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.



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

it is still impossible to break such a scheme. and has infinite computing re-sources. 1. the theory basis is under research and the application costs very much. their security is based on Heinsberg's Uncertainty Principle. (ii) Difficult to realize and expensive to apply.9 Comparisons among DNA cryptography. Any behavior of eavesdropping will change the cipher so it can be detected. 1. that is to say. Differently.2 Security Only computational security can be achieved for traditional cryptographic schemes except for the one-time pad. 1. So. an adversary with infinite power of computation can break them theoretically. All the practical ciphers can be seen as traditional ones. we believe that this biological problem is difficult and will last a relatively long time. they have not been plunged into practical use. Related theory is almost sound. 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. By and large. It is shown that quantum computers have great and striking computational potential. traditional cryptography and quantum cryptography 1.1 Development Traditional cryptography can be traced back to Caesar cipher 2000 years ago or even earlier. he must choose two primer sequences from about 10^23 kinds of sequences (the number of combination taking 2 sequences from 420 candidates). so much as P=NP. If an adversary without knowing the correct two primer pairs wants to pick out the message encoded sequence by PCR amplification. It is a special function in PCR amplification that having the correct primer pairs. DNA cryptography has only nearly ten years history.8 Limitations Of DNA Cryptography (i) Lack of the related theoretical basis. Even if an eavesdropper is given the ability to do whatever he wants. Although there is uncertainty about the computational power of quantum computers.DNA CRYPTOGRAPHY long. It is impossible for an adversary to obtain a totally NIT KURUKSHETRA 6 . and the theory basis has been prepared while implementation is difficult.9.9. Quantum cryptographic schemes are unbreakable under current theories. It would still be extremely difficult to amplify the message-encoded sequence without knowing the correct two primer pairs.

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

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

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

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

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

1. C. he can easily find the secrete-message DNA sequence. he could retrieve the plaintext M sended from Alice from the reverse preprocess operation using his secret key d. Since the intended receiver Bob had gotten the correct PCR two primer pairs through a secure way.1 Fig. the dummy is generated by sonicating human DNA to roughly 60 to 160 nucleotide pairs (average size) and denaturing it. Decryption After the intended receiver Bob gets the DNA mixture. Thus.12. Then. each 20-mer oligo nucleotides long. the secrete-message DNA sequence is prepared. After coding. 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. The last process of this encryption is that Alice generates a certain number of dummies and puts the secrete-message DNA sequence among them. Alice translates the binary ciphertext C_ into the DNA sequence according to the DNA digital coding technology. This decryption process is not only a mathematic computation. After Bob amplifies the secrete-message DNA sequence.12. Alice synthesizes the secret-message DNA sequence which is flanked by forward and reverse PCR primers. 1.1 Data pre(post)treatment flow chart NIT KURUKSHETRA 12 . In this scheme. he could amplify the secret-message DNA sequence by perform PCR on DNA mixture. The pretreatment data flow chart is described in Fig.DNA CRYPTOGRAPHY PCR primers. but also a biological process. Alice sends the DNA mixture to Bob using an open communication channel.

The result of the PCR amplification is shown in fig.DNA CRYPTOGRAPHY In the following part of this section. we thoroughly discuss details of this encryption scheme with an example shown in fig. 1. Step 2: Data pretreatment. This operation could increase the security of this encryption scheme.12. the intended PCR two primer pairs was not independent designed by sender or receiver. 1. but respectively designed complete cooperation by sender and receiver.3. The encryption and decryption keys are a pair of PCR primers. only when both of the primer sequences were correct. the amplification could be successful. that is: “47 45 4E 45 43 52 59 50 54 4F 47 52 41 50 48 59”. Then we translate hexadecimal code into binary plaintext M_ by using third-party software. In this scheme. We first convert this sentence into hexadecimal code by using the built-in computer code. The message-sender Alice and the message-receiver Bob respectively design and exchange a pair of PCR primers over a secure communication channel. Here we choose “GENECRYPTOGRAPHY” (gene cryptography) as plaintext to encrypt. the amplification was not efficient when one of a primer pair is incorrect. that is: 01000111 01000101 01001110 01000101 01000011 01010010 01011001 01010000 01010100 01001111 01000111 01010010 01000001 01010000 01001000 01011001 NIT KURUKSHETRA 13 .2. because even if an adversary somehow caught one of a primer pair.12. Step 1: Key Generation.

1. After that. he can easily pick out the secret-message DNA sequence by using the correct primer pairs. the secrete-message DNA is prepared. Step 4: Decryption. such as DNA ink or DNA book. After the binary plaintext M_ has been recovered. 1.12. Fig.12. Both the comma code and the alternating code. Bob can decrypt the binary ciphertext C_ into the binary plaintext M_ by using his secret key e. the comma code and the alternating code. The Huffman code is the most economical and would be the best for encrypting text for short-term storage. Bob translates the secret-message DNA sequence into the binary ciphertext C_ by using the DNA digital coding technology. Finally. It should be stated at the outset that none of them fulfill all the criteria listed above. After mixing the secrete-message DNA sequence with a certain number of dummies. Step 5: data post-treatment. 1. while the most NIT KURUKSHETRA 14 . Alice sends the DNA mixture to Bob using an open communication channel. After the intended receiver Bob gets the DNA mixture. Alice converts the binary ciphertext C_ into the DNA sequence by using the DNA digital coding technology. a secret-message DNA sequence containing an encoded message 64 nucleotides long flanked by forward and reverse PCR primers.3. Flow chart of Encryption scheme system. Bob can retrieve the plaintext M.13 The codes The three codes described in detail in this paper are referred to as the Huffman code.DNA CRYPTOGRAPHY Fig. providing that this text lacked any sort of punctuation. Result of the PCR amplification Step 3: Encryption. symbols or numbers. “GENECRYPTOGRAPHY” from the binary plaintext M_ by using data posttreatment. Thus.2. Then. Alice will encrypt the binary plaintext M_ into the binary ciphertext C_ by using Bob’s public key e.

and so would be best suited to the encryption of information for long-term storage. shorter than the codons of any of the other codes described in this paper. The Huffman code constructed with the four DNA bases A. The average codon length is 2. That is. no obvious pattern emerges when they are joined together to encode a message. have the advantage that they generate base sequences which are obviously artificial. For instance.13. As well as being compact. One of the best ways of constructing an economical code is to use Huffman’s method (Huffman 1952). The unambiguous nature of the Huffman code shown in Table 1 can be seen by encoding any group of letters with it and then decoding them from the beginning of the sequence: there is only one way it can be done. the most frequently used letter in the English language).e. the Huffman makes the most economical use of DNA. C and T for the letters of the English alphabet is shown in Table 1.2 bases. and the longest codon is five bases long (representing q and z. Given a suitable start signal. the most infrequent letters in the English language). C and T). the message generated by a Huffman code is unambiguous. once the start point has been specified. 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. the shortest codon is just one base long (representing e. One could counteract this problem by using three instead of four bases (e. In the code. codes in which the text is encrypted by the minimum number of symbols – it is as short as it can possibly be. with the most frequent character being given the least number of symbols and the least frequent the most number of symbols. G. it does have two disadvantages. While of the three codes discussed here. such a code is straightforward to construct (Materials and methods).13. i. The naive investigator might confuse it with natural DNA and therefore not appreciate its significance. the base sequence CATGTAGTCG can only be read from the beginning as hester – no other interpretation of the message is possible.g. A. Consequently they cannot be included when deriving the Huffman code. The Huffman code is the only code discussed in this paper with variable length codons. 1. The second disadvantage of the Huffman code relates to its possible use in long-term storage of information.DNA CRYPTOGRAPHY uneconomical of the codes. at the expense of economy. The first is that it does not cater for any symbols or numbers. as the frequency of these characters will be heavily text-dependent. there is only one way in which the stream of symbols comprising the message can be read.1 Given the frequencies of occurrence of these letters. Because of the variable length of the codons. The others all have NIT KURUKSHETRA 15 . the alternating code is also unambiguous.

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

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

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

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


NIT KURUKSHETRA 21 .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. Hide the biological complexity involved in basic processing of DNA cryptography. Allow users to apply the encoding on textual information.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. are available in the market this project aims at Although many encoding techniques Cryptography) for encoding text.DNA CRYPTOGRAPHY 2. 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. To obtain an encoded text as desired.

DNA CRYPTOGRAPHY Chapter 3 System Requirement Analysis NIT KURUKSHETRA 22 .

~ Encoding the text using DNA cryptography and PCR amplifications.2 System Requirements The following requirements must be fulfilled to run the software on any computer system . 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.DNA CRYPTOGRAPHY 3 System Requirement Analysis: 3.1 Characteristics The important characteristics of the system being developed: FUNCTIONS ~ Loading the text file from source.  HARDWARE SPECIFICATIONS Processor Intel Pentium III or higher Color Monitor 800 x 600 or higher resolution PCR (Polymerase Chain Reaction) Monitor Amplifier Amplifier NIT KURUKSHETRA 23 .

3 Technology Used Windows 9x / XP/ NT / 2000 JVM and JRE installed.4 Use Case Diagram 3.0 Programming Language JAVA 5 3.4.1 Encoder Fig 3. NetBeans 6.1 Usecase diagram(encoder) NIT KURUKSHETRA 24 .DNA CRYPTOGRAPHY  SOFTWARE SUPPORT Operating System Framework 3.4.

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

DNA CRYPTOGRAPHY Chapter 4 Project Overview NIT KURUKSHETRA 26 .

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


T. Decryption 5. Key generation 2. STEPS: 1.T.T. = EKA (P.2 Flow Diagrams 5.2.1 Encoder Fig 5.)) = P. T.T.1 Methodology OF Encryption Scheme The encryption process is: C.DNA CRYPTOGRAPHY 5 Software Design 5.2. Encryption 3.) The decryption process is: DKB (C.) = DKB (EKA (P.1 Flow Diagram(encoder) NIT KURUKSHETRA 29 .

DNA CRYPTOGRAPHY 5.2 Flow Diagram(decoder) NIT KURUKSHETRA 30 .2 Decoder Fig 5.2.2.

3.3 Class Diagrams 5.3.1 Encoder Fig 5.1 Class diagram(encoder) NIT KURUKSHETRA 31 .DNA CRYPTOGRAPHY 5.

DNA CRYPTOGRAPHY 5.2 Class diagram(decoder) NIT KURUKSHETRA 32 .3.2 Decoder Fig 5.3.

DNA CRYPTOGRAPHY 5.3.3 Class diagram(keyGen) NIT KURUKSHETRA 33 .3 KeyGen Fig 5.3.

DNA CRYPTOGRAPHY Chapter 6 Software Testing NIT KURUKSHETRA 34 .

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

and  Test cases that tell us something about the presence or absence of classes of errors.3.2 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. Initialization and termination errors. attention is focused on the information domain. the number of additional test cases that must be designed to achieve reasonable testing. 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. we derive a set of test cases that satisfy the following criteria:  Test cases that reduce. Errors in data structures or external data base access. which is performed early in the testing process. Performance errors. Exercise all logical decisions on their true and false sides. * Unlike White Box Testing. 36 NIT KURUKSHETRA . 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. Black Box Testing tends to be applied during later stages of testing. Because Black Box Testing purposely disregards control structure. 6.DNA CRYPTOGRAPHY • • • • Interface errors. by a count that is greater than one. rather than errors associated only with the specific test at hand.

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

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

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

DNA CRYPTOGRAPHY Chapter 7 Project Snapshots NIT KURUKSHETRA 40 .

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

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

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


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

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

NIT KURUKSHETRA 47 .  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. and provide secure channel for communication.  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 .

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

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