DNA CRYPTOGRAPHY

Chapter 1
Introduction

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DNA CRYPTOGRAPHY

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Introduction

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

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

Fig 1.2.1 Double helix structure of DNA

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

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

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

TAA TAG TGA --???

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

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DNA CRYPTOGRAPHY

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

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

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

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

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

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

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

As we all know. The DNA sequence after preprocessing by DNA digital coding techniques is able to do digital computing and adapt to the existing computer-processing mode. which facilitates the direct conversion between biological information and encryption information in the cryptographyscheme. Take DNA digital coding into account. is the best coding pattern for the nucleotide bases. two DNA strands are held together complementary in terms of sequence. There are four kinds of bases. C.DNA CRYPTOGRAPHY In the information science. The binary digital coding of DNA sequences prevails over the character DNA coding with the following advantages: (1). which is anything can be encoded by two state 0 or 1 and a combination of 0 and 1. 1.12 System Design Of Encryption Scheme Now. T. that is 0(00) to 3(11) and 1(01) to 2(10). 0123/CATG. 1(01). the complementary rule that (~0)=1. The simplest coding patterns to encode the 4 nucleotide bases (A. This pattern could perfect reflect the biological characteristics of 4 nucleotide bases and have a certain biological significance. that is A to T and C to G according to Watson-Crick complementarity rule. 0123/TGCA. the traditional encryption method such as DES or RSA could be used to preprocess to the plaintext in the cryptography scheme. 3(11). whose security on the scheme is mainly based on the difficult biological problems and difficult mathematical problems. By using the technology of DNA digital coding. (2). (4). the most fundamental coding method is binary digital coding. The digital coding of DNA sequence is very convenient for mathematical operation and logical operation and may give a great impact on the DNA bio-computer. 0123/GATC. To decrease the redundancy of the information coding andimprove the coding efficiency compared to the traditional character DNA coding. 0123/CTAG. in a double helix DNA string. which are adenine (A) and thymine (T) or cytosine (C) and guanine (G) in DNA sequence. we will describe the system design of encryption scheme. and (~1=0) is proposed in this DNA digital coding. only 8 kinds of patterns (0123/CTAG. According to this complementary rule. 2(10). 0123/GTAC. It is suggested that the coding pattern in accordance with the sequence of molecular weight. So among these 24 patterns. it should reflect the biological characteristics of 4 nucleotide bases. 0123/TCGA. We will show the way of exchanging message safely just between specific two persons. Obviously. G) is by means of 4 digits: 0(00). 0123/AGCT) which are topologically identical fit the complementary rule of the nucleotide bases. (3). We shall call the NIT KURUKSHETRA 10 . there are 4!=24 possible coding patterns by this encoding format. 0123/ACGT.

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

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

This operation could increase the security of this encryption scheme. We first convert this sentence into hexadecimal code by using the built-in computer code. we thoroughly discuss details of this encryption scheme with an example shown in fig.12.12.DNA CRYPTOGRAPHY In the following part of this section. 1. that is: 01000111 01000101 01001110 01000101 01000011 01010010 01011001 01010000 01010100 01001111 01000111 01010010 01000001 01010000 01001000 01011001 NIT KURUKSHETRA 13 . the amplification could be successful. Step 1: Key Generation. The message-sender Alice and the message-receiver Bob respectively design and exchange a pair of PCR primers over a secure communication channel. but respectively designed complete cooperation by sender and receiver. the amplification was not efficient when one of a primer pair is incorrect.3. because even if an adversary somehow caught one of a primer pair. that is: “47 45 4E 45 43 52 59 50 54 4F 47 52 41 50 48 59”. the intended PCR two primer pairs was not independent designed by sender or receiver. Step 2: Data pretreatment. 1. Here we choose “GENECRYPTOGRAPHY” (gene cryptography) as plaintext to encrypt. Then we translate hexadecimal code into binary plaintext M_ by using third-party software. The encryption and decryption keys are a pair of PCR primers. The result of the PCR amplification is shown in fig. only when both of the primer sequences were correct.2. In this scheme.

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

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

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

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

or the only types of code. there were a number of suggestions as to what form it might take. One of these was the comma-free code. because CGG does not belong to the set. possible.4 Other codes The three codes detailed above are meant to be illustrative rather than exhaustive. showed that twenty 3-base codons could be selected to act in a comma-free manner. As the name suggests. a comma-free code is just a comma code without the commas. by restricting oneself to a set of fixed-length codons with particular base combinations. Three others are outlined briefly in this section.2 General features of the codes Table 1.3 Advantages of the codes 1. there is a set of fifty-seven 4-base codons that would be enough to carry out this task. Before experimental data for the nature of the genetic code became available.13. one could not begin reading one base in. in the sequence ACGGTGGTGACGAGG. There is nothing particularly wrong with the commaNIT KURUKSHETRA 18 . For instance. One might think that removing the commas would give a code without a reading frame. But.13. Any combination of these codons will give a sequence which can be read in only one way. They are by no means the only codes.DNA CRYPTOGRAPHY Table 1. Although twenty codons is not sufficient to comfortably encrypt text. the 3-base codons AGG. In their original paper on the subject. the codons in this set can be chosen such that only one reading frame is ever possible – all the others give nonsense.13. at CGG. For example. ACG and GTG are part of a comma free code.

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

DNA CRYPTOGRAPHY Chapter 2 Objective NIT KURUKSHETRA 20 .

are available in the market this project aims at Although many encoding techniques Cryptography) for encoding text. To obtain an encoded text as desired. 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 2.2 Product Perspective The main purpose or goal of the project is to implement the basic fundamentals of DNA Cryptography using the Java platform so as to produce an encoding tool capable of applying the elementary encoding transformations to the text. NIT KURUKSHETRA 21 . Hide the biological complexity involved in basic processing of DNA cryptography.DNA CRYPTOGRAPHY 2.1 Objective The aim of our project is to build a system which fulfills the following objectives : • • • • To implement the basic concepts of DNA Cryptography. Allow users to apply the encoding on textual information.

DNA CRYPTOGRAPHY Chapter 3 System Requirement Analysis NIT KURUKSHETRA 22 .

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.  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 .1 Characteristics The important characteristics of the system being developed: FUNCTIONS ~ Loading the text file from source. ~ 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 .

3 Technology Used Windows 9x / XP/ NT / 2000 JVM and JRE installed.1 Encoder Fig 3. NetBeans 6.DNA CRYPTOGRAPHY  SOFTWARE SUPPORT Operating System Framework 3.1 Usecase diagram(encoder) NIT KURUKSHETRA 24 .0 Programming Language JAVA 5 3.4.4.4 Use Case Diagram 3.

DNA CRYPTOGRAPHY 3.2 Decoder Fig 3.4.4.2 Usecase diagram(decoder) NIT KURUKSHETRA 25 .

DNA CRYPTOGRAPHY Chapter 4 Project Overview NIT KURUKSHETRA 26 .

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

DNA CRYPTOGRAPHY Chapter 5 Software Design NIT KURUKSHETRA 28 .

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

2 Flow Diagram(decoder) NIT KURUKSHETRA 30 .2 Decoder Fig 5.DNA CRYPTOGRAPHY 5.2.2.

3 Class Diagrams 5.3.1 Class diagram(encoder) NIT KURUKSHETRA 31 .DNA CRYPTOGRAPHY 5.1 Encoder Fig 5.3.

2 Class diagram(decoder) NIT KURUKSHETRA 32 .3.3.2 Decoder Fig 5.DNA CRYPTOGRAPHY 5.

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

DNA CRYPTOGRAPHY Chapter 6 Software Testing NIT KURUKSHETRA 34 .

2 Testing Objectives 1. 3. Black Box Testing is not an alternative to white-box techniques. The above objectives imply a dramatic change in viewpoint.1 Black-Box Testing Black box testing focuses on the functional requirements of the software. it is a complementary approach that is likely to uncover a different class of errors than white-box methods. It is used to detect errors. where the system to be tested is executed and the behavior of the system is observed. They move counter to the commonly held view that a successful test is one in which no errors are found.1 Testing Methodology Software testing is critical element of software quality assurance and represents the ultimate review of specification. 2.3 Testing Technique The techniques followed throughout the testing of the system are as follows: 6. NIT KURUKSHETRA 35 .DNA CRYPTOGRAPHY 6 Testing 6. 6. 4. Testing is a process of executing a program with the intent of finding an error. Our objective is to design tests that systematically uncover different classes of errors and do so with a minimum amount of time and effort. That is.Black-Box Testing attempts to find errors in the following categories: • Incorrect or missing functions. design and coding. 6.3. Black Box testing enables the software engineer to derive sets of input conditions that will fully exercise all functional requirements for a program. A good test case is one that has a high probability of finding an as-yetundiscovered error. A successful test is one that uncovers an as-yet-undiscovered error. Rather. Testing is a dynamic method for verification and validation.

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

6. NIT KURUKSHETRA 37 .3.3 Control Structure Testing 6.3 Dataflow Testing The dataflow testing method selects test paths of a program according to the location of definitions and uses of variables in the program. In this testing approach.1 Condition Testing Condition testing is a test case design method that exercises the logical conditions contained in a program module. Therefore types of errors in a condition include the following      Boolean operator error Boolean variable error Boolean parenthesis error Relational operator error Arithmetic expression error 6.3. Exercise internal data structures to ensure their validity. If a condition is incorrect then at least one component of the condition is incorrect.DNA CRYPTOGRAPHY   Execute all loops at their boundaries and within their operational bounds.3. Loop testing is a white-box testing technique that focuses exclusively on the validity of loop constructs.3.3.2 Loop Testing Loops are the corner stone for the vast majority of all algorithms implemented in software.3. Four different classes of loops:     Simple Loops Nested Loops Concatenated Loops Unstructured Loops 6. 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.3.

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

. Software. Although each test has a different purpose all work to verify that system elements have been properly integrated and perform allocated functions.g.DNA CRYPTOGRAPHY 6.4.System testing verifies that all elements mesh properly and that overall system function/performance is achieved. An important element of validation process is configuration review. It is intended for all the elements are properly configured and cataloged. must be combined with other system element (e. people. once validated. 6. NIT KURUKSHETRA 39 . It is a series of different tests whose primary purpose is to fully exercise the computer-based system.4 System Testing The last high-order testing step falls outside the boundary of software engineering and into tile broader context of computer system engineering.3 Validation Testing It is achieved through a series of Black Box tests.4. It is also called AUDIT. hardware. and database).

DNA CRYPTOGRAPHY Chapter 7 Project Snapshots NIT KURUKSHETRA 40 .

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

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

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

DNA CRYPTOGRAPHY Chapter 8 Conclusion NIT KURUKSHETRA 44 .

This project provides an insight into the various details of the DNA and its use in cryptography purposes. NIT KURUKSHETRA 45 .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.

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. and provide secure channel for communication.  The space complexity can be reduced by practical usage of PCR Amplifier.DNA CRYPTOGRAPHY 9 Future Prospects and Enhancements  This project can be extended to encrypt other data formats. NIT KURUKSHETRA 47 .

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 .

Magdy Saeb .∗ Some possible codes for encrypting data in DNA. IEEE 2008 [5] Sherif T. Limin Qin . Amin . JAVA2 Complete Reference.DNA CRYPTOGRAPHY Bibliography Books & Literature [1] “Herbert Schildt”. Smith. Yanfeng Wang . A DNA-based Implementation of YAEA Encryption Algorithm [6] Guangzhao Cui . Fiddes. Tata McGraw-Hill Publishing Company Limited . .Willey Publishing Inc. Streletchi Cosmin. 2003. Jonathan P. Ceridwyn C. NIT KURUKSHETRA 49 . 2004 [2] Scott W. A Java Crypto Implementation of DNAProvider Featuring Complexity in Theory and Practice. JAVA2 Enterprise Edition 1. 2003 [3] Java 5. Vaida Mircea-Florin .4 Bible . Xuncai Zhang An Encryption Scheme Using DNA Technology. A Pseudo DNA Cryptography Method [8] Geoff C. Borda Monica. Biotechnology Letters 25: 1125–1130.0 API Documentation Websites [4] Hodorogea Tatiana. Salah El-Gindi.L. IEEE 2008 [7] Ning Kang. Hawkins & Jonathan P. Amber . Fifth Edition. Cox.

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