native API. understanding the limitations and configurations needed to perform a new technique (DNA 2.DNA CRYPTOGRAPHY 2. Hide the biological complexity involved in basic processing of DNA cryptography. Allow users to apply the encoding on textual information.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. are available in the market this project aims at Although many encoding techniques Cryptography) for encoding text.

DNA CRYPTOGRAPHY Chapter 3 System Requirement Analysis NIT KURUKSHETRA 22 .

~ Encoding the text using DNA cryptography and PCR amplifications.  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 .2 System Requirements The following requirements must be fulfilled to run the software on any computer system .DNA CRYPTOGRAPHY 3 System Requirement Analysis: 3.1 Characteristics The important characteristics of the system being developed: FUNCTIONS ~ Loading the text file from source. 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.

1 Usecase diagram(encoder) NIT KURUKSHETRA 24 .DNA CRYPTOGRAPHY  SOFTWARE SUPPORT Operating System Framework 3.1 Encoder Fig 3.3 Technology Used Windows 9x / XP/ NT / 2000 JVM and JRE installed.4. NetBeans 6.0 Programming Language JAVA 5 3.4 Use Case Diagram 3.4.

4.4.DNA CRYPTOGRAPHY 3.2 Usecase diagram(decoder) NIT KURUKSHETRA 25 .2 Decoder Fig 3.

DNA CRYPTOGRAPHY Chapter 4 Project Overview NIT KURUKSHETRA 26 .

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


1 Flow Diagram(encoder) NIT KURUKSHETRA 29 .2. STEPS: 1.) The decryption process is: DKB (C.T.T. T. Encryption 3. Key generation 2.T.DNA CRYPTOGRAPHY 5 Software Design 5.2.2 Flow Diagrams 5. = EKA (P.1 Methodology OF Encryption Scheme The encryption process is: C.)) = P. Decryption 5.T.) = DKB (EKA (P.1 Encoder Fig 5.

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

3 Class Diagrams 5.3.3.DNA CRYPTOGRAPHY 5.1 Encoder Fig 5.1 Class diagram(encoder) NIT KURUKSHETRA 31 .

3.2 Class diagram(decoder) NIT KURUKSHETRA 32 .3.2 Decoder Fig 5.DNA CRYPTOGRAPHY 5.

DNA CRYPTOGRAPHY KeyGen Fig 5.3 Class diagram(keyGen) NIT KURUKSHETRA 33 .

DNA CRYPTOGRAPHY Chapter 6 Software Testing NIT KURUKSHETRA 34 .

3. Testing is a dynamic method for verification and validation. It is used to detect errors.3 Testing Technique The techniques followed throughout the testing of the system are as follows: 6. NIT KURUKSHETRA 35 . 6.3. That is. Our objective is to design tests that systematically uncover different classes of errors and do so with a minimum amount of time and effort. Rather.Black-Box Testing attempts to find errors in the following categories: • Incorrect or missing functions.2 Testing Objectives 1. 6.1 Testing Methodology Software testing is critical element of software quality assurance and represents the ultimate review of specification. They move counter to the commonly held view that a successful test is one in which no errors are found. where the system to be tested is executed and the behavior of the system is observed.1 Black-Box Testing Black box testing focuses on the functional requirements of the software. 2.DNA CRYPTOGRAPHY 6 Testing 6. 4. Testing is a process of executing a program with the intent of finding an error. Black Box Testing is not an alternative to white-box techniques. A successful test is one that uncovers an as-yet-undiscovered error. 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. design and coding. A good test case is one that has a high probability of finding an as-yetundiscovered error. Black Box testing enables the software engineer to derive sets of input conditions that will fully exercise all functional requirements for a program.

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. Errors in data structures or external data base access. * Unlike White Box 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. 36 NIT KURUKSHETRA .3. Performance errors. by a count that is greater than one. Exercise all logical decisions on their true and false sides. Because Black Box Testing purposely disregards control structure. Black Box Testing tends to be applied during later stages of testing. which is performed early in the testing process. the number of additional test cases that must be designed to achieve reasonable testing. attention is focused on the information domain. 6. 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. rather than errors associated only with the specific test at hand. Initialization and termination errors. and  Test cases that tell us something about the presence or absence of classes of errors.DNA CRYPTOGRAPHY • • • • Interface errors.

NIT KURUKSHETRA 37 . If a condition is incorrect then at least one component of the condition is incorrect.2 Loop Testing Loops are the corner stone for the vast majority of all algorithms implemented in software.3.3.DNA CRYPTOGRAPHY   Execute all loops at their boundaries and within their operational bounds.3 Control Structure Testing 6. Exercise internal data structures to ensure their validity.3.3. 6. In this testing approach. 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. Four different classes of loops:     Simple Loops Nested Loops Concatenated Loops Unstructured Loops 6.3. Loop testing is a white-box testing technique that focuses exclusively on the validity of loop constructs.1 Condition Testing Condition testing is a test case design method that exercises the logical conditions contained in a program module. 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 6.3.3 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.3.

1 Unit Testing Unit testing focuses verification efforts on the smallest unit of software design.  All error-handling paths are tested. 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.  Boundary conditions are tested to ensure that modules operate properly at boundary limits of processing. A software testing strategy should be flexible enough to promote a customized testing approach.interfacing at the same time conducting tests to uncover errors.  All independent paths are exercised to ensure all statements in a module have been executed at least once.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. Others consider a module for integration and use only after it has been unit tested satisfactorily.4.DNA CRYPTOGRAPHY It is useful for selecting test paths of a program containing nested if and loop statement.2 Integration Testing Integration testing focuses on design and construction of the software architecture.  The module interface is tested to ensure that information properly flows in and out of program. 6. However. NIT KURUKSHETRA 38 . the problems of measuring test coverage and selecting test paths for data flow testing are more difficult than the corresponding problems for condition testing.We followed a systematic technique for constructing the program structure that is “putting them together”. We took unit tested components and build a program that has been dictated by design. 6.4. 6.  Local data structure is examined to ensure that data stored temporarily maintain its integrity. This approach is effective for error detection. For example: . It is white box oriented.

once validated. people.g.4.. It is intended for all the elements are properly configured and cataloged. 6. hardware. Although each test has a different purpose all work to verify that system elements have been properly integrated and perform allocated functions. NIT KURUKSHETRA 39 . It is a series of different tests whose primary purpose is to fully exercise the computer-based system. must be combined with other system element (e. It is also called AUDIT. Software.3 Validation Testing It is achieved through a series of Black Box tests.System testing verifies that all elements mesh properly and that overall system function/performance is achieved.4.4 System Testing The last high-order testing step falls outside the boundary of software engineering and into tile broader context of computer system engineering.DNA CRYPTOGRAPHY 6. An important element of validation process is configuration review. and database).

DNA CRYPTOGRAPHY Chapter 7 Project Snapshots NIT KURUKSHETRA 40 .

1 Text file Fig 7.1 Snapshot(original text) NIT KURUKSHETRA 41 .DNA CRYPTOGRAPHY 7.

DNA CRYPTOGRAPHY 7.2 Snapshot(encoded text) NIT KURUKSHETRA 42 .2 Encoded file Fig 7.

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


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. This project provided us with an opportunity to analyse and practice all the phases of the Software Development Life Cycle. This project provides an insight into the various details of the DNA and its use in cryptography purposes. NIT KURUKSHETRA 45 .

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

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

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 .

A DNA-based Implementation of YAEA Encryption Algorithm [6] Guangzhao Cui . 2004 [2] Scott W. Streletchi Cosmin. Tata McGraw-Hill Publishing Company Limited . Xuncai Zhang An Encryption Scheme Using DNA Technology. . JAVA2 Enterprise Edition 1.0 API Documentation Websites [4] Hodorogea Tatiana. Yanfeng Wang . Amber . Vaida Mircea-Florin . IEEE 2008 [5] Sherif T. Borda Monica.4 Bible . Salah El-Gindi. Fifth Edition. Smith. IEEE 2008 [7] Ning Kang. Ceridwyn C. NIT KURUKSHETRA 49 . A Pseudo DNA Cryptography Method [8] Geoff C. Amin .DNA CRYPTOGRAPHY Bibliography Books & Literature [1] “Herbert Schildt”. Fiddes. Cox. JAVA2 Complete Reference. Limin Qin .∗ Some possible codes for encrypting data in DNA. Hawkins & Jonathan P.L.Willey Publishing Inc. 2003. Jonathan P. A Java Crypto Implementation of DNAProvider Featuring Complexity in Theory and Practice. 2003 [3] Java 5. Magdy Saeb . Biotechnology Letters 25: 1125–1130.

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