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.



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

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

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

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

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

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

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

DNA CRYPTOGRAPHY PCR primers. he could retrieve the plaintext M sended from Alice from the reverse preprocess operation using his secret key d.12. the secrete-message DNA sequence is prepared.12. 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. Alice sends the DNA mixture to Bob using an open communication channel. Then. This decryption process is not only a mathematic computation.1. After coding. the dummy is generated by sonicating human DNA to roughly 60 to 160 nucleotide pairs (average size) and denaturing it. Thus. he could amplify the secret-message DNA sequence by perform PCR on DNA mixture. In this scheme. each 20-mer oligo nucleotides long. C.1 Fig. Decryption After the intended receiver Bob gets the DNA mixture. but also a biological process. 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. After mixing the secretemessage DNA sequence with a certain number of dummies. It is necessary that each dummy has the same structure as the secretemessage DNA sequence. After Bob amplifies the secrete-message DNA sequence. 1.1 Data pre(post)treatment flow chart NIT KURUKSHETRA 12 . Alice synthesizes the secret-message DNA sequence which is flanked by forward and reverse PCR primers. The last process of this encryption is that Alice generates a certain number of dummies and puts the secrete-message DNA sequence among them.

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

Result of the PCR amplification Step 3: Encryption. Bob translates the secret-message DNA sequence into the binary ciphertext C_ by using the DNA digital coding technology. while the most NIT KURUKSHETRA 14 . After mixing the secrete-message DNA sequence with a certain number of dummies. Alice will encrypt the binary plaintext M_ into the binary ciphertext C_ by using Bob’s public key e.3.12. Step 4: Decryption. providing that this text lacked any sort of punctuation. symbols or numbers. Alice sends the DNA mixture to Bob using an open communication channel.DNA CRYPTOGRAPHY Fig.13 The codes The three codes described in detail in this paper are referred to as the Huffman code. It should be stated at the outset that none of them fulfill all the criteria listed above. such as DNA ink or DNA book. 1. The Huffman code is the most economical and would be the best for encrypting text for short-term storage. Bob can decrypt the binary ciphertext C_ into the binary plaintext M_ by using his secret key e. Finally. Alice converts the binary ciphertext C_ into the DNA sequence by using the DNA digital coding technology. “GENECRYPTOGRAPHY” from the binary plaintext M_ by using data posttreatment. 1. After that.2. 1. Fig.12. the secrete-message DNA is prepared. Both the comma code and the alternating code. a secret-message DNA sequence containing an encoded message 64 nucleotides long flanked by forward and reverse PCR primers. Step 5: data post-treatment. Then. After the binary plaintext M_ has been recovered. Flow chart of Encryption scheme system. he can easily pick out the secret-message DNA sequence by using the correct primer pairs. the comma code and the alternating code. Thus. After the intended receiver Bob gets the DNA mixture. Bob can retrieve the plaintext M.

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

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

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

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

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


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. 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. To obtain an encoded text as desired.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. Added to this it is aimed to obtain a clear understanding of the Java cryptography and its native API. NIT KURUKSHETRA 21 . Allow users to apply the encoding on textual information. 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. 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 .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 .DNA CRYPTOGRAPHY 3 System Requirement Analysis: 3.

4.1 Encoder Fig 3.4 Use Case Diagram 3.3 Technology Used Windows 9x / XP/ NT / 2000 JVM and JRE installed.4.0 Programming Language JAVA 5 3. NetBeans 6.DNA CRYPTOGRAPHY  SOFTWARE SUPPORT Operating System Framework 3.1 Usecase diagram(encoder) NIT KURUKSHETRA 24 .

2 Usecase diagram(decoder) NIT KURUKSHETRA 25 .DNA CRYPTOGRAPHY 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. The functions of each component is as described below. The computer is a general computer that can range from a PC to a supercomputer. 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. NIT KURUKSHETRA 27 . It consists of specialized modules that perform specific tasks.


1 Flow Diagram(encoder) NIT KURUKSHETRA 29 .T. STEPS: 1.) = DKB (EKA (P. Key generation 2.T.1 Methodology OF Encryption Scheme The encryption process is: C.T. Decryption 5. T.DNA CRYPTOGRAPHY 5 Software Design 5. = EKA (P. Encryption 3.2.2 Flow Diagrams 5.T.) The decryption process is: DKB (C.)) = P.1 Encoder Fig 5.2.

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

3 Class Diagrams 5.DNA CRYPTOGRAPHY 5.1 Encoder Fig 5.1 Class diagram(encoder) NIT KURUKSHETRA 31 .3.3.

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

DNA CRYPTOGRAPHY 5.3 Class diagram(keyGen) NIT KURUKSHETRA 33 .3.3 KeyGen Fig 5.3.

DNA CRYPTOGRAPHY Chapter 6 Software Testing NIT KURUKSHETRA 34 .

Black-Box Testing attempts to find errors in the following categories: • Incorrect or missing functions. Our objective is to design tests that systematically uncover different classes of errors and do so with a minimum amount of time and effort. design and coding. NIT KURUKSHETRA 35 . it is a complementary approach that is likely to uncover a different class of errors than white-box methods. 3. A successful test is one that uncovers an as-yet-undiscovered error.2 Testing Objectives 1.DNA CRYPTOGRAPHY 6 Testing 6.3. Rather.1 Black-Box Testing Black box testing focuses on the functional requirements of the software. The above objectives imply a dramatic change in viewpoint. Testing is a dynamic method for verification and validation. Black Box Testing is not an alternative to white-box techniques. 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. It is used to detect errors.1 Testing Methodology Software testing is critical element of software quality assurance and represents the ultimate review of specification. 6. Black Box testing enables the software engineer to derive sets of input conditions that will fully exercise all functional requirements for a program. 2. where the system to be tested is executed and the behavior of the system is observed. 4. Testing is a process of executing a program with the intent of finding an error. 6. A good test case is one that has a high probability of finding an as-yetundiscovered error. That is.

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

Four different classes of loops:     Simple Loops Nested Loops Concatenated Loops Unstructured Loops 6.3 Control Structure Testing 6.3. 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. 6.3. 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.DNA CRYPTOGRAPHY   Execute all loops at their boundaries and within their operational bounds. NIT KURUKSHETRA 37 . 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. If a condition is incorrect then at least one component of the condition is incorrect. Loop testing is a white-box testing technique that focuses exclusively on the validity of loop constructs.3.3.3. In this testing approach.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.3.2 Loop Testing Loops are the corner stone for the vast majority of all algorithms implemented in software.

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

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

DNA CRYPTOGRAPHY Chapter 7 Project Snapshots NIT KURUKSHETRA 40 .

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

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

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


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. This project provided us with an opportunity to analyse and practice all the phases of the Software Development Life Cycle. NIT KURUKSHETRA 45 .

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

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

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 Pseudo DNA Cryptography Method [8] Geoff C. Jonathan P. Streletchi Cosmin. Vaida Mircea-Florin . A DNA-based Implementation of YAEA Encryption Algorithm [6] Guangzhao Cui . Amber .DNA CRYPTOGRAPHY Bibliography Books & Literature [1] “Herbert Schildt”. Amin .0 API Documentation Websites [4] Hodorogea Tatiana. Xuncai Zhang An Encryption Scheme Using DNA Technology. JAVA2 Complete Reference. 2004 [2] Scott W. Fifth Edition.∗ Some possible codes for encrypting data in DNA. Cox. 2003.4 Bible . Fiddes. 2003 [3] Java 5. Salah El-Gindi. Biotechnology Letters 25: 1125–1130. Limin Qin . IEEE 2008 [5] Sherif T.L. NIT KURUKSHETRA 49 . Yanfeng Wang . Ceridwyn C. A Java Crypto Implementation of DNAProvider Featuring Complexity in Theory and Practice. Hawkins & Jonathan P. JAVA2 Enterprise Edition 1. IEEE 2008 [7] Ning Kang. Borda Monica.Willey Publishing Inc. Magdy Saeb . . Smith. Tata McGraw-Hill Publishing Company Limited .

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