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.
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 * ?
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.
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.
Here we provide basic terminology used in cryptography. An unbreakable cryptosystem is one for which successful cryptanalysis is not possible. and a single target DNA molecule can be amplified to 106 after 20 cycles in theory. Thus one can effectively amplify a lot of DNA strands within a very short time. The goal is to transmit a message between a sender and receiver such that an eavesdropper is unable to understand it.6 Cryptography
Data security and cryptography are critical aspects of conventional computing and may also be important to possible DNA database applications. Thinking about the highly stability of PCR. Polymerase Chain Reaction (PCR) is a fast DNA amplification technology based on Watson-Crick complementarity. such as that of a natural language. * The main goal of the research of DNA cryptography is exploring characteristics of DNA molecule and reaction. after which it is destroyed. Each piece of data is used once to encrypt a message by the sender and to decrypt it by the receiver. In this study. we selected each PCR primer 20-mer nucleotides
. discovering possible development directions. Two complementary oligonucleotide primers are annealed to double-stranded target DNA strands. and lay-ing the basis for future development.DNA CRYPTOGRAPHY
1. each PCR primer (20-27)-mer nucleotides long is a comparatively perfect selection. and the necessary target DNA can be amplified after a serial of polymerase enzyme. Such a system is the one-time-pad cipher. Encryption is the process of scrambling the plaintext using a known algorithm and a secret key. which transforms the encrypted message back to the original form using a key. It gets its name from the fact that the sender and receiver each possess identical notepads ¯lled with random data. The output is a sequence of characters known as the ciphertext. Decryption is the reverse process. The PCR is a very sensitive method. Plaintext refers to a sequence of characters drawn from a ¯nite alphabet.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”. establishing corresponding theories. The goal of encryption is to prevent decryption by an adversary who does not know the secret key. searching for simple methods of realizing DNA cryptography.
1. and is one of the most important inventions in modern biology.
he must choose two primer sequences from about 10^23 kinds of sequences (the number of combination taking 2 sequences from 420 candidates).9.2 Security
Only computational security can be achieved for traditional cryptographic schemes except for the one-time pad.
1. DNA cryptography has only nearly ten years history. an adversary with infinite power of computation can break them theoretically. It would still be extremely difficult to amplify the message-encoded sequence without knowing the correct two primer pairs. so much as P=NP. we believe that this biological problem is difficult and will last a relatively long time. and has infinite computing re-sources. It is impossible for an adversary to obtain a totally NIT KURUKSHETRA 6
. they have not been plunged into practical use. Differently. If an adversary without knowing the correct two primer pairs wants to pick out the message encoded sequence by PCR amplification.9 Comparisons among DNA cryptography. It is a special function in PCR amplification that having the correct primer pairs.
1. and the theory basis has been prepared while implementation is difficult.DNA CRYPTOGRAPHY long. Even if an eavesdropper is given the ability to do whatever he wants. Related theory is almost sound. So.8 Limitations Of DNA Cryptography
(i) Lack of the related theoretical basis.9. Any behavior of eavesdropping will change the cipher so it can be detected. that is to say. it is still impossible to break such a scheme. 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. their security is based on Heinsberg's Uncertainty Principle. By and large. It is shown that quantum computers have great and striking computational potential. All the practical ciphers can be seen as traditional ones. Although there is uncertainty about the computational power of quantum computers. traditional cryptography and quantum cryptography 1.1 Development
Traditional cryptography can be traced back to Caesar cipher 2000 years ago or even earlier. Quantum cryptographic schemes are unbreakable under current theories. the theory basis is under research and the application costs very much. (ii) Difficult to realize and expensive to apply.
this making it hard to predict the future.10 Development directions of DNA cryptography
Since DNA cryptography is still in its immature stage. Under the current level of techniques. which has nothing to do with the computing power and immunizes DNA cryptographic schemes against attacks using quantum computers. However. DNA can even be used to produce unforgeable contract. exceptional energy efficiency and extraordinary information density inherent in DNA molecules. in view of the development of biological techniques and the requirement of cryptography. 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. only by physical ways can the cipher text of DNA cryptography be transmitted. Using the traditional cryptography we can realize purposes as public and private key encryption. Therefore. Researches of all the three kinds of cryptography are still in progress. magnetic medium. Quantum cryptosystem is implemented on quantum channels of which main ad-vantage lies in real-time communication. and so on. The disadvantage lies in the secure data storage. and the storage can be CDs. it is too early to predict the future development precisely. authentication. which makes it infeasible to implement publickey encryption and digital signature as easily as traditional one does. thus the attempt to tamper but without being detected in vain. 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 and other storage medium.9. fiber. digital signature.DNA CRYPTOGRAPHY same the quanta with the intercepted one. such as secure data storage.3 Application
Traditional cryptosystems are the most convenient of which the computation can be executed by electronic. and a great many problems remains to be solved especially for DNA and quantum cryptography. identity authentication and digital signature. Nonetheless.
1. the main security basis is the restriction of biological techniques. DNA cryptography can have special advantages in some cryptographic purposes.
1. the data can be transmitted by wire. quantum as well as DNA computers. quantum key agreement schemes have unconditional security. For the DNA cryptography. we hold the following opinions:
. cash ticket and identification card. steganography. wireless channel and even by a messenger. Due to the vast parallelism.
i. they both satisfy the same characteristic of cryptography. it must be assumed that an attacker knows the basic biological method the designer used. that is. The only thing
. Thereby. 2) Security requirements :Regardless of the many differences between DNA and traditional cryptography. such as developing nanoscopic storage based on the tiny volume of DNA. The communication model for DNA encryption is also made up of two par-ties.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. these problems being se-curity basis cannot be excluded absolutely. realizing fast encryption and decryption based on the vast parallelism. Encryption and decryption algorithms hard to be implemented using electronic computers may be feasible using DNA ones with regard to their vast parallel computational ability. a sender and a receiver. More precisely. are easier to be implemented than physical and chemical ones in the present era of electronic computers and the Internet. 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. they should have properties such as higher security levels and storage density etc. if DNA cryptography is necessary to be developed.e. It is under this assumption that a cryptosystem can be said secure when any attacker cannot break it. if described by mathematical methods. and has enough knowledge and excellent laboratory devices to repeat the de-signer’s operations. The security requirements should also be founded upon the assumption proposed by Kirchoff that security should depend only on the secrecy of decryption key. If other kinds of cryptosystems are necessary to be researched and developed. their computational security will be inherited into DNA schemes. Since it has not been made sure whether quan-tum computers threaten the hardness of various mathematical hard problems. the advantages inherent in DNA should be fully explored. which obtain the secret key in a secure or authenticated way and then communicate securely with each other in an insecure or unauthenticated channel. Encryption and decryption are procedures of data transform which. an attacker should be fully aware of all the details of encryption and decryption except the decryption key. If these schemes withstand attacks by quantum computers. DNA cryptography does not absolutely repulse traditional cryptography and it is possible to construct a hybrid cryptosystem of them. Thus. which cannot be realized by electronic computers by using mathematical methods.
The cur-rent goal or difficulty is to find and make use of the utmost potential. to establish the theoretical basis and to accumulate the experience. and sometimes the experiment conditions.
1.11 DNA Digital Coding Technology
NIT KURUKSHETRA 9
. Scientists can easily operate DNA with the aid of kinds of restriction enzymes only after DNA strands are amplified with amplification technology such as PCR. Presently. It is more practical to make use of colony property of plentiful DNA for cryptographer. a key is usually some substances of biological materials or a preparation flow. although the related research is just in its initial stage. Sound theories have not been founded for both DNA computing and cryptography. the most important is to find the sound properties of DNA that can be used to computation and encryption. This motivates the research of DNA computing and cryptography. 4) Currently. In a DNA cryptosystem.DNA CRYPTOGRAPHY not known by the attacker is the key. The development of modern biological technology makes it possible to express data by DNA. A sound cryptosystem should be secure as well as easy to be implemented. 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. 3) For DNA cryptography. based on which the design of secure and practical DNA cryptosystems is possible. store data by DNA chips and read data by hybridization. it is still difficult to operate the nanoscopic DNA directly. For example. The method is easier to be implemented than encoding message into nucleotides directly while the storage density is somewhat lower. the current research target should lie first in security and feasibility. It is certainly urgent to find such a method similar to computational complexity. exceptional energy efficiency and extraordinary information density inherent in DNA. which makes the operations of input/output faster and more convenient. It can be proved that there are vast parallelism. If the only requirement is to improve the density of storage. the main task for DNA cryptographers is to establish the theory foundations and to accumulate the practical experience. it is hard to implement DNA cryptography at the present technique level. but the related research is in its initial stage. With the current technology. second in storage density. Modern biology lays particular stress on experiments rather than theories. it is also impossible to store all the worldwide data by using several grams of DNA. In fact.
it should reflect the biological characteristics of 4 nucleotide bases. 1(01). According to this complementary rule. 0123/CTAG. The DNA sequence after preprocessing by DNA digital coding techniques is able to do digital computing and adapt to the existing computer-processing mode. which are adenine (A) and thymine (T) or cytosine (C) and guanine (G) in DNA sequence. that is 0(00) to 3(11) and 1(01) to 2(10). in a double helix DNA string. we will describe the system design of encryption scheme.
1. 2(10). (3). We will show the way of exchanging message safely just between specific two persons. the most fundamental coding method is binary digital coding. Take DNA digital coding into account. There are four kinds of bases. We shall call the NIT KURUKSHETRA 10
. To decrease the redundancy of the information coding andimprove the coding efficiency compared to the traditional character DNA coding. there are 4!=24 possible coding patterns by this encoding format. that is A to T and C to G according to Watson-Crick complementarity rule.DNA CRYPTOGRAPHY In the information science. 0123/GTAC.12 System Design Of Encryption Scheme
Now. The simplest coding patterns to encode the 4 nucleotide bases (A. 0123/GATC. 0123/ACGT. 0123/AGCT) which are topologically identical fit the complementary rule of the nucleotide bases. As we all know. C. two DNA strands are held together complementary in terms of sequence. 0123/TCGA. The digital coding of DNA sequence is very convenient for mathematical operation and logical operation and may give a great impact on the DNA bio-computer. the traditional encryption method such as DES or RSA could be used to preprocess to the plaintext in the cryptography scheme. This pattern could perfect reflect the biological characteristics of 4 nucleotide bases and have a certain biological significance. which is anything can be encoded by two state 0 or 1 and a combination of 0 and 1. the complementary rule that (~0)=1. is the best coding pattern for the nucleotide bases. 0123/TGCA. G) is by means of 4 digits: 0(00). whose security on the scheme is mainly based on the difficult biological problems and difficult mathematical problems. 0123/CATG. 3(11). It is suggested that the coding pattern in accordance with the sequence of molecular weight. By using the technology of DNA digital coding. only 8 kinds of patterns (0123/CTAG. The binary digital coding of DNA sequences prevails over the character DNA coding with the following advantages: (1). (4). (2). which facilitates the direct conversion between biological information and encryption information in the cryptographyscheme. T. Obviously. and (~1=0) is proposed in this DNA digital coding. So among these 24 patterns.
KB and C are not limited to digital data. Here. 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. Using traditional cryptography RSA to preprocess to the plaintext. we can get an encryption key KA that is a pair of PCR primers and Bob’s public key e. and the intended receiver Bob. The intended receiver Bob has a pair of keys (e. Bob uses KB to translate the ciphertext C into the plaintext M by a translation D. we extend the definition of this encryption scheme as follows. Suppose there is a sender Alice who owns an encryption key KA.
B. d). but can be any method. data. we can get completely different ciphertext from the same plaintext. E and D are also not limited to mathematical calculations. material. 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. Above all. but can be any physical or chemical or biological or mathematical process such as traditional encryption method. Through this preprocess operation. Encryption
First of all. KA. We will describe the general process of the encryption scheme as follows. such as DNA sequence. We call this preprocess operation is pretreatment data process (data pre-treatment). We call translation E as encryption process and C as ciphertext. After a pair of PCR primers is respectively designed and exchanged over a secure communication channel.
A. and an intended receiver Bob who owns a decryption key KB (KA = KB or KA ≠ KB). the sender Alice will translate the plaintext M into hexadecimal code by using the built-in computer code. 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. which can effectively prevent attack from a possible word as NIT KURUKSHETRA 11
. Finally. 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. 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.DNA CRYPTOGRAPHY sender Alice.
This decryption process is not only a mathematic computation.12. Decryption
After the intended receiver Bob gets the DNA mixture. In this scheme.1 Data pre(post)treatment flow chart
. Since the intended receiver Bob had gotten the correct PCR two primer pairs through a secure way. The last process of this encryption is that Alice generates a certain number of dummies and puts the secrete-message DNA sequence among them. After mixing the secretemessage DNA sequence with a certain number of dummies.1.DNA CRYPTOGRAPHY PCR primers. After Bob amplifies the secrete-message DNA sequence.12. each 20-mer oligo nucleotides long. the dummy is generated by sonicating human DNA to roughly 60 to 160 nucleotide pairs (average size) and denaturing it. Alice synthesizes the secret-message DNA sequence which is flanked by forward and reverse PCR primers. the secrete-message DNA sequence is prepared. Alice translates the binary ciphertext C_ into the DNA sequence according to the DNA digital coding technology. he can easily find the secrete-message DNA sequence. The pretreatment data flow chart is described in Fig.1
C. It is necessary that each dummy has the same structure as the secretemessage DNA sequence. 1. Then. he could retrieve the plaintext M sended from Alice from the reverse preprocess operation using his secret key d. Thus. but also a biological process. Alice sends the DNA mixture to Bob using an open communication channel. he could amplify the secret-message DNA sequence by perform PCR on DNA mixture. After coding.
Step 2: Data pretreatment. only when both of the primer sequences were correct. the intended PCR two primer pairs was not independent designed by sender or receiver. because even if an adversary somehow caught one of a primer pair. In this scheme.12. 1. Then we translate hexadecimal code into binary plaintext M_ by using third-party software. that is: 01000111 01000101 01001110 01000101 01000011 01010010 01011001 01010000 01010100 01001111 01000111 01010010 01000001 01010000 01001000 01011001
. We first convert this sentence into hexadecimal code by using the built-in computer code. that is: “47 45 4E 45 43 52 59 50 54 4F 47 52 41 50 48 59”. The result of the PCR amplification is shown in fig. we thoroughly discuss details of this encryption scheme with an example shown in fig.12. The message-sender Alice and the message-receiver Bob respectively design and exchange a pair of PCR primers over a secure communication channel. The encryption and decryption keys are a pair of PCR primers. Step 1: Key Generation. 1. but respectively designed complete cooperation by sender and receiver.2. Here we choose “GENECRYPTOGRAPHY” (gene cryptography) as plaintext to encrypt.3. the amplification was not efficient when one of a primer pair is incorrect.DNA CRYPTOGRAPHY In the following part of this section. This operation could increase the security of this encryption scheme. the amplification could be successful.
After the binary plaintext M_ has been recovered.2. symbols or numbers.
Fig. Both the comma code and the alternating code. providing that this text lacked any sort of punctuation.12.13 The codes
The three codes described in detail in this paper are referred to as the Huffman code. Bob translates the secret-message DNA sequence into the binary ciphertext C_ by using the DNA digital coding technology. Step 4: Decryption. the comma code and the alternating code. 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. he can easily pick out the secret-message DNA sequence by using the correct primer pairs. Alice will encrypt the binary plaintext M_ into the binary ciphertext C_ by using Bob’s public key e. a secret-message DNA sequence containing an encoded message 64 nucleotides long flanked by forward and reverse PCR primers. After that. such as DNA ink or DNA book. Bob can retrieve the plaintext M. 1. Then. Flow chart of Encryption scheme system.DNA CRYPTOGRAPHY Fig. Bob can decrypt the binary ciphertext C_ into the binary plaintext M_ by using his secret key e. After mixing the secrete-message DNA sequence with a certain number of dummies. Finally.
1. Result of the PCR amplification Step 3: Encryption. Thus. It should be stated at the outset that none of them fulfill all the criteria listed above. “GENECRYPTOGRAPHY” from the binary plaintext M_ by using data posttreatment. The Huffman code is the most economical and would be the best for encrypting text for short-term storage.3. Alice sends the DNA mixture to Bob using an open communication channel. the secrete-message DNA is prepared. 1.12. while the most
. Step 5: data post-treatment.
and the longest codon is five bases long (representing q and z. Consequently they cannot be included when deriving the Huffman code.
1.g. For instance. In the code. Because of the variable length of the codons. the most infrequent letters in the English language). shorter than the codons of any of the other codes described in this paper. the alternating code is also unambiguous. While of the three codes discussed here. The second disadvantage of the Huffman code relates to its possible use in long-term storage of information. The average codon length is 2. no obvious pattern emerges when they are joined together to encode a message. C and T).DNA CRYPTOGRAPHY uneconomical of the codes. i. The naive investigator might confuse it with natural DNA and therefore not appreciate its significance.1 The Huffman code
By varying the number of symbols allotted to a character in a code. G. One could counteract this problem by using three instead of four bases (e. That is. with the most frequent character being given the least number of symbols and the least frequent the most number of symbols. the shortest codon is just one base long (representing e. The first is that it does not cater for any symbols or numbers.2 bases. Given a suitable start signal. The others all have NIT KURUKSHETRA 15
. it does have two disadvantages. as the frequency of these characters will be heavily text-dependent. it is possible to construct very economical codes. the Huffman makes the most economical use of DNA. once the start point has been specified.1 Given the frequencies of occurrence of these letters. codes in which the text is encrypted by the minimum number of symbols – it is as short as it can possibly be. The Huffman code is the only code discussed in this paper with variable length codons. The Huffman code constructed with the four DNA bases A. As well as being compact. One of the best ways of constructing an economical code is to use Huffman’s method (Huffman 1952).13. and so would be best suited to the encryption of information for long-term storage. 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.e. at the expense of economy. have the advantage that they generate base sequences which are obviously artificial. the message generated by a Huffman code is unambiguous. the base sequence CATGTAGTCG can only be read from the beginning as hester – no other interpretation of the message is possible. there is only one way in which the stream of symbols comprising the message can be read. A.13. such a code is straightforward to construct (Materials and methods). C and T for the letters of the English alphabet is shown in Table 1. the most frequently used letter in the English language).
and therefore the comma
. facilitating the construction of message DNA (‘Criteria for an optimal code’.g.2 The comma code
In the comma code. e.1 The Huffman code
1.DNA CRYPTOGRAPHY fixed length codons. We note that. the comma.
Table 1. The repetition of G every six bases must be construed by any careful sequence analyst as a deliberate device. in a similar manner to the above. the Huffman code has also been used to construct a ‘perfect’ genetic code comprising variable length codons. which is always the same: e. consecutive 5-base codons are separated by a single base.g. WWCWC or WCCWW). where W = A or T.13. G− − − − − G− − − − − G− − − −− G. The codons take the general form CWWWC. above).13. but not G. There are 80 codons in this set. A and T. This kind of an arrangement. The codons that slot into the gaps in the above framework are made up of the remaining bases C. 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. and the C’s and W’s can adopt any arrangement (e. Most (83%) point mutations give nonsense codons. with the C of the latter always being located in the top strand.g. ATCAC.suggested by unrelated work .
it offers some protection against deletion and insertion mutations. As in the comma code. or vice versa) and therefore the remaining 83% of single point mutations will given nonsense codons. there is no automatic reading frame. Of these 18 single point mutations. the alternating code has two other advantages of the comma code: it is isothermal. it might be difficult to orientate oneself with respect to the message. the number of G:C pairs will be the same as the number of A:T pairs. the reading frame is clear. 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. or be fixed in other arrangements such as YYYRRR or RRYYRY). As well as creating message DNA of an obviously artificial nature. since 67% of single point mutations result in nonsense codons.DNA CRYPTOGRAPHY code is good at detecting errors. Furthermore. when the commas are included.13. and it is error-detecting. It should also be noted that the base composition of the codons will give. but less so than the comma code. But the principal attraction of the comma code is the reading frame established by the regular pattern of repeating G’s. where R = A or G and Y = C or T (although there is no reason why the purines and pyrimidines should not alternate YRYRYR. and. unless a start point is specified.
1.3 The alternating code
The alternating code comprises sixty-four 6-base codons of alternating purines and pyrimidines: RYRYRY. With the comma code. which could further complicate the interpretation of the other codes. 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 . in a given piece of message DNA. Unlike the comma code. it is not difficult to spot the codon containing the deletion mutation in the following comma-coded sequence: GATCACGATTCCGCTATGACTCAG. Like the comma code it does not use DNA economically. the alternating structure has the unusual property that. and therefore there are 18 single point mutations altogether. Three possible point mutations can occur at each position of the codon GCWWWC (which includes the initial comma). three (17%) will produce sense codons (mutation of an A to a T. For example.
For instance. the 3-base codons AGG. in the sequence ACGGTGGTGACGAGG.DNA CRYPTOGRAPHY
Table 1.13. a comma-free code is just a comma code without the commas. possible. They are by no means the only codes. at CGG. there were a number of suggestions as to what form it might take. But. Before experimental data for the nature of the genetic code became available. one could not begin reading one base in.3 Advantages of the codes
1. showed that twenty 3-base codons could be selected to act in a comma-free manner. ACG and GTG are part of a comma free code. In their original paper on the subject. There is nothing particularly wrong with the commaNIT KURUKSHETRA 18
. Any combination of these codons will give a sequence which can be read in only one way. Three others are outlined briefly in this section.13.4 Other codes
The three codes detailed above are meant to be illustrative rather than exhaustive. One of these was the comma-free code. For example. by restricting oneself to a set of fixed-length codons with particular base combinations. Although twenty codons is not sufficient to comfortably encrypt text.13. there is a set of fifty-seven 4-base codons that would be enough to carry out this task. One might think that removing the commas would give a code without a reading frame. or the only types of code.2 General features of the codes
Table 1. the codons in this set can be chosen such that only one reading frame is ever possible – all the others give nonsense. As the name suggests. because CGG does not belong to the set.
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. since it is quite economical and establishes an automatic reading frame. Finally. There are no such absences in natural DNA. Like the alternating and comma codes. such that a degree of error-protection could be achieved. in a similar manner to the codons of the comma code. the commafree code would be error-detecting to a certain extent. it ought to be rather good. perhaps the most obvious code of all is one similar to the genetic code – a triplet code. We would probably use a 4-base codon version of this code. However. 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.DNA CRYPTOGRAPHY free code as a message-encoding scheme. In fact. as the comma-free code forbids these. message DNA has already been constructed with a 3-base codon version of this code. to give a larger codon set (34 = 81 as opposed to 33 = 27). Codon assignment in this case may be done in a non-random fashion.g. In fact.g. CTT to encode for ’<’ and AAG for ’>’). AAAA).
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.1
The aim of our project is to build a system which fulfills the following objectives : • • • • To implement the basic concepts of DNA Cryptography. Added to this it is aimed to obtain a clear understanding of the Java cryptography and its native API. are available in the market this project aims at
Although many encoding techniques Cryptography) for encoding text. To obtain an encoded text as desired.
. Hide the biological complexity involved in basic processing of DNA cryptography.DNA CRYPTOGRAPHY
understanding the limitations and configurations needed to perform a new technique (DNA
2. Allow users to apply the encoding on textual information.
System Requirement Analysis
The important characteristics of the system being developed:
FUNCTIONS ~ Loading the text file from source.
Intel Pentium III or higher Color Monitor 800 x 600 or higher resolution PCR (Polymerase Chain Reaction)
~ 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 .DNA CRYPTOGRAPHY
System Requirement Analysis:
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
Operating System Framework 3.0
3.4 Use Case Diagram 3.1 Usecase diagram(encoder)
Fig 3.3 Technology Used
Windows 9x / XP/ NT / 2000 JVM and JRE installed.4.4. NetBeans 6.
2 Usecase diagram(decoder)
PCR Amplifier is the hardware component that will be used for converting the text into a graphical format which reduces the space consumed. The functions of each component is as described below.
Network (To Receiver)
Fig 4.1 Project overview
The above figure shows the basic components comprising a typical general-purpose system used for dna cryptography. It consists of specialized modules that perform specific tasks. The computer is a general computer that can range from a PC to a supercomputer. In dedicated applications sometimes specialized computers are used to achieve the desired level of performance. Text File is a user input that has to be encoded.
5. = EKA (P.T. Encryption 3. STEPS: 1.T.T. T.1 Methodology OF Encryption Scheme
The encryption process is: C.DNA CRYPTOGRAPHY
5.2 Flow Diagrams 5.) The decryption process is: DKB (C.2.1 Encoder
Fig 5.) = DKB (EKA (P.)) = P.2.1 Flow Diagram(encoder)
. Key generation 2.
Fig 5.DNA CRYPTOGRAPHY
5.2 Flow Diagram(decoder)
3 Class Diagrams 5.3.1 Encoder
Fig 5.1 Class diagram(encoder)
Fig 5.3.2 Class diagram(decoder)
Fig 5.3 Class diagram(keyGen)
3 Testing Technique
The techniques followed throughout the testing of the system are as follows:
6. Testing is a dynamic method for verification and validation. They move counter to the commonly held view that a successful test is one in which no errors are found. 3.1 Black-Box Testing
Black box testing focuses on the functional requirements of the software.
. That is.
6. 2. 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. A good test case is one that has a high probability of finding an as-yetundiscovered error. Rather. where the system to be tested is executed and the behavior of the system is observed.DNA CRYPTOGRAPHY
6.1 Testing Methodology
Software testing is critical element of software quality assurance and represents the ultimate review of specification.3. It is used to detect errors. A successful test is one that uncovers an as-yet-undiscovered error.
6. 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.2 Testing Objectives
1. design and coding. Black Box Testing is not an alternative to white-box techniques.Black-Box Testing attempts to find errors in the following categories: • Incorrect or missing functions. Our objective is to design tests that systematically uncover different classes of errors and do so with a minimum amount of time and effort. 4.
6.2 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. Exercise all logical decisions on their true and false sides. 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. Performance errors. the number of additional test cases that must be designed to achieve reasonable testing.3. rather than errors associated only with the specific test at hand. and Test cases that tell us something about the presence or absence of classes of errors.DNA CRYPTOGRAPHY • • • • Interface errors. Initialization and termination errors. Errors in data structures or external data base access. 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. which is performed early in the testing process. 36
* Unlike White Box Testing. Black Box Testing tends to be applied during later stages of testing. attention is focused on the information domain. Because Black Box Testing purposely disregards control structure. by a count that is greater than one.
6. Loop testing is a white-box testing technique that focuses exclusively on the validity of loop constructs. 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 Dataflow Testing
The dataflow testing method selects test paths of a program according to the location of definitions and uses of variables in the program.3. Exercise internal data structures to ensure their validity.3.3. Therefore types of errors in a condition include the following Boolean operator error Boolean variable error Boolean parenthesis error Relational operator error Arithmetic expression error
6.3.3 Control Structure Testing 6. Four different classes of loops: Simple Loops Nested Loops Concatenated Loops Unstructured Loops
6.1 Condition Testing
Condition testing is a test case design method that exercises the logical conditions contained in a program module.
.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. In this testing approach. If a condition is incorrect then at least one component of the condition is incorrect.
4.4 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. 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. This approach is effective for error detection.DNA CRYPTOGRAPHY It is useful for selecting test paths of a program containing nested if and loop statement.
6. The module interface is tested to ensure that information properly flows in and out of program. However.We followed a systematic technique for constructing the program structure that is “putting them together”. We took unit tested components and build a program that has been dictated by design.
6.1 Unit Testing
Unit testing focuses verification efforts on the smallest unit of software design.4.
6. Others consider a module for integration and use only after it has been unit tested satisfactorily. A software testing strategy should be flexible enough to promote a customized testing approach. All error-handling paths are tested. Boundary conditions are tested to ensure that modules operate properly at boundary limits of processing. For example: .interfacing at the same time conducting tests to uncover errors. It is white box oriented. 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 independent paths are exercised to ensure all statements in a module have been executed at least once. Local data structure is examined to ensure that data stored temporarily maintain its integrity.
.2 Integration Testing
Integration testing focuses on design and construction of the software architecture.
3 Validation Testing
It is achieved through a series of Black Box tests.4. Although each test has a different purpose all work to verify that system elements have been properly integrated and perform allocated functions. people. hardware.System testing verifies that all elements mesh properly and that overall system function/performance is achieved.
6. It is intended for all the elements are properly configured and cataloged.4.4 System Testing
The last high-order testing step falls outside the boundary of software engineering and into tile broader context of computer system engineering.DNA CRYPTOGRAPHY
6. It is also called AUDIT. once validated. An important element of validation process is configuration review. Software.. and database). must be combined with other system element (e. It is a series of different tests whose primary purpose is to fully exercise the computer-based system.g.
1 Text file
Fig 7.DNA CRYPTOGRAPHY
7.1 Snapshot(original text)
7.2 Snapshot(encoded text)
.2 Encoded file
7.3 Decoded file
Fig 7.3 Snapshot(decoded text)
This project provides an insight into the various details of the DNA and its use in cryptography purposes. This project provided us with an opportunity to analyse and practice all the phases of the Software Development Life Cycle.DNA CRYPTOGRAPHY
The main purpose or goal of the project was to study and implement the basic fundamentals of DNA cryptography on textual information.
Future Prospects & Enhancements
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. DNA Cryptography can be used to prevent cyber crimes like hacking.
. Ongoing researches could be used for the future enhancement of this project.
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
Borda Monica. Xuncai Zhang An Encryption Scheme Using DNA Technology. Cox. 2003  Java 5. Yanfeng Wang . .∗ Some possible codes for encrypting data in DNA.Willey Publishing Inc. A Pseudo DNA Cryptography Method  Geoff C. Tata McGraw-Hill Publishing Company Limited . Amber . Fifth Edition. A DNA-based Implementation of YAEA Encryption Algorithm  Guangzhao Cui .DNA CRYPTOGRAPHY
Bibliography Books & Literature
 “Herbert Schildt”. Biotechnology Letters 25: 1125–1130. Jonathan P. Vaida Mircea-Florin . Fiddes. A Java Crypto Implementation of DNAProvider Featuring Complexity in Theory and Practice. Salah El-Gindi. Smith. 2004  Scott W. Streletchi Cosmin. 2003. Magdy Saeb . JAVA2 Enterprise Edition 1.4 Bible . Hawkins & Jonathan P. IEEE 2008  Sherif T.L. JAVA2 Complete Reference. Amin .
. Limin Qin . Ceridwyn C. IEEE 2008  Ning Kang.0 API Documentation
 Hodorogea Tatiana.